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Conserved domains on  [gi|663855578|ref|NP_001287725|]
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GTP-binding nuclear protein Ran isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RAN super family cl30510
Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the ...
1-127 3.45e-99

Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the active transport of proteins through nuclear pores.


The actual alignment was detected with superfamily member smart00176:

Pssm-ID: 128473 [Multi-domain]  Cd Length: 200  Bit Score: 282.29  E-value: 3.45e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578     1 MFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 80
Cdd:smart00176  74 MFDVTARVTYKNVPNWHRDLVRVCENIPIVLCGNKVDVKDRKVKAKSITFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 153
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 663855578    81 IGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDD 127
Cdd:smart00176 154 IGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAATTALPDEDDD 200
 
Name Accession Description Interval E-value
RAN smart00176
Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the ...
1-127 3.45e-99

Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the active transport of proteins through nuclear pores.


Pssm-ID: 128473 [Multi-domain]  Cd Length: 200  Bit Score: 282.29  E-value: 3.45e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578     1 MFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 80
Cdd:smart00176  74 MFDVTARVTYKNVPNWHRDLVRVCENIPIVLCGNKVDVKDRKVKAKSITFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 153
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 663855578    81 IGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDD 127
Cdd:smart00176 154 IGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAATTALPDEDDD 200
PTZ00132 PTZ00132
GTP-binding nuclear protein Ran; Provisional
1-128 8.41e-92

GTP-binding nuclear protein Ran; Provisional


Pssm-ID: 240284 [Multi-domain]  Cd Length: 215  Bit Score: 264.25  E-value: 8.41e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 80
Cdd:PTZ00132  88 MFDVTSRITYKNVPNWHRDIVRVCENIPIVLVGNKVDVKDRQVKARQITFHRKKNLQYYDISAKSNYNFEKPFLWLARRL 167
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 663855578  81 IGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL 128
Cdd:PTZ00132 168 TNDPNLVFVGAPALAPEEIQIDPELVAQAEKELQAAANVPLPDDDDDL 215
Ran cd00877
Ras-related nuclear proteins (Ran)/TC4 family of small GTPases; Ran GTPase is involved in ...
1-88 8.54e-67

Ras-related nuclear proteins (Ran)/TC4 family of small GTPases; Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is bound to chromatin and confined to the nucleus. Ran itself is mobile and is actively imported into the nucleus by a mechanism involving NTF-2. Together with the compartmentalization of its regulators, this is thought to produce a relatively high concentration of RanGTP in the nucleus.


Pssm-ID: 206643 [Multi-domain]  Cd Length: 166  Bit Score: 199.06  E-value: 8.54e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 80
Cdd:cd00877   79 MFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKPKQITFHRKKNLQYYEISAKSNYNFEKPFLWLARKL 158

                 ....*...
gi 663855578  81 IGDPNLEF 88
Cdd:cd00877  159 LGNPNLEF 166
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
1-81 1.88e-29

Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.


Pssm-ID: 425451 [Multi-domain]  Cd Length: 162  Bit Score: 104.13  E-value: 1.88e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578    1 MFDVTSRVTYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKD-RKVKAKS-IVFHRKKNLQYYDISAKSNYNFEKPFLWLA 77
Cdd:pfam00071  78 VYDITSRDSFENVKKWVEEILRHAdENVPIVLVGNKCDLEDqRVVSTEEgEALAKELGLPFMETSAKTNENVEEAFEELA 157

                  ....
gi 663855578   78 RKLI 81
Cdd:pfam00071 158 REIL 161
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
1-73 8.73e-05

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 39.66  E-value: 8.73e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663855578    1 MFDVTSRV-TYKNVPN-WHRDLVRVCE-NIPIVLCGNKVDIKDRKVKAKSI-VFHRKKNLQYYDISAKSNYNFEKPF 73
Cdd:TIGR00231  81 VFDIVILVlDVEEILEkQTKEIIHHADsGVPIILVGNKIDLKDADLKTHVAsEFAKLNGEPIIPLSAETGKNIDSAF 157
 
Name Accession Description Interval E-value
RAN smart00176
Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the ...
1-127 3.45e-99

Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the active transport of proteins through nuclear pores.


Pssm-ID: 128473 [Multi-domain]  Cd Length: 200  Bit Score: 282.29  E-value: 3.45e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578     1 MFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 80
Cdd:smart00176  74 MFDVTARVTYKNVPNWHRDLVRVCENIPIVLCGNKVDVKDRKVKAKSITFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 153
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 663855578    81 IGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDD 127
Cdd:smart00176 154 IGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAATTALPDEDDD 200
PTZ00132 PTZ00132
GTP-binding nuclear protein Ran; Provisional
1-128 8.41e-92

GTP-binding nuclear protein Ran; Provisional


Pssm-ID: 240284 [Multi-domain]  Cd Length: 215  Bit Score: 264.25  E-value: 8.41e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 80
Cdd:PTZ00132  88 MFDVTSRITYKNVPNWHRDIVRVCENIPIVLVGNKVDVKDRQVKARQITFHRKKNLQYYDISAKSNYNFEKPFLWLARRL 167
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 663855578  81 IGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL 128
Cdd:PTZ00132 168 TNDPNLVFVGAPALAPEEIQIDPELVAQAEKELQAAANVPLPDDDDDL 215
PLN03071 PLN03071
GTP-binding nuclear protein Ran; Provisional
1-128 3.85e-87

GTP-binding nuclear protein Ran; Provisional


Pssm-ID: 178620 [Multi-domain]  Cd Length: 219  Bit Score: 252.36  E-value: 3.85e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 80
Cdd:PLN03071  92 MFDVTARLTYKNVPTWHRDLCRVCENIPIVLCGNKVDVKNRQVKAKQVTFHRKKNLQYYEISAKSNYNFEKPFLYLARKL 171
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 663855578  81 IGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL 128
Cdd:PLN03071 172 AGDPNLHFVESPALAPPEVQIDLAAQQQHEAELAAAAAQPLPDDDDDA 219
Ran cd00877
Ras-related nuclear proteins (Ran)/TC4 family of small GTPases; Ran GTPase is involved in ...
1-88 8.54e-67

Ras-related nuclear proteins (Ran)/TC4 family of small GTPases; Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is bound to chromatin and confined to the nucleus. Ran itself is mobile and is actively imported into the nucleus by a mechanism involving NTF-2. Together with the compartmentalization of its regulators, this is thought to produce a relatively high concentration of RanGTP in the nucleus.


Pssm-ID: 206643 [Multi-domain]  Cd Length: 166  Bit Score: 199.06  E-value: 8.54e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 80
Cdd:cd00877   79 MFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKPKQITFHRKKNLQYYEISAKSNYNFEKPFLWLARKL 158

                 ....*...
gi 663855578  81 IGDPNLEF 88
Cdd:cd00877  159 LGNPNLEF 166
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
1-81 1.88e-29

Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.


Pssm-ID: 425451 [Multi-domain]  Cd Length: 162  Bit Score: 104.13  E-value: 1.88e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578    1 MFDVTSRVTYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKD-RKVKAKS-IVFHRKKNLQYYDISAKSNYNFEKPFLWLA 77
Cdd:pfam00071  78 VYDITSRDSFENVKKWVEEILRHAdENVPIVLVGNKCDLEDqRVVSTEEgEALAKELGLPFMETSAKTNENVEEAFEELA 157

                  ....
gi 663855578   78 RKLI 81
Cdd:pfam00071 158 REIL 161
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
1-78 6.16e-19

Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible.


Pssm-ID: 206640 [Multi-domain]  Cd Length: 159  Bit Score: 77.11  E-value: 6.16e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKDRKVKAKSIV--FHRKKNLQYYDISAKSNYNFEKPFLWLA 77
Cdd:cd00154   79 VYDVTNRESFENLDKWLNELKEYApPNIPIILVGNKSDLEDERQVSTEEAqqFAKENGLLFFETSAKTGENVDEAFESLA 158

                 .
gi 663855578  78 R 78
Cdd:cd00154  159 R 159
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
1-81 1.20e-15

Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 68.69  E-value: 1.20e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578     1 MFDVTSRVTYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKD-RKVK---AKSivFHRKKNLQYYDISAKSNYNFEKPFLW 75
Cdd:smart00175  79 VYDITNRESFENLENWLKELREYAsPNVVIMLVGNKSDLEEqRQVSreeAEA--FAEEHGLPFFETSAKTNTNVEEAFEE 156

                   ....*.
gi 663855578    76 LARKLI 81
Cdd:smart00175 157 LAREIL 162
Ras cd00876
Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases); The Ras family of the ...
1-80 4.27e-12

Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases); The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206642 [Multi-domain]  Cd Length: 160  Bit Score: 59.46  E-value: 4.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKD-RKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWL 76
Cdd:cd00876   77 VYSITSRESFEEIKNIREQILRVkdKEDVPIVLVGNKCDLENeRQVsTEEGEALAEEWGCPFLETSAKTNINIDELFNTL 156

                 ....
gi 663855578  77 ARKL 80
Cdd:cd00876  157 VREI 160
RAS smart00173
Ras subfamily of RAS small GTPases; Similar in fold and function to the bacterial EF-Tu GTPase. ...
2-78 2.52e-11

Ras subfamily of RAS small GTPases; Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades


Pssm-ID: 214541 [Multi-domain]  Cd Length: 164  Bit Score: 57.57  E-value: 2.52e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578     2 FDVTSRVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKD-RKV---KAKSIVfhRKKNLQYYDISAKSNYNFEKPFLW 75
Cdd:smart00173  79 YSITDRQSFEEIKKFREQILRVkdRDDVPIVLVGNKCDLESeRVVsteEGKELA--RQWGCPFLETSAKERVNVDEAFYD 156

                   ...
gi 663855578    76 LAR 78
Cdd:smart00173 157 LVR 159
Rab7 cd01862
Rab GTPase family 7 (Rab7); Rab7 subfamily. Rab7 is a small Rab GTPase that regulates ...
2-81 3.29e-11

Rab GTPase family 7 (Rab7); Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206655 [Multi-domain]  Cd Length: 172  Bit Score: 57.29  E-value: 3.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRD-LVRVC----ENIPIVLCGNKVDIKDRKVKAKSIVFH---RKKNLQYYDISAKSNYNFEKPF 73
Cdd:cd01862   80 YDVTNPKSFESLDSWRDEfLIQASprdpENFPFVVLGNKIDLEEKRQVSTKKAQQwckSKGNIPYFETSAKEAINVDQAF 159

                 ....*...
gi 663855578  74 LWLARKLI 81
Cdd:cd01862  160 ETIARLAL 167
Rab1_Ypt1 cd01869
Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in ...
2-81 3.48e-11

Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206661 [Multi-domain]  Cd Length: 166  Bit Score: 56.95  E-value: 3.48e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVR-VCENIPIVLCGNKVDIKDRKV----KAKSivFHRKKNLQYYDISAKSNYNFEKPFLWL 76
Cdd:cd01869   82 YDVTDQESFNNVKQWLQEIDRyASENVNKLLVGNKCDLTDKKVvdytEAKE--FADELGIPFLETSAKNATNVEEAFMTM 159

                 ....*
gi 663855578  77 ARKLI 81
Cdd:cd01869  160 AREIK 164
Rab21 cd04123
Rab GTPase family 21 (Rab21); The localization and function of Rab21 are not clearly defined, ...
2-81 4.80e-11

Rab GTPase family 21 (Rab21); The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133323 [Multi-domain]  Cd Length: 162  Bit Score: 56.46  E-value: 4.80e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKDRKVKAKSIV--FHRKKNLQYYDISAKSNYNFEKPFLWLAR 78
Cdd:cd04123   80 YDITDADSFQKVKKWIKELKQMRgNNISLVIVGNKIDLERQRVVSKSEAeeYAKSVGAKHFETSAKTGKGIEELFLSLAK 159

                 ...
gi 663855578  79 KLI 81
Cdd:cd04123  160 RMI 162
RabL2 cd04124
Rab GTPase-like family 2 (Rab-like2); RabL2 (Rab-like2) subfamily. RabL2s are novel Rab ...
2-73 5.49e-11

Rab GTPase-like family 2 (Rab-like2); RabL2 (Rab-like2) subfamily. RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share > 98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.


Pssm-ID: 133324 [Multi-domain]  Cd Length: 161  Bit Score: 56.41  E-value: 5.49e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIkDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPF 73
Cdd:cd04124   80 FDVTRKITYKNLSKWYEELREYRPEIPCIVVANKIDL-DPSVTQKKFNFAEKHNLPLYYVSAADGTNVVKLF 150
small_GTPase smart00010
Small GTPase of the Ras superfamily; ill-defined subfamily; SMART predicts Ras-like small ...
2-78 6.48e-11

Small GTPase of the Ras superfamily; ill-defined subfamily; SMART predicts Ras-like small GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies. Others that could not be classified in this way are predicted to be members of the small GTPase superfamily without predictions of the subfamily.


Pssm-ID: 197466 [Multi-domain]  Cd Length: 166  Bit Score: 56.41  E-value: 6.48e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578     2 FDVTSRVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKD-RKV---KAKSIVfhRKKNLQYYDISAKSNYNFEKPFLW 75
Cdd:smart00010  81 YSITDRQSFEEIAKFREQILRVkdRDDVPIVLVGNKCDLENeRVVsteEGKELA--RQWGCPFLETSAKERINVDEAFYD 158

                   ...
gi 663855578    76 LAR 78
Cdd:smart00010 159 LVR 161
Rab27A cd04127
Rab GTPase family 27a (Rab27a); The Rab27a subfamily consists of Rab27a and its highly ...
1-71 1.47e-09

Rab GTPase family 27a (Rab27a); The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated insulin secretion, making it a potential target for diabetes therapy. When bound to JFC1 in prostate cells, Rab27a is believed to regulate the exocytosis of prostate- specific markers. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206700 [Multi-domain]  Cd Length: 180  Bit Score: 52.89  E-value: 1.47e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVR--VCENIPIVLCGNKVDIKDRKVKAKSIV--FHRKKNLQYYDISAKSNYNFEK 71
Cdd:cd04127   93 MFDLTSEQSFLNVRNWMSQLQAhaYCENPDIVLIGNKADLPDQREVSERQAreLADKYGIPYFETSAATGQNVEK 167
Rap1 cd04175
Rap1 family GTPase consists of Rap1a and Rap1b isoforms; The Rap1 subgroup is part of the Rap ...
2-81 1.88e-09

Rap1 family GTPase consists of Rap1a and Rap1b isoforms; The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature. Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. High expression of Rap1 has been observed in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines; interestingly, in the SCCs, the active GTP-bound form localized to the nucleus, while the inactive GDP-bound form localized to the cytoplasm. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. Rap1a, which is stimulated by T-cell receptor (TCR) activation, is a positive regulator of T cells by directing integrin activation and augmenting lymphocyte responses. In murine hippocampal neurons, Rap1b determines which neurite will become the axon and directs the recruitment of Cdc42, which is required for formation of dendrites and axons. In murine platelets, Rap1b is required for normal homeostasis in vivo and is involved in integrin activation. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133375 [Multi-domain]  Cd Length: 164  Bit Score: 52.52  E-value: 1.88e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKDRKV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLA 77
Cdd:cd04175   80 YSITAQSTFNDLQDLREQILRVkdTEDVPMILVGNKCDLEDERVvgKEQGQNLARQWGCAFLETSAKAKINVNEIFYDLV 159

                 ....
gi 663855578  78 RKLI 81
Cdd:cd04175  160 RQIN 163
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
1-78 3.43e-09

Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 51.69  E-value: 3.43e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNwHRDLVRVCENIPIVLCGNKVDIKDRKVKAK---SIVFHRKKNLQYYDISAKSNYNFEKPFLWLA 77
Cdd:cd00882   82 VVDSTDRESEEDAKL-LILRRLRKEGIPIILVGNKIDLLEEREVEEllrLEELAKILGVPVFEVSAKTGEGVDELFEKLI 160

                 .
gi 663855578  78 R 78
Cdd:cd00882  161 E 161
Rab23_like cd04106
Rab GTPase family 23 (Rab23)-like; Rab23-like subfamily. Rab23 is a member of the Rab family ...
2-79 5.61e-09

Rab GTPase family 23 (Rab23)-like; Rab23-like subfamily. Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signaling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133306 [Multi-domain]  Cd Length: 162  Bit Score: 51.29  E-value: 5.61e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARK 79
Cdd:cd04106   82 FSTTDRESFEAIESWKEKVEAECGDIPMVLVQTKIDLLDQAVitNEEAEALAKRLQLPLFRTSVKDDFNVTELFEYLAEK 161
Rab8_Rab10_Rab13_like cd01867
Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to ...
2-78 6.59e-09

Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206659 [Multi-domain]  Cd Length: 167  Bit Score: 51.11  E-value: 6.59e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVR-VCENIPIVLCGNKVDIKDRKV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLAR 78
Cdd:cd01867   83 YDITDEKSFENIKNWMRNIDEhASEDVERMLVGNKCDMEEKRVvsKEEGEALAREYGIKFLETSAKANINVEEAFLTLAK 162
M_R_Ras_like cd04145
R-Ras2/TC21, M-Ras/R-Ras3; The M-Ras/R-Ras-like subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, ...
2-78 7.74e-09

R-Ras2/TC21, M-Ras/R-Ras3; The M-Ras/R-Ras-like subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133345 [Multi-domain]  Cd Length: 164  Bit Score: 50.87  E-value: 7.74e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKD-RKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLA 77
Cdd:cd04145   81 FSVTDRGSFEEVDKFHTQILRVkdRDEFPMILVGNKADLEHqRQVsREEGQELARQLKIPYIETSAKDRVNVDKAFHDLV 160

                 .
gi 663855578  78 R 78
Cdd:cd04145  161 R 161
Rab18 cd01863
Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ...
2-80 9.66e-09

Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206656 [Multi-domain]  Cd Length: 161  Bit Score: 50.39  E-value: 9.66e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVRVC--ENIPIVLCGNKVDIKDRKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLAR 78
Cdd:cd01863   80 YDVTRRDTFDNLDTWLNELDTYStnPDAVKMLVGNKIDKENREVtREEGQKFARKHNMLFIETSAKTRIGVQQAFEELVE 159

                 ..
gi 663855578  79 KL 80
Cdd:cd01863  160 KI 161
Rab5_related cd01860
Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The ...
2-81 1.27e-08

Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The Rab5-related subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206653 [Multi-domain]  Cd Length: 163  Bit Score: 50.24  E-value: 1.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVR-VCENIPIVLCGNKVDIKD-RKVKAKSI-VFHRKKNLQYYDISAKSNYNFEKPFLWLAR 78
Cdd:cd01860   81 YDITSEESFEKAKSWVKELQEhGPPNIVIALAGNKADLESkRQVSTEEAqEYADENGLLFMETSAKTGENVNELFTEIAR 160

                 ...
gi 663855578  79 KLI 81
Cdd:cd01860  161 KLP 163
RabL4 cd04101
Rab GTPase-like family 4 (Rab-like4); RabL4 (Rab-like4) subfamily. RabL4s are novel proteins ...
1-78 1.31e-08

Rab GTPase-like family 4 (Rab-like4); RabL4 (Rab-like4) subfamily. RabL4s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL4 lacks a prenylation site at the C-terminus. The specific function of RabL4 remains unknown.


Pssm-ID: 206688 [Multi-domain]  Cd Length: 167  Bit Score: 50.22  E-value: 1.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWhRDLVR---VCENIPIVLCGNKVDIKDRK--VKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLW 75
Cdd:cd04101   83 VYDVTNEVSFNNCSRW-INRVRthsHGLHTPGVLVGNKCDLTDRRevDAAQAQALAQANTLKFYETSAKEGVGYEAPFLS 161

                 ...
gi 663855578  76 LAR 78
Cdd:cd04101  162 LAR 164
Rab2 cd01866
Rab GTPase family 2 (Rab2); Rab2 is localized on cis-Golgi membranes and interacts with Golgi ...
2-80 1.81e-08

Rab GTPase family 2 (Rab2); Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206658 [Multi-domain]  Cd Length: 168  Bit Score: 49.73  E-value: 1.81e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDlVR--VCENIPIVLCGNKVDIKDRKV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLA 77
Cdd:cd01866   84 YDITRRETFNHLTSWLED-ARqhSNSNMTIMLIGNKCDLESRREvsYEEGEAFAREHGLIFMETSAKTASNVEEAFINTA 162

                 ...
gi 663855578  78 RKL 80
Cdd:cd01866  163 KEI 165
Rab4 cd04113
Rab GTPase family 4 (Rab4); Rab4 subfamily. Rab4 has been implicated in numerous functions ...
2-80 1.99e-08

Rab GTPase family 4 (Rab4); Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206696 [Multi-domain]  Cd Length: 161  Bit Score: 49.74  E-value: 1.99e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDlVR--VCENIPIVLCGNKVDIK-DRKVK-AKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLA 77
Cdd:cd04113   80 YDITSRESFNALTNWLTD-ARtlASPDIVIILVGNKKDLEdDREVTfLEASRFAQENGLLFLETSALTGENVEEAFLKCA 158

                 ...
gi 663855578  78 RKL 80
Cdd:cd04113  159 RSI 161
Rab11_like cd01868
Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25; Rab11a, Rab11b, and ...
2-73 3.47e-08

Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25; Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206660 [Multi-domain]  Cd Length: 165  Bit Score: 49.10  E-value: 3.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNW------HRDlvrvcENIPIVLCGNKVDIK-DRKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPF 73
Cdd:cd01868   83 YDITKKSTFENVERWlkelrdHAD-----SNIVIMLVGNKSDLRhLRAVpTEEAKAFAEKNGLSFIETSALDGTNVEEAF 157
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
1-37 3.95e-08

Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial Rho proteins (Miro-1, and Miro-2) and atypical Rho GTPases. Full-length proteins have a unique domain organization, with tandem GTP-binding domains and two EF hand domains (pfam00036) that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.


Pssm-ID: 462490 [Multi-domain]  Cd Length: 114  Bit Score: 47.89  E-value: 3.95e-08
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 663855578    1 MFDVTsrvTYKNVPNWHRDLVRVCENIPIVLCGNKVD 37
Cdd:pfam08477  81 VYDSR---TFSNLKYWLRELKKYAGNSPVILVGNKID 114
H_N_K_Ras_like cd04138
Ras GTPase family containing H-Ras,N-Ras and K-Ras4A/4B; H-Ras/N-Ras/K-Ras subfamily. H-Ras, ...
2-80 4.82e-08

Ras GTPase family containing H-Ras,N-Ras and K-Ras4A/4B; H-Ras/N-Ras/K-Ras subfamily. H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1. Others are proposed to play negative regulatory roles in oncogenesis, including RASSF and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133338 [Multi-domain]  Cd Length: 162  Bit Score: 48.57  E-value: 4.82e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKDRKV-------KAKSIvfhrkkNLQYYDISAKSNYNFEKP 72
Cdd:cd04138   80 FAINSRKSFEDIHTYREQIKRVkdSDDVPMVLVGNKCDLAARTVstrqgqdLAKSY------GIPYIETSAKTRQGVEEA 153

                 ....*...
gi 663855578  73 FLWLARKL 80
Cdd:cd04138  154 FYTLVREI 161
Rab19 cd01864
Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. ...
2-80 8.22e-08

Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet characterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133267 [Multi-domain]  Cd Length: 165  Bit Score: 48.20  E-value: 8.22e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVRV-CENIPIVLCGNKVDIKDRkvkaKSIVFHRKKNL-QYYDI------SAKSNYNFEKPF 73
Cdd:cd01864   83 YDITRRSSFESVPHWIEEVEKYgASNVVLLLIGNKCDLEEQ----REVLFEEACTLaEHYGIlavletSAKESSNVEEAF 158

                 ....*..
gi 663855578  74 LWLARKL 80
Cdd:cd01864  159 LLMATEL 165
RalA_RalB cd04139
Ral (Ras-like) family containing highly homologous RalA and RalB; The Ral (Ras-like) subfamily ...
2-80 1.61e-07

Ral (Ras-like) family containing highly homologous RalA and RalB; The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (>80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exocyst and for localizing the exocyst to the leading edge of migrating cells. In human cancer cells, RalA is required to support anchorage-independent proliferation and RalB is required to suppress apoptosis. RalA has been shown to localize to the plasma membrane while RalB is localized to the intracellular vesicles. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206710 [Multi-domain]  Cd Length: 163  Bit Score: 47.42  E-value: 1.61e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKDRKVKAKSIV--FHRKKNLQYYDISAKSNYNFEKPFLWLA 77
Cdd:cd04139   79 FSITDMESFTALAEFREQILRVkeDDNVPLLLVGNKCDLEDKRQVSVEEAanLAEQWGVNYVETSAKTRANVDKVFFDLV 158

                 ...
gi 663855578  78 RKL 80
Cdd:cd04139  159 REI 161
Rab35 cd04110
Rab GTPase family 35 (Rab35); Rab35 is one of several Rab proteins to be found to participate ...
1-81 1.88e-07

Rab GTPase family 35 (Rab35); Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133310 [Multi-domain]  Cd Length: 199  Bit Score: 47.54  E-value: 1.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLAR 78
Cdd:cd04110   85 VYDVTNGESFVNVKRWLQEIEQNCDDVCKVLVGNKNDDPERKVveTEDAYKFAGQMGISLFETSAKENINVEEMFNCITE 164

                 ...
gi 663855578  79 KLI 81
Cdd:cd04110  165 LVL 167
Rab6 cd01861
Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways ...
2-73 2.24e-07

Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206654 [Multi-domain]  Cd Length: 161  Bit Score: 46.85  E-value: 2.24e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVRVCENIP-IVLCGNKVDIKDRKVkaKSIV----FHRKKNLQYYDISAKSNYNFEKPF 73
Cdd:cd01861   80 YDITNRQSFDNTDKWIDDVRDERGNDViIVLVGNKTDLSDKRQ--VSTEegekKAKENNAMFIETSAKAGHNVKQLF 154
Rab14 cd04122
Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, ...
1-80 1.03e-06

Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133322 [Multi-domain]  Cd Length: 166  Bit Score: 45.21  E-value: 1.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVCE-NIPIVLCGNKVDIKD-RKVK-AKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLA 77
Cdd:cd04122   81 VYDITRRSTYNHLSSWLTDARNLTNpNTVIFLIGNKADLEAqRDVTyEEAKQFADENGLLFLECSAKTGENVEDAFLETA 160

                 ...
gi 663855578  78 RKL 80
Cdd:cd04122  161 KKI 163
PLN03118 PLN03118
Rab family protein; Provisional
1-86 1.13e-06

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 45.43  E-value: 1.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPN-WHRDLVRVCENIPIV--LCGNKVDIKDRKV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLW 75
Cdd:PLN03118  92 VYDVTRRETFTNLSDvWGKEVELYSTNQDCVkmLVGNKVDRESERDvsREEGMALAKEHGCLFLECSAKTRENVEQCFEE 171
                         90
                 ....*....|.
gi 663855578  76 LARKLIGDPNL 86
Cdd:PLN03118 172 LALKIMEVPSL 182
Rab30 cd04114
Rab GTPase family 30 (Rab30); Rab30 subfamily. Rab30 appears to be associated with the Golgi ...
2-81 1.35e-06

Rab GTPase family 30 (Rab30); Rab30 subfamily. Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133314 [Multi-domain]  Cd Length: 169  Bit Score: 44.89  E-value: 1.35e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWHRDLVRVCEN-IPIVLCGNKVDIKDRKVKAKSIV--FHRKKNLQYYDISAKSNYNFEKPFLWLAR 78
Cdd:cd04114   87 YDITCEESFRCLPEWLREIEQYANNkVITILVGNKIDLAERREVSQQRAeeFSDAQDMYYLETSAKESDNVEKLFLDLAC 166

                 ...
gi 663855578  79 KLI 81
Cdd:cd04114  167 RLI 169
Rho cd00157
Ras homology family (Rho) of small guanosine triphosphatases (GTPases); Members of the Rho ...
2-40 1.63e-06

Ras homology family (Rho) of small guanosine triphosphatases (GTPases); Members of the Rho (Ras homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Since crystal structures often lack C-terminal residues, this feature is not available for annotation in many of the CDs in the hierarchy.


Pssm-ID: 206641 [Multi-domain]  Cd Length: 171  Bit Score: 44.46  E-value: 1.63e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPN-WHRDLVRVCENIPIVLCGNKVDIKD 40
Cdd:cd00157   79 FSVDSPSSFENVKTkWYPEIKHYCPNVPIILVGTKIDLRD 118
PLN03110 PLN03110
Rab GTPase; Provisional
1-124 1.78e-06

Rab GTPase; Provisional


Pssm-ID: 178657 [Multi-domain]  Cd Length: 216  Bit Score: 44.92  E-value: 1.78e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVCE-NIPIVLCGNKVDIKD-RKVKAK-SIVFHRKKNLQYYDISAKSNYNFEKPFLWLA 77
Cdd:PLN03110  91 VYDITKRQTFDNVQRWLRELRDHADsNIVIMMAGNKSDLNHlRSVAEEdGQALAEKEGLSFLETSALEATNVEKAFQTIL 170
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 663855578  78 RKLIgdpnlefvampalappEVVMDPALAAQyehdlEVAQTTALPDE 124
Cdd:PLN03110 171 LEIY----------------HIISKKALAAQ-----EAAANSGLPGQ 196
Ras2 cd04144
Rat sarcoma (Ras) family 2 of small guanosine triphosphatases (GTPases); The Ras2 subfamily, ...
1-80 3.26e-06

Rat sarcoma (Ras) family 2 of small guanosine triphosphatases (GTPases); The Ras2 subfamily, found exclusively in fungi, was first identified in Ustilago maydis. In U. maydis, Ras2 is regulated by Sql2, a protein that is homologous to GEFs (guanine nucleotide exchange factors) of the CDC25 family. Ras2 has been shown to induce filamentous growth, but the signaling cascade through which Ras2 and Sql2 regulate cell morphology is not known. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.


Pssm-ID: 133344 [Multi-domain]  Cd Length: 190  Bit Score: 44.07  E-value: 3.26e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVCEN----IPIVLCGNKVD-IKDRKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFL 74
Cdd:cd04144   77 VYSITSRSTFERVERFREQIQRVKDEsaadVPIMIVGNKCDkVYEREVsTEEGAALARRLGCEFIEASAKTNVNVERAFY 156

                 ....*.
gi 663855578  75 WLARKL 80
Cdd:cd04144  157 TLVRAL 162
RJL cd04119
Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with ...
1-65 3.30e-06

Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.


Pssm-ID: 133319 [Multi-domain]  Cd Length: 168  Bit Score: 43.88  E-value: 3.30e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVC------ENIPIVLCGNKVDIKDRKVKAKS--IVFHRKKNLQYYDISAKS 65
Cdd:cd04119   79 VYDVTDRQSFEALDSWLKEMKQEGgphgnmENIVVVVCANKIDLTKHRAVSEDegRLWAESKGFKYFETSACT 151
Rab12 cd04120
Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was ...
1-83 3.94e-06

Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206699 [Multi-domain]  Cd Length: 202  Bit Score: 43.85  E-value: 3.94e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVR-VCENIPIVLCGNKVDIK-DRKV-KAKSIVF-HRKKNLQYYDISAKSNYNFEKPFLwl 76
Cdd:cd04120   79 VYDITKKETFDDLPKWMKMIDKyASEDAELLLVGNKLDCEtDREItRQQGEKFaQQITGMRFCEASAKDNFNVDEIFL-- 156

                 ....*..
gi 663855578  77 arKLIGD 83
Cdd:cd04120  157 --KLVDD 161
Rab32_Rab38 cd04107
Rab GTPase families 18 (Rab18) and 32 (Rab32); Rab38/Rab32 subfamily. Rab32 and Rab38 are ...
1-81 4.09e-06

Rab GTPase families 18 (Rab18) and 32 (Rab32); Rab38/Rab32 subfamily. Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206692 [Multi-domain]  Cd Length: 201  Bit Score: 43.84  E-value: 4.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDL---VRVC--ENIPIVLCGNKVDIKDRKVKAKSIVFHR--KKN--LQYYDISAKSNYNFEK 71
Cdd:cd04107   80 VFDVTRPSTFEAVLKWKADLdskVTLPngEPIPALLLANKCDLKKERLAKDPEQMDQfcKENgfIGWFETSAKENINIEE 159
                         90
                 ....*....|
gi 663855578  72 PFLWLARKLI 81
Cdd:cd04107  160 AMRFLVKNIL 169
Rab39 cd04111
Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell ...
1-78 4.66e-06

Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines. It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133311 [Multi-domain]  Cd Length: 211  Bit Score: 43.98  E-value: 4.66e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDlVRV---CENIPIVLCGNKVD-IKDRKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLW 75
Cdd:cd04111   82 VFDITNRESFEHVHDWLEE-ARShiqPHRPVFILVGHKCDlESQRQVtREEAEKLAKDLGMKYIETSARTGDNVEEAFEL 160

                 ...
gi 663855578  76 LAR 78
Cdd:cd04111  161 LTQ 163
RSR1 cd04177
RSR1/Bud1p family GTPase; RSR1/Bud1p is a member of the Rap subfamily of the Ras family that ...
1-81 5.84e-06

RSR1/Bud1p family GTPase; RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.


Pssm-ID: 133377 [Multi-domain]  Cd Length: 168  Bit Score: 43.24  E-value: 5.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKDRKV--KAKSIVFHRK-KNLQYYDISAKSNYNFEKPFLW 75
Cdd:cd04177   79 VYSVTSEASLNELGELREQVLRIkdSDNVPMVLVGNKADLEDDRQvsREDGVSLSQQwGNVPFYETSARKRTNVDEVFID 158

                 ....*.
gi 663855578  76 LARKLI 81
Cdd:cd04177  159 LVRQII 164
Rap2 cd04176
Rap2 family GTPase consists of Rap2a, Rap2b, and Rap2c; The Rap2 subgroup is part of the Rap ...
1-80 6.92e-06

Rap2 family GTPase consists of Rap2a, Rap2b, and Rap2c; The Rap2 subgroup is part of the Rap subfamily of the Ras family. It consists of Rap2a, Rap2b, and Rap2c. Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton. In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments. In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway. The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation. A number of additional effector proteins for Rap2 have been identified, including the RalGEFs RalGDS, RGL, and Rlf, which also interact with Rap1 and Ras. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133376 [Multi-domain]  Cd Length: 163  Bit Score: 42.90  E-value: 6.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDIK-DRKVK-AKSIVFHRKKNLQYYDISAKSNYNFEKPFLWL 76
Cdd:cd04176   79 VYSLVNQQTFQDIKPMRDQIVRVkgYEKVPIILVGNKVDLEsEREVSsAEGRALAEEWGCPFMETSAKSKTMVNELFAEI 158

                 ....
gi 663855578  77 ARKL 80
Cdd:cd04176  159 VRQM 162
RheB cd04137
Ras Homolog Enriched in Brain (RheB) is a small GTPase; Rheb (Ras Homolog Enriched in Brain) ...
1-73 1.55e-05

Ras Homolog Enriched in Brain (RheB) is a small GTPase; Rheb (Ras Homolog Enriched in Brain) subfamily. Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that leads to cell growth and cell-cycle progression. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.


Pssm-ID: 206709 [Multi-domain]  Cd Length: 180  Bit Score: 42.23  E-value: 1.55e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVC--ENIPIVLCGNKVDIKD-RKVKAKS-IVFHRKKNLQYYDISAKSNYNFEKPF 73
Cdd:cd04137   79 VYSVTSRKSFEVVKVIYDKILDMLgkESVPIVLVGNKSDLHMeRQVSAEEgKKLAESWGAAFLESSAKENENVEEAF 155
PTZ00369 PTZ00369
Ras-like protein; Provisional
1-80 1.97e-05

Ras-like protein; Provisional


Pssm-ID: 240385 [Multi-domain]  Cd Length: 189  Bit Score: 41.77  E-value: 1.97e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVCEN--IPIVLCGNKVDIK-DRKVK-AKSIVFHRKKNLQYYDISAKSNYNFEKPFLWL 76
Cdd:PTZ00369  83 VYSITSRSSFEEIASFREQILRVKDKdrVPMILVGNKCDLDsERQVStGEGQELAKSFGIPFLETSAKQRVNVDEAFYEL 162

                 ....
gi 663855578  77 ARKL 80
Cdd:PTZ00369 163 VREI 166
Rap_like cd04136
Rap-like family consists of Rap1, Rap2 and RSR1; The Rap subfamily consists of the Rap1, Rap2, ...
1-81 2.22e-05

Rap-like family consists of Rap1, Rap2 and RSR1; The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. Rap2 is involved in multiple functions, including activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton and activation of the Wnt/beta-catenin signaling pathway in embryonic Xenopus. A number of effector proteins for Rap2 have been identified, including isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK), and the RalGEFs RalGDS, RGL, and Rlf, which also interact with Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and Rap2. In budding yeasts, it is involved in selecting a site for bud growth, which directs the establishment of cell polarization. The Rho family GTPase Cdc42 and its GEF, Cdc24, then establish an axis of polarized growth. It is believed that Cdc42 interacts directly with RSR1 in vivo. In filamentous fungi such as Ashbya gossypii, RSR1 is a key regulator of polar growth in the hypha. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206708 [Multi-domain]  Cd Length: 164  Bit Score: 41.39  E-value: 2.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKDRKVKAKS--IVFHRK-KNLQYYDISAKSNYNFEKPFLW 75
Cdd:cd04136   79 VYSITAQQSFNDLQDLREQILRVkdTEDVPMILVGNKCDLEDERVVSKEegQNLARQwGNCPFLETSAKSKINVDEIFYD 158

                 ....*.
gi 663855578  76 LARKLI 81
Cdd:cd04136  159 LVRQIN 164
RHO smart00174
Rho (Ras homology) subfamily of Ras-like small GTPases; Members of this subfamily of Ras-like ...
2-42 2.68e-05

Rho (Ras homology) subfamily of Ras-like small GTPases; Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.


Pssm-ID: 197554 [Multi-domain]  Cd Length: 174  Bit Score: 41.45  E-value: 2.68e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 663855578     2 FDVTSRVTYKNVPN-WHRDLVRVCENIPIVLCGNKVDIKDRK 42
Cdd:smart00174  77 FSVDSPASFENVKEkWYPEVKHFCPNVPIILVGTKLDLRNDK 118
Rho4_like cd04132
Ras homology family 4 (Rho4) of small guanosine triphosphatases (GTPases)-like; Rho4 is a ...
2-73 3.45e-05

Ras homology family 4 (Rho4) of small guanosine triphosphatases (GTPases)-like; Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.


Pssm-ID: 206704 [Multi-domain]  Cd Length: 197  Bit Score: 41.17  E-value: 3.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPN-WHRDLVRVCENIPIVLCGNKVDI-KDRKVKAKS-------IVFHRKKNL-------QYYDISAKS 65
Cdd:cd04132   83 YSVDNPTSLDNVEDkWYPEVNHFCPGTPIVLVGLKTDLrKDKNSVSKLraqglepVTPEQGESVaksigavAYIECSAKL 162

                 ....*...
gi 663855578  66 NYNFEKPF 73
Cdd:cd04132  163 MENVDEVF 170
Rhes_like cd04143
Ras homolog enriched in striatum (Rhes) and activator of G-protein signaling 1 (Dexras1/AGS1); ...
27-77 4.25e-05

Ras homolog enriched in striatum (Rhes) and activator of G-protein signaling 1 (Dexras1/AGS1); This subfamily includes Rhes (Ras homolog enriched in striatum) and Dexras1/AGS1 (activator of G-protein signaling 1). These proteins are homologous, but exhibit significant differences in tissue distribution and subcellular localization. Rhes is found primarily in the striatum of the brain, but is also expressed in other areas of the brain, such as the cerebral cortex, hippocampus, inferior colliculus, and cerebellum. Rhes expression is controlled by thyroid hormones. In rat PC12 cells, Rhes is farnesylated and localizes to the plasma membrane. Rhes binds and activates PI3K, and plays a role in coupling serpentine membrane receptors with heterotrimeric G-protein signaling. Rhes has recently been shown to be reduced under conditions of dopamine supersensitivity and may play a role in determining dopamine receptor sensitivity. Dexras1/AGS1 is a dexamethasone-induced Ras protein that is expressed primarily in the brain, with low expression levels in other tissues. Dexras1 localizes primarily to the cytoplasm, and is a critical regulator of the circadian master clock to photic and nonphotic input. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.


Pssm-ID: 133343 [Multi-domain]  Cd Length: 247  Bit Score: 41.27  E-value: 4.25e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 663855578  27 IPIVLCGNKVDIKD-RKVKAKSI--VFHRKKNLQYYDISAKSNYNFEKPFLWLA 77
Cdd:cd04143  114 IPMVICGNKADRDFpREVQRDEVeqLVGGDENCAYFEVSAKKNSNLDEMFRALF 167
Rab40 cd04121
Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c; The Rab40 subfamily contains ...
1-78 7.33e-05

Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c; The Rab40 subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133321 [Multi-domain]  Cd Length: 189  Bit Score: 40.30  E-value: 7.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIK-DRKVKAKSI-VFHRKKNLQYYDISAKSNYNFEKPFLWLAR 78
Cdd:cd04121   85 VYDITNRWSFDGIDRWIKEIDEHAPGVPKILVGNRLHLAfKRQVATEQAqAYAERNGMTFFEVSPLCNFNITESFTELAR 164
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
1-73 8.73e-05

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 39.66  E-value: 8.73e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663855578    1 MFDVTSRV-TYKNVPN-WHRDLVRVCE-NIPIVLCGNKVDIKDRKVKAKSI-VFHRKKNLQYYDISAKSNYNFEKPF 73
Cdd:TIGR00231  81 VFDIVILVlDVEEILEkQTKEIIHHADsGVPIILVGNKIDLKDADLKTHVAsEFAKLNGEPIIPLSAETGKNIDSAF 157
Rab3 cd01865
Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, ...
1-73 1.06e-04

Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206657 [Multi-domain]  Cd Length: 165  Bit Score: 39.51  E-value: 1.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKDRKVkaksIVFHRKKNL------QYYDISAKSNYNFEKPF 73
Cdd:cd01865   80 MYDITNEESFNAVQDWSTQIKTYSwDNAQVILVGNKCDMEDERV----VSAERGRQLadqlgfEFFEASAKENINVKQVF 155
Rop_like cd04133
Rho-related protein from plants (Rop)-like; The Rop (Rho-related protein from plants) ...
2-42 1.75e-04

Rho-related protein from plants (Rop)-like; The Rop (Rho-related protein from plants) subfamily plays a role in diverse cellular processes, including cytoskeletal organization, pollen and vegetative cell growth, hormone responses, stress responses, and pathogen resistance. Rops are able to regulate several downstream pathways to amplify a specific signal by acting as master switches early in the signaling cascade. They transmit a variety of extracellular and intracellular signals. Rops are involved in establishing cell polarity in root-hair development, root-hair elongation, pollen-tube growth, cell-shape formation, responses to hormones such as abscisic acid (ABA) and auxin, responses to abiotic stresses such as oxygen deprivation, and disease resistance and disease susceptibility. An individual Rop can have a unique function or an overlapping function shared with other Rop proteins; in addition, a given Rop-regulated function can be controlled by one or multiple Rop proteins. For example, Rop1, Rop3, and Rop5 are all involved in pollen-tube growth; Rop2 plays a role in response to low-oxygen environments, cell-morphology, and root-hair development; root-hair development is also regulated by Rop4 and Rop6; Rop6 is also responsible for ABA response, and ABA response is also regulated by Rop10. Plants retain some of the regulatory mechanisms that are shared by other members of the Rho family, but have also developed a number of unique modes for regulating Rops. Unique RhoGEFs have been identified that are exclusively active toward Rop proteins, such as those containing the domain PRONE (plant-specific Rop nucleotide exchanger). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206705 [Multi-domain]  Cd Length: 173  Bit Score: 39.06  E-value: 1.75e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 663855578   2 FDVTSRVTYKNV-PNWHRDLVRVCENIPIVLCGNKVDIKDRK 42
Cdd:cd04133   80 FSLISKASYENVlKKWIPELRHYAPGVPIVLVGTKLDLRDDK 121
Rab9 cd04116
Rab GTPase family 9 (Rab9); Rab9 is found in late endosomes, together with mannose 6-phosphate ...
2-73 1.89e-04

Rab GTPase family 9 (Rab9); Rab9 is found in late endosomes, together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kD (TIP47). Rab9 is a key mediator of vesicular transport from late endosomes to the trans-Golgi network (TGN) by redirecting the MPRs. Rab9 has been identified as a key component for the replication of several viruses, including HIV1, Ebola, Marburg, and measles, making it a potential target for inhibiting a variety of viruses. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206697 [Multi-domain]  Cd Length: 170  Bit Score: 39.09  E-value: 1.89e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 663855578   2 FDVTSRVTYKNVPNWHRDL-----VRVCENIPIVLCGNKVDIKDRKVKAKSIV--FHRKKNLQYYDISAKSNYNFEKPF 73
Cdd:cd04116   85 FSVDDSQSFQNLSNWKKEFiyyadVKEPESFPFVILGNKIDIPERQVSTEEAQawCRDNGDYPYFETSAKDATNVAAAF 163
Rit_Rin_Ric cd04141
Ras-like protein in all tissues (Rit), Ras-like protein in neurons (Rin) and Ras-related ...
2-80 3.20e-04

Ras-like protein in all tissues (Rit), Ras-like protein in neurons (Rin) and Ras-related protein which interacts with calmodulin (Ric); Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to signal in parallel with the Ras pathway or stimulate the Ras pathway at some upstream point, and binding of calmodulin to Ric may negatively regulate Ric activity.


Pssm-ID: 206712 [Multi-domain]  Cd Length: 172  Bit Score: 38.30  E-value: 3.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWhRDL---VRVCENIPIVLCGNKVDIKD-RKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWL 76
Cdd:cd04141   81 YSVTDRHSFQEASEF-KELitrVRLTEDIPLVLVGNKVDLEQqRQVtTEEGRNLAREFNCPFFETSAALRFYIDDAFHGL 159

                 ....
gi 663855578  77 ARKL 80
Cdd:cd04141  160 VREI 163
Ras_dva cd04147
Ras - dorsal-ventral anterior localization (Ras-dva) family; Ras-dva subfamily. Ras-dva (Ras - ...
1-106 9.64e-04

Ras - dorsal-ventral anterior localization (Ras-dva) family; Ras-dva subfamily. Ras-dva (Ras - dorsal-ventral anterior localization) subfamily consists of a set of proteins characterized only in Xenopus leavis, to date. In Xenopus Ras-dva expression is activated by the transcription factor Otx2 and begins during gastrulation throughout the anterior ectoderm. Ras-dva expression is inhibited in the anterior neural plate by factor Xanf1. Downregulation of Ras-dva results in head development abnormalities through the inhibition of several regulators of the anterior neural plate and folds patterning, including Otx2, BF-1, Xag2, Pax6, Slug, and Sox9. Downregulation of Ras-dva also interferes with the FGF-8a signaling within the anterior ectoderm. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.


Pssm-ID: 206714 [Multi-domain]  Cd Length: 197  Bit Score: 37.13  E-value: 9.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   1 MFDVTSRVTYKNVPNWHRDLVRVCEN--IPIVLCGNKVD-IKDRKVKAKSI--VFHRKKNLQYYDISAKSNYNFEKPFlw 75
Cdd:cd04147   77 VYSVDDPESFEEVKRLREEILEVKEDkfVPIVVVGNKIDsLAERQVEAADAlsTVELDWNNGFVEASAKDNENVTEVF-- 154
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 663855578  76 laRKLIGDPNLEFVAMPAL------APPEVVMDPALA 106
Cdd:cd04147  155 --KELLQQANLPSWLSPALrrrresAPSEIQRRPPMN 189
RhoG cd01875
Ras homolog family, member G (RhoG) of small guanosine triphosphatases (GTPases); RhoG is a ...
2-42 1.44e-03

Ras homolog family, member G (RhoG) of small guanosine triphosphatases (GTPases); RhoG is a GTPase with high sequence similarity to members of the Rac subfamily, including the regions involved in effector recognition and binding. However, RhoG does not bind to known Rac1 and Cdc42 effectors, including proteins containing a Cdc42/Rac interacting binding (CRIB) motif. Instead, RhoG interacts directly with Elmo, an upstream regulator of Rac1, in a GTP-dependent manner and forms a ternary complex with Dock180 to induce activation of Rac1. The RhoG-Elmo-Dock180 pathway is required for activation of Rac1 and cell spreading mediated by integrin, as well as for neurite outgrowth induced by nerve growth factor. Thus RhoG activates Rac1 through Elmo and Dock180 to control cell morphology. RhoG has also been shown to play a role in caveolar trafficking and has a novel role in signaling the neutrophil respiratory burst stimulated by G protein-coupled receptor (GPCR) agonists. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.


Pssm-ID: 133277 [Multi-domain]  Cd Length: 191  Bit Score: 36.53  E-value: 1.44e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 663855578   2 FDVTSRVTYKNVPN-WHRDLVRVCENIPIVLCGNKVDIKDRK 42
Cdd:cd01875   82 FSIASPSSYENVRHkWHPEVCHHCPNVPILLVGTKKDLRNDA 123
Rab33B_Rab33A cd04115
Rab GTPase family 33 includes Rab33A and Rab33B; Rab33B/Rab33A subfamily. Rab33B is ...
2-80 1.87e-03

Rab GTPase family 33 includes Rab33A and Rab33B; Rab33B/Rab33A subfamily. Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133315 [Multi-domain]  Cd Length: 170  Bit Score: 36.26  E-value: 1.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663855578   2 FDVTSRVTYKNVPNWhrdlVRVCEN------IPIVLCGNKVDIKD-RKVKA-KSIVFHRKKNLQYYDISAK---SNYNFE 70
Cdd:cd04115   83 YDVTNMASFHSLPSW----IEECEQhslpneVPRILVGNKCDLREqIQVPTdLAQRFADAHSMPLFETSAKdpsENDHVE 158
                         90
                 ....*....|
gi 663855578  71 KPFLWLARKL 80
Cdd:cd04115  159 AIFMTLAHKL 168
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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