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Conserved domains on  [gi|568906665|ref|XP_006496192|]
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RUN and FYVE domain-containing protein 4 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RUN super family cl45896
RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new ...
 17-161 4.82e-73

RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new molecule containing SH3 at the carboxyl-terminus), is a less conserved protein motif that comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases. RUN domains are often found in proteins linked particularly to the functions of GTPases in the Rap and Rab families, suggesting the RUN domain may be involved in Rab-mediated membrane trafficking, possibly as a Rab-binding site. RUN domain-containing proteins could hence play important roles in multiple Ras-like GTPase signalling pathways.


The actual alignment was detected with superfamily member cd17697:

Pssm-ID: 459241  Cd Length: 150  Bit Score: 230.45  E-value: 4.82e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  17 AVSAILQGYGDGQE-PVTETSAELHRLCGCLELLLQFDQKEQRSFLGARKDYWDFLFTALRRHRGYTEQMSFICSQDKLK 95
Cdd:cd17697    5 ASIAELQKDQEEQQlPITDGSPELHRLCARLEYLLQFDQKEKKSFFGSRKDYWDFLCLCLNRHRGGTEGIHFVNSTDKLK 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568906665  96 TSLGKGRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAFNL 161
Cdd:cd17697   85 TPLGKGRAFIRYCLVQQQLAESLQLCLLNPELTGEWYYARSPFLSPELRSDILDSLYELNGVNFDL 150
FYVE_RUFY4 cd15745
FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar ...
 544-586 8.31e-11

FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins; RUFY4 belongs to the FUFY protein family which is characterized by the presence of an N-terminal RUN domain and a C-terminal FYVE domain. The FYVE domain of RUFY4 resembles the FYVE-related domain as it lacks the WxxD motif (x for any residue). The biological function of RUFY4 still remains unclear.


:

Pssm-ID: 277284 [Multi-domain]  Cd Length: 52  Bit Score: 57.51  E-value: 8.31e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 568906665 544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACSVDYK--------KRERCCPTC 586
Cdd:cd15745    1 ACAICAKAFSLFRRKYVCRLCGGVVCHSCSSEDLvlsvpdtcIYLRVCKTC 51
OmpH pfam03938
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
 448-527 4.03e-05

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.


:

Pssm-ID: 461098 [Multi-domain]  Cd Length: 140  Bit Score: 43.72  E-value: 4.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  448 QLAKEQAQCQEQLRAQEAELQALQEQLsrcQKERALLQVKLEQKQQEAERRDAMYQTELEGQRDLVQAMKRRVLELIHEK 527
Cdd:pfam03938  23 QLEKKFKKRQAELEAKQKELQKLYEEL---QKDGALLEEEREEKEQELQKKEQELQQLQQKAQQELQKKQQELLQPIQDK 99
CCDC22 super family cl25503
Coiled-coil domain-containing protein 22; Human coiled-coil domain-containing protein 22 ...
 236-537 1.92e-03

Coiled-coil domain-containing protein 22; Human coiled-coil domain-containing protein 22 (CCDC22) is involved in regulation of NF-kappa-B signalling; the function may involve association with COMMD8 and a CUL1-dependent E3 ubiquitin ligase complex. It is part of the OMMD/CCDC22/CCDC93 (CCC) complex, which interacts with the multisubunit WASH complex required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer. This entry also includes CCDC22 homologs from animals and plants.


The actual alignment was detected with superfamily member pfam05667:

Pssm-ID: 461708 [Multi-domain]  Cd Length: 600  Bit Score: 41.17  E-value: 1.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  236 SRGEQLQEPdTGGTSCLQDATREDRTPDLCKPLQPSHLPTflEEKREDSRSLsCPQSTWETEREGFQLDQKDGGPKPRKF 315
Cdd:pfam05667 111 ESSEAADQP-VGKSAVLQRAIAAAIRSQLAAPWLPPECKP--HQRRQGSRAL-RPFHTQTLVLPGRKGKTLKNSKELKEF 186

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  316 LENSTASIQQQRSRAKDVKMQLTGRKVEGKGSLSGTEDQRTTEGIQKRAADWDLGQGLMAPGLQGREDA--ELGYRCEWN 393
Cdd:pfam05667 187 YSEYLPPVTAQPSSRASVVPSLLERNAAELAAAQEWEEEWNSQGLASRLTPEEYRKRKRTKLLKRIAEQlrSAALAGTEA 266

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  394 QPDVLRQSWVLGTKKSSPTEKPQEWTGVTSGTMQEDGSEVPLQQEvikDPGYGLQLAKEQAQCQEQLRAQEAELQALQEQ 473
Cdd:pfam05667 267 TSGASRSAQDLAELLSSFSGSSTTDTGLTKGSRFTHTEKLQFTNE---APAATSSPPTKVETEEELQQQREEELEELQEQ 343

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568906665  474 LSRCQ-------KERALLQVKLEQKQQEAERRDAMyQTELEGQRDLvqamKRRVLELIHEKDLQWQRLQQL 537
Cdd:pfam05667 344 LEDLEssiqeleKEIKKLESSIKQVEEELEELKEQ-NEELEKQYKV----KKKTLDLLPDAEENIAKLQAL 409
 
Name Accession Description Interval E-value
RUN_RUFY4 cd17697
RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins; ...
 17-161 4.82e-73

RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins; RUFY4 acts as a positive regulator that enhances autophagy and lysosome tethering in response to Interleukin-4. It is expressed in a cell-specific manner or under specific immunological conditions associated with IL4 expression such as allergic asthma. RUFY4 belongs to the FUFY protein family which is characterized by the presence of an N-terminal RUN domain and a C-terminal FYVE domain; this model represents the RUN domain of RUFY4.


Pssm-ID: 439059  Cd Length: 150  Bit Score: 230.45  E-value: 4.82e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  17 AVSAILQGYGDGQE-PVTETSAELHRLCGCLELLLQFDQKEQRSFLGARKDYWDFLFTALRRHRGYTEQMSFICSQDKLK 95
Cdd:cd17697    5 ASIAELQKDQEEQQlPITDGSPELHRLCARLEYLLQFDQKEKKSFFGSRKDYWDFLCLCLNRHRGGTEGIHFVNSTDKLK 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568906665  96 TSLGKGRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAFNL 161
Cdd:cd17697   85 TPLGKGRAFIRYCLVQQQLAESLQLCLLNPELTGEWYYARSPFLSPELRSDILDSLYELNGVNFDL 150
FYVE_RUFY4 cd15745
FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar ...
 544-586 8.31e-11

FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins; RUFY4 belongs to the FUFY protein family which is characterized by the presence of an N-terminal RUN domain and a C-terminal FYVE domain. The FYVE domain of RUFY4 resembles the FYVE-related domain as it lacks the WxxD motif (x for any residue). The biological function of RUFY4 still remains unclear.


Pssm-ID: 277284 [Multi-domain]  Cd Length: 52  Bit Score: 57.51  E-value: 8.31e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 568906665 544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACSVDYK--------KRERCCPTC 586
Cdd:cd15745    1 ACAICAKAFSLFRRKYVCRLCGGVVCHSCSSEDLvlsvpdtcIYLRVCKTC 51
FYVE pfam01363
FYVE zinc finger; The FYVE zinc finger is named after four proteins that it has been found in: ...
 544-589 1.27e-07

FYVE zinc finger; The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. We have included members which do not conserve these histidine residues but are clearly related.


Pssm-ID: 426221 [Multi-domain]  Cd Length: 68  Bit Score: 48.92  E-value: 1.27e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568906665  544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACS---------VDYKKRERCCPTCAQQ 589
Cdd:pfam01363  11 VCMICSKPFTFFRRRHHCRNCGRVFCSACSskkisllpeLGSNKPVRVCDACYDT 65
FYVE smart00064
Protein present in Fab1, YOTB, Vac1, and EEA1; The FYVE zinc finger is named after four ...
 544-588 9.12e-07

Protein present in Fab1, YOTB, Vac1, and EEA1; The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PHD finger and the RING finger. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. The FYVE finger functions in the membrane recruitment of cytosolic proteins by binding to phosphatidylinositol 3-phosphate (PI3P), which is prominent on endosomes. The R+HHC+XCG motif is critical for PI3P binding.


Pssm-ID: 214499 [Multi-domain]  Cd Length: 68  Bit Score: 46.27  E-value: 9.12e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 568906665   544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACS--------VDYKKRERCCPTCAQ 588
Cdd:smart00064  12 NCMGCGKEFNLTKRRHHCRNCGRIFCSKCSskkaplpkLGIERPVRVCDDCYE 64
RUN pfam02759
RUN domain; This domain is present in several proteins that are linked to the functions of ...
 41-163 2.15e-06

RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.


Pssm-ID: 460679  Cd Length: 134  Bit Score: 47.27  E-value: 2.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665   41 RLCGCLELLLQ------FDQKEQRSFLGARKDYWDFL------FTALRRHRGYTEQMSFICSqdkLKTSLGKGRAFIRLC 108
Cdd:pfam02759   1 QLCAALEALLShglkrsSLLILRAAGLLPERSFWALLervgklVPPAEELLSSVQELEQIHT---PYSPDGRGRAWIRLA 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568906665  109 LARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAFNLDL 163
Cdd:pfam02759  78 LNEKLLDQWLKLLLSNKELLSEYYEPWALLADPEFGEILLGLLVGLSALDFNLCL 132
RUN smart00593
domain involved in Ras-like GTPase signaling;
101-163 2.32e-05

domain involved in Ras-like GTPase signaling;


Pssm-ID: 214736 [Multi-domain]  Cd Length: 64  Bit Score: 42.22  E-value: 2.32e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568906665   101 GRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAFNLDL 163
Cdd:smart00593   1 FRAWIRLALNEKLLSSWLNLLLSDEELLSKYYEPWAFLRDPEEGEQLLGLLVGLSALDFNLPV 63
OmpH pfam03938
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
 448-527 4.03e-05

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.


Pssm-ID: 461098 [Multi-domain]  Cd Length: 140  Bit Score: 43.72  E-value: 4.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  448 QLAKEQAQCQEQLRAQEAELQALQEQLsrcQKERALLQVKLEQKQQEAERRDAMYQTELEGQRDLVQAMKRRVLELIHEK 527
Cdd:pfam03938  23 QLEKKFKKRQAELEAKQKELQKLYEEL---QKDGALLEEEREEKEQELQKKEQELQQLQQKAQQELQKKQQELLQPIQDK 99
OmpH smart00935
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
 448-526 4.54e-05

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.


Pssm-ID: 214922 [Multi-domain]  Cd Length: 140  Bit Score: 43.73  E-value: 4.54e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665   448 QLAKEQAQCQEQLRAQEAELQALQEQLSR-----CQKERALLQVKLEQKQQEAERRDAMYQTELEG-QRDLVQAMKRRVL 521
Cdd:smart00935  22 QLEKEFKKRQAELEKLEKELQKLKEKLQKdaatlSEAAREKKEKELQKKVQEFQRKQQKLQQDLQKrQQEELQKILDKIN 101


                   ....*
gi 568906665   522 ELIHE 526
Cdd:smart00935 102 KAIKE 106
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 448-536 1.07e-04

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 45.31  E-value: 1.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAMYQ------TELEGQRDLVQAMKRRVL 521
Cdd:COG1196  236 ELEAELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYellaelARLEQDIARLEERRRELE 315

                         90
                 ....*....|....*
gi 568906665 522 ELIHEKDLQWQRLQQ 536
Cdd:COG1196  316 ERLEELEEELAELEE 330
STAT5_CCD cd16855
Coiled-coil domain of Signal Transducer and Activator of Transcription 5 (STAT5); This family ...
 455-538 8.84e-04

Coiled-coil domain of Signal Transducer and Activator of Transcription 5 (STAT5); This family consists of the coiled-coil (alpha) domain of the STAT5 proteins (Signal Transducer and Activator of Transcription 5, or Signal Transduction And Transcription 5) which include STAT5A and STAT5B, both of which are >90% identical despite being encoded by separate genes. The coiled-coil domain (CCD) of STAT5A and STAT5B appears to be required for constitutive nuclear localization signals (NLS) function; small deletions within the CCD can abrogate nuclear import. Studies show that the CCD binds to the importin-alpha3 NLS adapter in most cells. STAT5A and STAT5B regulate erythropoiesis, lymphopoiesis, and the maintenance of the hematopoietic stem cell population. STAT5A and STAT5B have overlapping and redundant functions; both isoforms can be activated by the same set of cytokines, but some cytokines preferentially activate either STAT5A or STAT5B, e.g. during pregnancy and lactation, STAT5A rather than STAT5B is required for the production of luminal progenitor cells from mammary stem cells and is essential for the differentiation of milk producing alveolar cells during pregnancy. STAT5 has been found to be constitutively phosphorylated in cancer cells, and therefore constantly activated, either by aberrant cell signaling expression or by mutations. It differentially regulates cellular behavior in human mammary carcinoma. Prolactin (PRL) in the prostate gland can induce growth and survival of prostate cancer cells and tissues through the activation of STAT5, its downstream target; PRL expression and STAT5 activation correlates with disease severity. STAT5A and STAT5B are central signaling molecules in leukemias driven by Abelson fusion tyrosine kinases, displaying unique nuclear shuttling mechanisms and having a key role in resistance of leukemic cells against treatment with tyrosine kinase inhibitors (TKI). In addition, STAT5A and STAT5B promote survival of leukemic stem cells. STAT5 is a key transcription factor for IL-3-mediated inhibition of RANKL-induced osteoclastogenesis via the induction of the expression of Id genes. Autosomal recessive STAT5B mutations are associated with severe growth failure, insulin-like growth factor (IGF) deficiency and growth hormone insensitivity (GHI) syndrome. STAT5B deficiency can lead to potentially fatal primary immunodeficiency.


Pssm-ID: 341080 [Multi-domain]  Cd Length: 194  Bit Score: 40.71  E-value: 8.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 455 QCQEQLRAQeAELQALQEQ-LSRCQKERALLQVKLEQKQQEAerrDAMYQTELEGQRDLVQAMK------RRVLELIHEK 527
Cdd:cd16855   37 QYQESQKIQ-AQLQQLQQQpQNERIELEQQLQQQKEQLEQLL---NAKAQELLQLRMELADKFKktiqllSKLQSRVLDE 112

                         90
                 ....*....|..
gi 568906665 528 DL-QWQRLQQLS 538
Cdd:cd16855  113 ELiQWKRQQQLA 124
CCDC22 pfam05667
Coiled-coil domain-containing protein 22; Human coiled-coil domain-containing protein 22 ...
 236-537 1.92e-03

Coiled-coil domain-containing protein 22; Human coiled-coil domain-containing protein 22 (CCDC22) is involved in regulation of NF-kappa-B signalling; the function may involve association with COMMD8 and a CUL1-dependent E3 ubiquitin ligase complex. It is part of the OMMD/CCDC22/CCDC93 (CCC) complex, which interacts with the multisubunit WASH complex required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer. This entry also includes CCDC22 homologs from animals and plants.


Pssm-ID: 461708 [Multi-domain]  Cd Length: 600  Bit Score: 41.17  E-value: 1.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  236 SRGEQLQEPdTGGTSCLQDATREDRTPDLCKPLQPSHLPTflEEKREDSRSLsCPQSTWETEREGFQLDQKDGGPKPRKF 315
Cdd:pfam05667 111 ESSEAADQP-VGKSAVLQRAIAAAIRSQLAAPWLPPECKP--HQRRQGSRAL-RPFHTQTLVLPGRKGKTLKNSKELKEF 186

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  316 LENSTASIQQQRSRAKDVKMQLTGRKVEGKGSLSGTEDQRTTEGIQKRAADWDLGQGLMAPGLQGREDA--ELGYRCEWN 393
Cdd:pfam05667 187 YSEYLPPVTAQPSSRASVVPSLLERNAAELAAAQEWEEEWNSQGLASRLTPEEYRKRKRTKLLKRIAEQlrSAALAGTEA 266

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  394 QPDVLRQSWVLGTKKSSPTEKPQEWTGVTSGTMQEDGSEVPLQQEvikDPGYGLQLAKEQAQCQEQLRAQEAELQALQEQ 473
Cdd:pfam05667 267 TSGASRSAQDLAELLSSFSGSSTTDTGLTKGSRFTHTEKLQFTNE---APAATSSPPTKVETEEELQQQREEELEELQEQ 343

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568906665  474 LSRCQ-------KERALLQVKLEQKQQEAERRDAMyQTELEGQRDLvqamKRRVLELIHEKDLQWQRLQQL 537
Cdd:pfam05667 344 LEDLEssiqeleKEIKKLESSIKQVEEELEELKEQ-NEELEKQYKV----KKKTLDLLPDAEENIAKLQAL 409
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 448-539 2.53e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.81  E-value: 2.53e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665   448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAMYQ---TELEGQRDLVQAMKRRVLELI 524
Cdd:TIGR02168  313 NLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEeleSRLEELEEQLETLRSKVAQLE 392

                           90
                   ....*....|....*
gi 568906665   525 HEKDLQWQRLQQLST 539
Cdd:TIGR02168  393 LQIASLNNEIERLEA 407
 
Name Accession Description Interval E-value
RUN_RUFY4 cd17697
RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins; ...
 17-161 4.82e-73

RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins; RUFY4 acts as a positive regulator that enhances autophagy and lysosome tethering in response to Interleukin-4. It is expressed in a cell-specific manner or under specific immunological conditions associated with IL4 expression such as allergic asthma. RUFY4 belongs to the FUFY protein family which is characterized by the presence of an N-terminal RUN domain and a C-terminal FYVE domain; this model represents the RUN domain of RUFY4.


Pssm-ID: 439059  Cd Length: 150  Bit Score: 230.45  E-value: 4.82e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  17 AVSAILQGYGDGQE-PVTETSAELHRLCGCLELLLQFDQKEQRSFLGARKDYWDFLFTALRRHRGYTEQMSFICSQDKLK 95
Cdd:cd17697    5 ASIAELQKDQEEQQlPITDGSPELHRLCARLEYLLQFDQKEKKSFFGSRKDYWDFLCLCLNRHRGGTEGIHFVNSTDKLK 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568906665  96 TSLGKGRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAFNL 161
Cdd:cd17697   85 TPLGKGRAFIRYCLVQQQLAESLQLCLLNPELTGEWYYARSPFLSPELRSDILDSLYELNGVNFDL 150
RUN_FYCO1 cd17698
RUN domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar ...
 9-161 5.41e-49

RUN domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins; FYCO1, also called zinc finger FYVE domain-containing protein 7 (ZFYVE7), is a multidomain autophagy adaptor protein that interacts with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7, and Phosphatidylinositol 3-phosphate (PI3P), to mediate microtubule plus-end-directed autophagosome transport. This model represents the RUN domain of FYCO1.


Pssm-ID: 439060  Cd Length: 158  Bit Score: 167.57  E-value: 5.41e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665   9 KISRSLKNAVSAILQGYGDGQEPVTETSAELHRLCGCLELLLQFDQKEQRSFLGARKDYWDFLFTALRRHRGYTEQMSFI 88
Cdd:cd17698    6 KIIRDLQDCVTELKKEFEETGEPITDDSTTLHKFCAKLEYLLQFDQKEKTTLLGGRKDYWDYFCECLAKVKGLNDGIRFV 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568906665  89 CSQDKLKTSLGKGRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAFNL 161
Cdd:cd17698   86 KSLKEVRTSLGKGRAFIRYSLVHQRLADTLQQCVMNGKVTSDWYYPRSVFLNHKYSSDIINSLYDLNEVQFDL 158
RUN_RUFY4_like cd17682
RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4), FYVE and coiled-coil ...
 14-161 1.39e-40

RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4), FYVE and coiled-coil domain-containing protein 1 (FYCO1), and similar proteins; The family includes RUFY4 and FYCO1. RUFY4 acts as a positive regulator that enhances autophagy and lysosome tethering in response to Interleukin-4. It is expressed in a cell-specific manner or under specific immunological conditions associated with IL4 expression such as allergic asthma. FYCO1, also called zinc finger FYVE domain-containing protein 7 (ZFYVE7), is a multidomain autophagy adaptor protein that interacts with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7, and phosphatidylinositol 3-phosphate (PI3P), to mediate microtubule plus-end-directed autophagosome transport. Both RUFY4 and FYCO1 contain an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain.


Pssm-ID: 439044  Cd Length: 150  Bit Score: 144.29  E-value: 1.39e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  14 LKNAVSAILQGYGDGQEPvteTSAELHRLCGCLELLLQFDQKEQRSFLGARKDYWDFLFTALRRH----RGYTEQMSFIC 89
Cdd:cd17682    2 LKGCVLDLKSEFGEITDP---DNPYLRPFCETLEKILRKGLKEKVSLGGRRKDYWDWLEELLKKLnkipKSLSDAVKFVK 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568906665  90 SQDKLKTSLGKGRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAFNL 161
Cdd:cd17682   79 SCKKVKTNQGRGRLFIRYALNKKCLHDPVQQLVKNPKLLSDYYSPDSILGNEILSEILLSLLYQLNEINFDL 150
RUN cd17671
RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new ...
 17-161 2.61e-28

RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new molecule containing SH3 at the carboxyl-terminus), is a less conserved protein motif that comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases. RUN domains are often found in proteins linked particularly to the functions of GTPases in the Rap and Rab families, suggesting the RUN domain may be involved in Rab-mediated membrane trafficking, possibly as a Rab-binding site. RUN domain-containing proteins could hence play important roles in multiple Ras-like GTPase signalling pathways.


Pssm-ID: 439038  Cd Length: 154  Bit Score: 110.59  E-value: 2.61e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  17 AVSAILQGYGDGQE-------PVTETSAELHRLCGCLELLLQFDQKEqRSFLGARKDYWDFL--FTALRRHRGYTEQMSF 87
Cdd:cd17671    2 AVKELLESFADNGEaddsaalTLTDDDPVVGRLCAALEAILSHGLKP-KRFGGGKVSFWDFLeaLEKLLPAPSLKQAIRD 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568906665  88 ICSQDKLKTSLGKGRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAFNL 161
Cdd:cd17671   81 INSLSNVKTDDGRGRAWIRLALNEKSLESYLAALLSDQSLLRKYYEPWALLRDPEEAELFLSLLVGLSSLDFNL 154
RUN_RUFY1_like cd17681
RUN domain found in RUN and FYVE domain-containing proteins, RUFY1, RUFY2, RUFY3 and similar ...
 31-161 5.40e-12

RUN domain found in RUN and FYVE domain-containing proteins, RUFY1, RUFY2, RUFY3 and similar proteins; This family includes RUN and FYVE domain-containing protein RUFY1, RUFY2, and RUFY3. RUFY1, also called FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homolog of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY2, also called Rab4-interacting protein related, is a novel embryonic factor that is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. RUFY1, RUFY2, and RUFY3 contain an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain.


Pssm-ID: 439043  Cd Length: 155  Bit Score: 64.13  E-value: 5.40e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  31 PVTETSAELHRLCGCLELLLQFDQKEQRSFLGARKDYWDFLFTALRRHRGYTEQMSFICSQDKLKTSLGKGRAFIRLCLA 110
Cdd:cd17681   26 TLDSDHVPLQQFFVILEHVLRHGLKVKKSFLGPNKSFWPVLEHVEKLVPEANEITASVRDLPGIKTPLGRARAWLRLALM 105

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 568906665 111 RGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEdILDSLYALNGVAFNL 161
Cdd:cd17681  106 QKKLADYFRALIENKDLLSEFYEPGALMMSEEAVV-IAGLLVGLNVIDCNL 155
FYVE_RUFY4 cd15745
FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar ...
 544-586 8.31e-11

FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins; RUFY4 belongs to the FUFY protein family which is characterized by the presence of an N-terminal RUN domain and a C-terminal FYVE domain. The FYVE domain of RUFY4 resembles the FYVE-related domain as it lacks the WxxD motif (x for any residue). The biological function of RUFY4 still remains unclear.


Pssm-ID: 277284 [Multi-domain]  Cd Length: 52  Bit Score: 57.51  E-value: 8.31e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 568906665 544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACSVDYK--------KRERCCPTC 586
Cdd:cd15745    1 ACAICAKAFSLFRRKYVCRLCGGVVCHSCSSEDLvlsvpdtcIYLRVCKTC 51
RUN_RUNDC3 cd17684
RUN domain found in RUN domain-containing protein 3 (RUNDC3) and similar proteins; RUNDC3 ...
 30-161 1.23e-09

RUN domain found in RUN domain-containing protein 3 (RUNDC3) and similar proteins; RUNDC3 contains two isoforms, RUNDC3A and RUNDC3B. RUNDC3A, also called Rap2-interacting protein 8 (RPIP8), may act as an effector of Rap2A GTPase in neuronal cells. RUNDC3B, also called Rap2-binding protein 9, or Rap2-interacting protein 9 (RPIP-9), contains a RUN domain in its N-terminal region that mediates interaction with Rap2, an important component of the Mitogen-Activated Protein Kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. It also contains characteristic binding sites for MAPK intermediates. Both RUNDC3A and RUNDC3B contain a RUN domain.


Pssm-ID: 439046  Cd Length: 150  Bit Score: 57.02  E-value: 1.23e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  30 EPVTETSAELHRLCGCLELLLQFDQKEQRSFLGA--RKDYWDFLFTAlrrHRGYTEQ-MSFICSQDKLKTSLGKGRAFIR 106
Cdd:cd17684   20 ETIDDSSEELINFAAILEQILSHRLKPVKPWYGSeePRTFWDYIRVA---CKKVPQNcIASIEQMENIKSPKAKGRAWIR 96

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 568906665 107 LCLARGQLAESMQLCLLNPQLTREWYGPRSPLlcaeLQED---ILDSLYALNGVAFNL 161
Cdd:cd17684   97 VALMEKRLSEYLSTALKQTRLTRNFYQDGAIM----LSEDatvLCGMLIGLNAIDFSF 150
FYVE_like_SF cd00065
FYVE domain like superfamily; FYVE domain is a 60-80 residue double zinc finger ...
 544-587 3.13e-09

FYVE domain like superfamily; FYVE domain is a 60-80 residue double zinc finger motif-containing module named after the four proteins, Fab1, YOTB, Vac1, and EEA1. The canonical FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif, which form a compact phosphatidylinositol 3-phosphate (PtdIns3P, also termed PI3P)-binding site. They are found in many membrane trafficking regulators, including EEA1, Hrs, Vac1p, Vps27p, and FENS-1, which locate to early endosomes, specifically bind PtdIns3P, and play important roles in vesicular traffic and in signal transduction. Some proteins, such as rabphilin-3A and alpha-Rab3-interacting molecules (RIMs), are also involved in membrane trafficking and bind to members of the Rab subfamily of GTP hydrolases. However, they contain FYVE-related domains that are structurally similar to the canonical FYVE domains but lack the three signature sequences. At this point, they may not bind to phosphoinositides. In addition, this superfamily also contains the third group of proteins, caspase-associated ring proteins CARP1 and CARP2. They do not localize to membranes in the cell and are involved in the negative regulation of apoptosis, specifically targeting two initiator caspases, caspase 8 and caspase 10, which are distinguished from other FYVE-type proteins. Moreover, these proteins have an altered sequence in the basic ligand binding patch and lack the WxxD motif that is conserved only in phosphoinositide binding FYVE domains. Thus they constitute a family of unique FYVE-type domains called FYVE-like domains. The FYVE domain is structurally similar to the RING domain and the PHD finger. This superfamily also includes ADDz zinc finger domain, which is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger.


Pssm-ID: 277249 [Multi-domain]  Cd Length: 52  Bit Score: 52.92  E-value: 3.13e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 568906665 544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACSV--------DYKKRERCCPTCA 587
Cdd:cd00065    1 RCMLCGKKFSLFRRRHHCRRCGRVFCSKCSSkklplpsfGSGKPVRVCDSCY 52
RUN1_DENND5 cd17677
RUN1 domain found in DENN domain-containing protein 5 (DENND5) and similar proteins; DENND5 ...
 85-160 9.06e-08

RUN1 domain found in DENN domain-containing protein 5 (DENND5) and similar proteins; DENND5 has been characterized as Rab6-interacting protein which is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. It functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. DENND5 has two isoforms, DENND5A and DENND5B. This model represents the first RUN domain of DENND5.


Pssm-ID: 439039  Cd Length: 183  Bit Score: 52.40  E-value: 9.06e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568906665  85 MSFICSQDKLKTSLGKGRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAFN 160
Cdd:cd17677  101 MKNVQNMKEIKTDVGYARAWIRLALEKKLLSKHLKTLLSNQDLLRSLYKRYAFLRCEDEREQFLYHLLSLNAVDYF 176
RUN_PLEKHM1 cd17679
RUN domain found in pleckstrin homology domain-containing family M member 1 (PLEKHM1) and ...
 9-163 1.19e-07

RUN domain found in pleckstrin homology domain-containing family M member 1 (PLEKHM1) and similar proteins; PLEKHM1, also called PH domain-containing family M member 1, or 162 kDa adapter protein (AP162), may act as a multivalent adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. This model represents the RUN domain of PLEKHM1.


Pssm-ID: 439041 [Multi-domain]  Cd Length: 171  Bit Score: 51.82  E-value: 1.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665   9 KISRSLKNAVSAILQGYGDGQEPVTETSAELHRLCGCLE-LLLQ-----FDQKEqRSFLGAR------KDYWDFL--FTa 74
Cdd:cd17679    3 SLTKELSSSVKELQLEYVSSDEVVTSSDDGANTLCCVLEaIFLHglkdkFISKV-SSVFSGDvdklpePNFWPLLlkFS- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  75 lrrHRGYTEQmsfICSQDKLKTSLGKGRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYAL 154
Cdd:cd17679   81 ---HRDVIDQ---IEHLSQITTDVGRCRAWIRLALNDGLLESYLEAILKDKSALKSYYNPSAFLRDPEQLDILKSLLQGL 154


                 ....*....
gi 568906665 155 NGVAFNLDL 163
Cdd:cd17679  155 ESFQFELPY 163
FYVE pfam01363
FYVE zinc finger; The FYVE zinc finger is named after four proteins that it has been found in: ...
 544-589 1.27e-07

FYVE zinc finger; The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. We have included members which do not conserve these histidine residues but are clearly related.


Pssm-ID: 426221 [Multi-domain]  Cd Length: 68  Bit Score: 48.92  E-value: 1.27e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568906665  544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACS---------VDYKKRERCCPTCAQQ 589
Cdd:pfam01363  11 VCMICSKPFTFFRRRHHCRNCGRVFCSACSskkisllpeLGSNKPVRVCDACYDT 65
FYVE_FYCO1 cd15726
FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar ...
 544-587 1.74e-07

FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins; FYCO1, also termed zinc finger FYVE domain-containing protein 7, is a phosphatidylinositol 3-phosphate (PtdIns3P or PI3P)-binding protein that is associated with the exterior of autophagosomes and mediates microtubule plus-end-directed vesicle transport. It acts as an effector of GTP-bound Rab7, a GTPase that recruits FYCO1 to autophagosomes and has been implicated in autophagosome-lysosomal fusion. FYCO1 also interacts with two microtubule motor proteins, kinesin (KIF) 5B and KIF23, and thus functions as a platform for assembly of vesicle fusion and trafficking factors. FYCO1 contains an N-terminal alpha-helical RUN domain followed by a long central coiled-coil region, a FYVE domain and a GOLD (Golgi dynamics) domain in C-terminus.


Pssm-ID: 277265 [Multi-domain]  Cd Length: 58  Bit Score: 48.32  E-value: 1.74e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 568906665 544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACSVDY------KKRERCCPTCA 587
Cdd:cd15726    9 HCLDCKSEFSWMVRRHHCRLCGRIFCYACSNFYvltahgGKKERCCKACF 58
RUN_RUNDC3B cd17700
RUN domain found in RUN domain-containing protein 3B (RUNDC3B) and similar proteins; RUN ...
 30-161 3.13e-07

RUN domain found in RUN domain-containing protein 3B (RUNDC3B) and similar proteins; RUN domain-containing protein 3B (RUNDC3B), also called Rap2-binding protein 9, or Rap2-interacting protein 9 (RPIP-9), contains a RUN domain in its N-terminal region that mediates interaction with Rap2, an important component of the Mitogen-Activated Protein Kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. It also contains characteristic binding sites for MAPK intermediates. RUNDC3B contains a RUN domain.


Pssm-ID: 439062  Cd Length: 151  Bit Score: 50.35  E-value: 3.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  30 EPVTETSAELHRLCGCLELLLQFDQKEQRSFLG--ARKDYWDFLFTALRRhrgytEQMSFICS---QDKLKTSLGKGRAF 104
Cdd:cd17700   20 ETIDDSSPEFVNFAAILEQILSHRLKGQVTWFGyeSPRSFWDYIRVACSK-----VPHNCICSienMENVSSSRAKGRAW 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 568906665 105 IRLCLARGQLAESMQLCLLNPQLTREWYgPRSPLLCAELQEDILDSLYALNGVAFNL 161
Cdd:cd17700   95 IRVALMEKRLSEYISTALRDFKTTRRFY-EDGAIVLGEEANMLAGMLLGLNAIDFSF 150
FYVE_RBNS5 cd15716
FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and ...
 545-586 7.50e-07

FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins; Rbsn-5, also termed zinc finger FYVE domain-containing protein 20, is a novel Rab5 effector that is complexed to the Sec1-like protein VPS45 and recruited in a phosphatidylinositol-3-kinase-dependent fashion to early endosomes. It also binds to Rab4 and EHD1/RME-1, two regulators of the recycling route, and is involved in cargo recycling to the plasma membrane. Moreover, Rbsn-5 regulates endocytosis at the apical side of the wing epithelium and plays a role of the apical endocytic trafficking of Fmi in the establishment of planar cell polarity (PCP).


Pssm-ID: 277256 [Multi-domain]  Cd Length: 61  Bit Score: 46.57  E-value: 7.50e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 568906665 545 CIGCNKVFRRLSRRYPCRLCGGLVCHACSVDYKKRERCCPTC 586
Cdd:cd15716   13 CPDCGKKFNLARRRHHCRLCGSIMCNKCSQFLPLHIRCCHHC 54
FYVE smart00064
Protein present in Fab1, YOTB, Vac1, and EEA1; The FYVE zinc finger is named after four ...
 544-588 9.12e-07

Protein present in Fab1, YOTB, Vac1, and EEA1; The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PHD finger and the RING finger. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. The FYVE finger functions in the membrane recruitment of cytosolic proteins by binding to phosphatidylinositol 3-phosphate (PI3P), which is prominent on endosomes. The R+HHC+XCG motif is critical for PI3P binding.


Pssm-ID: 214499 [Multi-domain]  Cd Length: 68  Bit Score: 46.27  E-value: 9.12e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 568906665   544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACS--------VDYKKRERCCPTCAQ 588
Cdd:smart00064  12 NCMGCGKEFNLTKRRHHCRNCGRIFCSKCSskkaplpkLGIERPVRVCDDCYE 64
RUN pfam02759
RUN domain; This domain is present in several proteins that are linked to the functions of ...
 41-163 2.15e-06

RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.


Pssm-ID: 460679  Cd Length: 134  Bit Score: 47.27  E-value: 2.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665   41 RLCGCLELLLQ------FDQKEQRSFLGARKDYWDFL------FTALRRHRGYTEQMSFICSqdkLKTSLGKGRAFIRLC 108
Cdd:pfam02759   1 QLCAALEALLShglkrsSLLILRAAGLLPERSFWALLervgklVPPAEELLSSVQELEQIHT---PYSPDGRGRAWIRLA 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568906665  109 LARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAFNLDL 163
Cdd:pfam02759  78 LNEKLLDQWLKLLLSNKELLSEYYEPWALLADPEFGEILLGLLVGLSALDFNLCL 132
RUN1_DENND5B cd17691
RUN1 domain found in DENN domain-containing protein 5B (DENND5B) and similar proteins; DENND5B, ...
 83-159 2.99e-06

RUN1 domain found in DENN domain-containing protein 5B (DENND5B) and similar proteins; DENND5B, also called Rab6-interacting protein 1 (Rab6IP1)-like protein, functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. This model represents the first RUN domain of DENND5B.


Pssm-ID: 439053 [Multi-domain]  Cd Length: 206  Bit Score: 48.51  E-value: 2.99e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568906665  83 EQMSFICSQDKLKTSLGKGRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAF 159
Cdd:cd17691  122 QDMRHIQNMSEIKTDVGRARAWIRLSLEKKLLSQHLKQLLSNQALTKKLYKRYAFLRCEEEKEQFLYHLLSLNAVDY 198
RUN_SNX29 cd17689
RUN domain found in sorting nexin-29 (SNX29) and similar proteins; SNX29, also called RUN ...
 14-162 5.83e-06

RUN domain found in sorting nexin-29 (SNX29) and similar proteins; SNX29, also called RUN domain-containing protein 2A (RUNDC2A), belongs to the sorting nexin family. Sorting nexins are a large group of proteins that are localized in the cytoplasm and have the potential for membrane association either through their lipid-binding PX domain, a phospholipid-binding motif, or through protein-protein interactions with membrane-associated protein complexes. Some sorting nexin family members have been shown to facilitate protein sorting. This model contains the RUN domain of SNX29.


Pssm-ID: 439051  Cd Length: 166  Bit Score: 46.84  E-value: 5.83e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  14 LKNAVSAILQGYGDGQEPVTETSAELHRLCGCLELLLQ----------FDQKEQRSFLGARKD---------YWDFLFTA 74
Cdd:cd17689    2 LLDAVKQCQIRFGGKTELATESDSRVSCLCAQLEAVLQhglktsrspnLVSSAVTQVSGLAGSlgsaeteptFWPFVKEH 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  75 LRRHrgytEQMSFICSQDkLKTSLGKGRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYAL 154
Cdd:cd17689   82 LTKH----ELERFELLKN-IWTDIGRGRAWLRSALNEHSLERYLHILLSNENLLRQYYEDWAFLRDEERSSMLPNMAAGL 156


                 ....*...
gi 568906665 155 NGVAFNLD 162
Cdd:cd17689  157 GSILFALS 164
RUN_PLEKHM2 cd17680
RUN domain found in pleckstrin homology domain-containing family M member 2 (PLEKHM2) and ...
 12-161 2.03e-05

RUN domain found in pleckstrin homology domain-containing family M member 2 (PLEKHM2) and similar proteins; PLEKHM2, also called PH domain-containing family M member 2, or Salmonella-induced filaments A (SifA) and Kinesin-Interacting Protein (SKIP), is the lysosome, melanosome and lytic granule cargo adaptor that controls lysosome positioning using a composite kinesin-1 heavy and light chain-binding domain. In addition to kinesin-1, it also interacts with several Rabs to affect endosomal trafficking. This model represents the RUN domain of PLEKHM2.


Pssm-ID: 439042  Cd Length: 145  Bit Score: 44.54  E-value: 2.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  12 RSLKNAVSAI--LQGY----GDGQEPVTETSAELHRLCGCLELLLQFdqkeqrSFLGARKDYWDFLFTALRRhrgytEQM 85
Cdd:cd17680    1 RILRNISEAIksLQSYsssqEEEDVLITNENRELQRLCEALDHALLH------GLRRGNRGYWPFVKEFTHK-----ETI 69

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568906665  86 SFICSQDKLKTSLGKGRAFIRLCLARGQLaES-MQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAFNL 161
Cdd:cd17680   70 KQIENLPNVTTDLGRGRAWLYLALNEGSL-ESyLRSFLENRKLVKKFYHKHALLRDSQRLELLLTLLSGLEFVQFDL 145
RUN smart00593
domain involved in Ras-like GTPase signaling;
101-163 2.32e-05

domain involved in Ras-like GTPase signaling;


Pssm-ID: 214736 [Multi-domain]  Cd Length: 64  Bit Score: 42.22  E-value: 2.32e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568906665   101 GRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAFNLDL 163
Cdd:smart00593   1 FRAWIRLALNEKLLSSWLNLLLSDEELLSKYYEPWAFLRDPEEGEQLLGLLVGLSALDFNLPV 63
RUN_RUNDC3A cd17699
RUN domain found in RUN domain-containing protein 3A (RUNDC3A) and similar proteins; RUN ...
 17-132 3.29e-05

RUN domain found in RUN domain-containing protein 3A (RUNDC3A) and similar proteins; RUN domain-containing protein 3A (RUNDC3A), also called Rap2-interacting protein 8 (RPIP8), may act as an effector of Rap2A GTPase in neuronal cells. It contains a RUN domain.


Pssm-ID: 439061  Cd Length: 151  Bit Score: 44.25  E-value: 3.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  17 AVSAILQGYGdgQEPVTETSAELHRLCGCLELLLQFDQKEQRSFLGA--RKDYWDFLFTALRRHRgyTEQMSFICSQDKL 94
Cdd:cd17699    9 SVKTLLEKYT--AEPIDDSSEEFVNFAAILEQILSHRFKGPVSWFSSdgQRGFWDYIRLACSKVP--NNCISSIENMENI 84

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 568906665  95 KTSLGKGRAFIRLCLARGQLAESMQLCLLNPQLTREWY 132
Cdd:cd17699   85 STSRAKGRAWIRVALMEKRLSEYIATALRDTRTTRRFY 122
OmpH pfam03938
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
 448-527 4.03e-05

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.


Pssm-ID: 461098 [Multi-domain]  Cd Length: 140  Bit Score: 43.72  E-value: 4.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  448 QLAKEQAQCQEQLRAQEAELQALQEQLsrcQKERALLQVKLEQKQQEAERRDAMYQTELEGQRDLVQAMKRRVLELIHEK 527
Cdd:pfam03938  23 QLEKKFKKRQAELEAKQKELQKLYEEL---QKDGALLEEEREEKEQELQKKEQELQQLQQKAQQELQKKQQELLQPIQDK 99
OmpH smart00935
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
 448-526 4.54e-05

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.


Pssm-ID: 214922 [Multi-domain]  Cd Length: 140  Bit Score: 43.73  E-value: 4.54e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665   448 QLAKEQAQCQEQLRAQEAELQALQEQLSR-----CQKERALLQVKLEQKQQEAERRDAMYQTELEG-QRDLVQAMKRRVL 521
Cdd:smart00935  22 QLEKEFKKRQAELEKLEKELQKLKEKLQKdaatlSEAAREKKEKELQKKVQEFQRKQQKLQQDLQKrQQEELQKILDKIN 101


                   ....*
gi 568906665   522 ELIHE 526
Cdd:smart00935 102 KAIKE 106
RUN_RUFY3 cd17696
RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; ...
 37-161 6.81e-05

RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. This model represents the RUN domain of RUFY3.


Pssm-ID: 439058  Cd Length: 156  Bit Score: 43.45  E-value: 6.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  37 AELHRLCGCLELLLQFDQKEQRSFLGARKDYWDFLFTALRRHRGYTEQMSFICSQDKLKTSLGKGRAFIRLCLARGQLAE 116
Cdd:cd17696   32 APLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVGRGRAWLRLALMQKKLSE 111

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 568906665 117 SMQLCLLNPQLTREWYGPRSpLLCAELQEDILDSLYALNGVAFNL 161
Cdd:cd17696  112 YMKALINRKDLLSEFYEPNA-LMMEEEGAIIAGLLVGLNVIDANF 155
FYVE_RUFY1_like cd15721
FYVE domain found in RUN and FYVE domain-containing protein RUFY1, RUFY2 and similar proteins; ...
 544-586 9.64e-05

FYVE domain found in RUN and FYVE domain-containing protein RUFY1, RUFY2 and similar proteins; This family includes RUN and FYVE domain-containing protein RUFY1 and RUFY2. RUFY1, also termed FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homologue of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY2, also termed Rab4-interacting protein related, is a novel embryonic factor that is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. Both RUFY1 and RUFY2 contain an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between.


Pssm-ID: 277261 [Multi-domain]  Cd Length: 58  Bit Score: 40.44  E-value: 9.64e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 568906665 544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACS------VDYKKRERCCPTC 586
Cdd:cd15721    9 HCQQCEKEFSLSRRKHHCRNCGGIFCNSCSdntmplPSSAKPVRVCDTC 57
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 448-536 1.07e-04

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 45.31  E-value: 1.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAMYQ------TELEGQRDLVQAMKRRVL 521
Cdd:COG1196  236 ELEAELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYellaelARLEQDIARLEERRRELE 315

                         90
                 ....*....|....*
gi 568906665 522 ELIHEKDLQWQRLQQ 536
Cdd:COG1196  316 ERLEELEEELAELEE 330
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 457-538 1.53e-04

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 44.93  E-value: 1.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 457 QEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAmyqtELEGQRDLVQAMKRRVLELIHEKDLQWQRLQQ 536
Cdd:COG1196  238 EAELEELEAELEELEAELEELEAELAELEAELEELRLELEELEL----ELEEAQAEEYELLAELARLEQDIARLEERRRE 313


                 ..
gi 568906665 537 LS 538
Cdd:COG1196  314 LE 315
RUN_RUFY1 cd17694
RUN domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins; ...
 46-161 1.58e-04

RUN domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins; RUFY1, also called FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homolog of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY1 contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain.


Pssm-ID: 439056  Cd Length: 156  Bit Score: 42.58  E-value: 1.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  46 LELLLQFDQKEQRSFLGARKDYWDFLFTALRRHRGYTEQMSFICSQDKLKTSLGKGRAFIRLCLARGQLAESMQLCLLNP 125
Cdd:cd17694   41 LEHCLKHGLKVKKSFIGQNKSFFGPLELVEKLCPEASDIATSARNLPELKTAVGRGRAWLHLALMQKKLADYLKVLIDRK 120

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 568906665 126 QLTREWYGPRSpLLCAELQEDILDSLYALNGVAFNL 161
Cdd:cd17694  121 DLLSEFYEPGA-LMMEEEGAVIVGLLVGLNVIDANL 155
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 448-537 2.04e-04

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 44.54  E-value: 2.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAMYQTELEGQRDLVQAMKRRVLELIHEK 527
Cdd:COG1196  313 ELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEAL 392

                         90
                 ....*....|
gi 568906665 528 DLQWQRLQQL 537
Cdd:COG1196  393 RAAAELAAQL 402
RUN1_DENND5A cd17690
RUN1 domain found in DENN domain-containing protein 5A (DENND5A) and similar proteins; DENND5A, ...
 82-159 2.61e-04

RUN1 domain found in DENN domain-containing protein 5A (DENND5A) and similar proteins; DENND5A, also called Rab6-interacting protein 1 (Rab6IP1), is present predominantly in developing neuronal tissue, and functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. This model represents the first RUN domain of DENND5A.


Pssm-ID: 439052 [Multi-domain]  Cd Length: 209  Bit Score: 42.69  E-value: 2.61e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568906665  82 TEQMSFICSQDKLKTSLGKGRAFIRLCLARGQLAESMQLCLLNPQLTREWYGPRSPLLCAELQEDILDSLYALNGVAF 159
Cdd:cd17690  124 IQDMRHIQNIGEIKTDVGKARAWVRLSMEKKLLSRHLKQLLSDHELTKKLYKRYAFLRCDDEKEQFLYHLLSFNAVDY 201
DUF4670 pfam15709
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ...
 448-536 3.26e-04

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.


Pssm-ID: 464815 [Multi-domain]  Cd Length: 522  Bit Score: 43.40  E-value: 3.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKE--RALLQVKLEQKQQEAERRDAMYQTELEGQRDLVQAMKrRVLELIH 525
Cdd:pfam15709 395 RLEEERQRQEEEERKQRLQLQAAQERARQQQEEfrRKLQELQRKKQQEEAERAEAEKQRQKELEMQLAEEQK-RLMEMAE 473

                          90
                  ....*....|.
gi 568906665  526 EKDLQWQRLQQ 536
Cdd:pfam15709 474 EERLEYQRQKQ 484
RUN_RUFY2 cd17695
RUN domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins; ...
 46-161 3.63e-04

RUN domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins; RUFY2, also called Rab4-interacting protein related, is a novel embryonic factor that contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between. It is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. This model represents the RUN domain of RUFY2.


Pssm-ID: 439057  Cd Length: 156  Bit Score: 41.50  E-value: 3.63e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  46 LELLLQFDQKEQRSFLGARKDYWDFLFTALRRHRGYTEQMSFICSQDKLKTSLGKGRAFIRLCLARGQLAESMQLCLLNP 125
Cdd:cd17695   41 MEHCLKHGLKVRKSFLSYNKTIWGPLELVEKLCPEAEEIAASVRDLPGLKTPLGRARAWLRLALMQKKLADYLRCLIIRR 120

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 568906665 126 QLTREWYgPRSPLLCAELQEDILDSLYALNGVAFNL 161
Cdd:cd17695  121 DLLSEFY-EYHALMMEEEGAVIVGLLVGLNVIDANL 155
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 448-536 3.65e-04

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 43.77  E-value: 3.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAMYQT------ELEGQRDLVQAMKRRVL 521
Cdd:COG1196  292 ELLAELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEaeeeleEAEAELAEAEEALLEAE 371

                         90
                 ....*....|....*
gi 568906665 522 ELIHEKDLQWQRLQQ 536
Cdd:COG1196  372 AELAEAEEELEELAE 386
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 448-538 4.64e-04

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 43.39  E-value: 4.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAMYQTELEGQRDLVQAMKRRVLELIHEK 527
Cdd:COG1196  320 ELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELA 399

                         90
                 ....*....|.
gi 568906665 528 DLQWQRLQQLS 538
Cdd:COG1196  400 AQLEELEEAEE 410
FYVE_MTMR4 cd15733
FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins; MTMR4, also ...
 541-573 4.92e-04

FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins; MTMR4, also termed FYVE domain-containing dual specificity protein phosphatase 2 (FYVE-DSP2), or zinc finger FYVE domain-containing protein 11, is an dual specificity protein phosphatase that specifically dephosphorylates phosphatidylinositol 3-phosphate (PtdIns3P or PI3P). It is localizes to early endosomes, as well as to Rab11- and Sec15-positive recycling endosomes, and regulates sorting from early endosomes. Moreover, MTMR4 is preferentially associated with and dephosphorylated the activated regulatory Smad proteins (R-Smads) in cytoplasm to keep transforming growth factor (TGF) beta signaling in homeostasis. It also functions as an essential negative modulator for the homeostasis of bone morphogenetic protein (BMP)/decapentaplegic (Dpp) signaling. In addition, MTMR4 acts as a novel interactor of the ubiquitin ligase Nedd4 (neural-precursor-cell-expressed developmentally down-regulated 4) and may play a role in the biological process of muscle breakdown. MTMR4 contains an N-terminal PH-GRAM (PH-G) domain, a MTM phosphatase domain, a coiled-coil region, and a C-terminal FYVE domain.


Pssm-ID: 277272 [Multi-domain]  Cd Length: 60  Bit Score: 38.57  E-value: 4.92e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 568906665 541 APGHCIGCNKVFRRLSRRYPCRLCGGLVCHACS 573
Cdd:cd15733    6 AASHCFGCDCEFWLAKRKHHCRNCGNVFCADCS 38
FYVE_RUFY1 cd15758
FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins; ...
 544-586 5.10e-04

FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins; RUFY1, also termed FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homologue of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY1 contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between.


Pssm-ID: 277297 [Multi-domain]  Cd Length: 71  Bit Score: 38.89  E-value: 5.10e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 568906665 544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACSVD------YKKRERCCPTC 586
Cdd:cd15758   14 HCKQCEKEFSISRRKHHCRNCGHIFCNTCSSNelalpsYPKPVRVCDSC 62
STAT5_CCD cd16855
Coiled-coil domain of Signal Transducer and Activator of Transcription 5 (STAT5); This family ...
 455-538 8.84e-04

Coiled-coil domain of Signal Transducer and Activator of Transcription 5 (STAT5); This family consists of the coiled-coil (alpha) domain of the STAT5 proteins (Signal Transducer and Activator of Transcription 5, or Signal Transduction And Transcription 5) which include STAT5A and STAT5B, both of which are >90% identical despite being encoded by separate genes. The coiled-coil domain (CCD) of STAT5A and STAT5B appears to be required for constitutive nuclear localization signals (NLS) function; small deletions within the CCD can abrogate nuclear import. Studies show that the CCD binds to the importin-alpha3 NLS adapter in most cells. STAT5A and STAT5B regulate erythropoiesis, lymphopoiesis, and the maintenance of the hematopoietic stem cell population. STAT5A and STAT5B have overlapping and redundant functions; both isoforms can be activated by the same set of cytokines, but some cytokines preferentially activate either STAT5A or STAT5B, e.g. during pregnancy and lactation, STAT5A rather than STAT5B is required for the production of luminal progenitor cells from mammary stem cells and is essential for the differentiation of milk producing alveolar cells during pregnancy. STAT5 has been found to be constitutively phosphorylated in cancer cells, and therefore constantly activated, either by aberrant cell signaling expression or by mutations. It differentially regulates cellular behavior in human mammary carcinoma. Prolactin (PRL) in the prostate gland can induce growth and survival of prostate cancer cells and tissues through the activation of STAT5, its downstream target; PRL expression and STAT5 activation correlates with disease severity. STAT5A and STAT5B are central signaling molecules in leukemias driven by Abelson fusion tyrosine kinases, displaying unique nuclear shuttling mechanisms and having a key role in resistance of leukemic cells against treatment with tyrosine kinase inhibitors (TKI). In addition, STAT5A and STAT5B promote survival of leukemic stem cells. STAT5 is a key transcription factor for IL-3-mediated inhibition of RANKL-induced osteoclastogenesis via the induction of the expression of Id genes. Autosomal recessive STAT5B mutations are associated with severe growth failure, insulin-like growth factor (IGF) deficiency and growth hormone insensitivity (GHI) syndrome. STAT5B deficiency can lead to potentially fatal primary immunodeficiency.


Pssm-ID: 341080 [Multi-domain]  Cd Length: 194  Bit Score: 40.71  E-value: 8.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 455 QCQEQLRAQeAELQALQEQ-LSRCQKERALLQVKLEQKQQEAerrDAMYQTELEGQRDLVQAMK------RRVLELIHEK 527
Cdd:cd16855   37 QYQESQKIQ-AQLQQLQQQpQNERIELEQQLQQQKEQLEQLL---NAKAQELLQLRMELADKFKktiqllSKLQSRVLDE 112

                         90
                 ....*....|..
gi 568906665 528 DL-QWQRLQQLS 538
Cdd:cd16855  113 ELiQWKRQQQLA 124
FYVE_PKHF cd15717
FYVE domain found in protein containing both PH and FYVE domains 1 (phafin-1), 2 (phafin-2), ...
 545-586 9.80e-04

FYVE domain found in protein containing both PH and FYVE domains 1 (phafin-1), 2 (phafin-2), and similar proteins; This family includes protein containing both PH and FYVE domains 1 (phafin-1) and 2 (phafin-2). Phafin-1 is a representative of a novel family of PH and FYVE domain-containing proteins called phafins. It is a ubiquitously expressed pro-apoptotic protein via translocating to lysosomes, facilitating apoptosis induction through a lysosomal-mitochondrial apoptotic pathway. Phafin-2 is a ubiquitously expressed endoplasmic reticulum-associated protein that facilitates tumor necrosis factor alpha (TNF-alpha)-triggered cellular apoptosis through endoplasmic reticulum (ER)-mitochondrial apoptotic pathway. It is an endosomal phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) effector, as well as an interactor of the endosomal-tethering protein EEA1. It regulates endosome fusion upstream of Rab5. Phafin-2 also functions as a novel regulator of endocytic epidermal growth factor receptor (EGFR) degradation through a role in endosomal fusion.


Pssm-ID: 277257 [Multi-domain]  Cd Length: 61  Bit Score: 37.73  E-value: 9.80e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 568906665 545 CIGCNKV-FRRLSRRYPCRLCGGLVCHACS-------VDYKKRERCCPTC 586
Cdd:cd15717   11 CMHCKKTkFTAINRRHHCRKCGAVVCGACSskkfllpHQSSKPLRVCDTC 60
PilN COG3166
Type IV pilus assembly protein PilN [Cell motility, Extracellular structures];
457-542 1.65e-03

Type IV pilus assembly protein PilN [Cell motility, Extracellular structures];


Pssm-ID: 442399 [Multi-domain]  Cd Length: 185  Bit Score: 39.95  E-value: 1.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 457 QEQLRAQEAELQALQEQLSrcqkerallqvKLEQKQQEAErrdamyqtELEGQRDLVQAmKRRVLELIHEKDLQWQR-LQ 535
Cdd:COG3166   44 QGQIAQQQARNAALQQEIA-----------KLDKQIAEIK--------ELKKQKAELLA-RLQVIEQLQQSRPPWVHlLD 103


                 ....*..
gi 568906665 536 QLSTVAP 542
Cdd:COG3166  104 ELARLLP 110
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 448-541 1.72e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 41.46  E-value: 1.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAMYQTELEGQRDLVQAMKRRVLELIHEK 527
Cdd:COG1196  334 ELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALL 413

                         90
                 ....*....|....
gi 568906665 528 DLQWQRLQQLSTVA 541
Cdd:COG1196  414 ERLERLEEELEELE 427
CCDC22 pfam05667
Coiled-coil domain-containing protein 22; Human coiled-coil domain-containing protein 22 ...
 236-537 1.92e-03

Coiled-coil domain-containing protein 22; Human coiled-coil domain-containing protein 22 (CCDC22) is involved in regulation of NF-kappa-B signalling; the function may involve association with COMMD8 and a CUL1-dependent E3 ubiquitin ligase complex. It is part of the OMMD/CCDC22/CCDC93 (CCC) complex, which interacts with the multisubunit WASH complex required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer. This entry also includes CCDC22 homologs from animals and plants.


Pssm-ID: 461708 [Multi-domain]  Cd Length: 600  Bit Score: 41.17  E-value: 1.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  236 SRGEQLQEPdTGGTSCLQDATREDRTPDLCKPLQPSHLPTflEEKREDSRSLsCPQSTWETEREGFQLDQKDGGPKPRKF 315
Cdd:pfam05667 111 ESSEAADQP-VGKSAVLQRAIAAAIRSQLAAPWLPPECKP--HQRRQGSRAL-RPFHTQTLVLPGRKGKTLKNSKELKEF 186

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  316 LENSTASIQQQRSRAKDVKMQLTGRKVEGKGSLSGTEDQRTTEGIQKRAADWDLGQGLMAPGLQGREDA--ELGYRCEWN 393
Cdd:pfam05667 187 YSEYLPPVTAQPSSRASVVPSLLERNAAELAAAQEWEEEWNSQGLASRLTPEEYRKRKRTKLLKRIAEQlrSAALAGTEA 266

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  394 QPDVLRQSWVLGTKKSSPTEKPQEWTGVTSGTMQEDGSEVPLQQEvikDPGYGLQLAKEQAQCQEQLRAQEAELQALQEQ 473
Cdd:pfam05667 267 TSGASRSAQDLAELLSSFSGSSTTDTGLTKGSRFTHTEKLQFTNE---APAATSSPPTKVETEEELQQQREEELEELQEQ 343

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568906665  474 LSRCQ-------KERALLQVKLEQKQQEAERRDAMyQTELEGQRDLvqamKRRVLELIHEKDLQWQRLQQL 537
Cdd:pfam05667 344 LEDLEssiqeleKEIKKLESSIKQVEEELEELKEQ-NEELEKQYKV----KKKTLDLLPDAEENIAKLQAL 409
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
448-537 2.08e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 40.66  E-value: 2.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQ---QEAERRDAMYQTELEGQRDLVQAMKRRVLELI 524
Cdd:COG4372   42 KLQEELEQLREELEQAREELEQLEEELEQARSELEQLEEELEELNeqlQAAQAELAQAQEELESLQEEAEELQEELEELQ 121

                         90
                 ....*....|...
gi 568906665 525 HEKDLQWQRLQQL 537
Cdd:COG4372  122 KERQDLEQQRKQL 134
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 448-539 2.53e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.81  E-value: 2.53e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665   448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAMYQ---TELEGQRDLVQAMKRRVLELI 524
Cdd:TIGR02168  313 NLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEeleSRLEELEEQLETLRSKVAQLE 392

                           90
                   ....*....|....*
gi 568906665   525 HEKDLQWQRLQQLST 539
Cdd:TIGR02168  393 LQIASLNNEIERLEA 407
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 448-537 2.94e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 40.69  E-value: 2.94e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQvKLEQKQQEAERRDAMYQTELEGQRDLVQAMKRRVLELIHEK 527
Cdd:COG1196  366 ALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLE-ELEEAEEALLERLERLEEELEELEEALAELEEEEEEEEEAL 444

                         90
                 ....*....|
gi 568906665 528 DLQWQRLQQL 537
Cdd:COG1196  445 EEAAEEEAEL 454
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
441-536 3.20e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 40.52  E-value: 3.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 441 KDPGYGLQLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAM------YQTELEGQRDLVQ 514
Cdd:COG4717   64 RKPELNLKELKELEEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLlqllplYQELEALEAELAE 143

                         90       100
                 ....*....|....*....|..
gi 568906665 515 AMKRrvLELIHEKDLQWQRLQQ 536
Cdd:COG4717  144 LPER--LEELEERLEELRELEE 163
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 448-519 3.31e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 40.13  E-value: 3.31e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAMYQTELEGQRDLVQAMKRR 519
Cdd:COG4942  164 ALRAELEAERAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQEAEELEALIARLEAE 235
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
448-539 3.64e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 39.89  E-value: 3.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAM---YQTELEGQRDLVQAMKRRVLELI 524
Cdd:COG4372   63 QLEEELEQARSELEQLEEELEELNEQLQAAQAELAQAQEELESLQEEAEELQEEleeLQKERQDLEQQRKQLEAQIAELQ 142

                         90
                 ....*....|....*
gi 568906665 525 HEKDLQWQRLQQLST 539
Cdd:COG4372  143 SEIAEREEELKELEE 157
CwlO1 COG3883
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ...
 448-516 3.88e-03

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];


Pssm-ID: 443091 [Multi-domain]  Cd Length: 379  Bit Score: 39.81  E-value: 3.88e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRdamyQTELEGQRDLVQAM 516
Cdd:COG3883   27 ELQAELEAAQAELDALQAELEELNEEYNELQAELEALQAEIDKLQAEIAEA----EAEIEERREELGER 91
FYVE_scVPS27p_like cd15760
FYVE domain found in Saccharomyces cerevisiae vacuolar protein sorting-associated protein 27 ...
 544-587 5.88e-03

FYVE domain found in Saccharomyces cerevisiae vacuolar protein sorting-associated protein 27 (scVps27p) and similar proteins; scVps27p, also termed Golgi retention defective protein 11, is the putative yeast counterpart of the mammalian protein Hrs and is involved in endosome maturation. It is a mono-ubiquitin-binding protein that interacts with ubiquitinated cargoes, such as Hse1p, and is required for protein sorting into the multivesicular body. Vps27p forms a complex with Hse1p. The complex binds ubiquitin and mediates endosomal protein sorting. At the endosome, Vps27p and a trimeric protein complex, ESCRT-1, bind ubiquitin and are important for multivesicular body (MVB) sorting. Vps27p contains an N-terminal VHS (Vps27/Hrs/STAM) domain, a FYVE domain that binds PtdIns3P, followed by two ubiquitin-interacting motifs (UIMs), and a C-terminal clathrin-binding motif.


Pssm-ID: 277299 [Multi-domain]  Cd Length: 59  Bit Score: 35.35  E-value: 5.88e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 568906665 544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACS---------VDYKKRERCCPTCA 587
Cdd:cd15760    7 RCDVCRKKFGLFKRRHHCRNCGDSFCSEHSsrriplphlGPLGVPQRVCDRCF 59
F-BAR_FCHSD2 cd07677
The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH and double SH3 domains 2 ...
 418-519 6.24e-03

The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH and double SH3 domains 2 (FCHSD2); F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FCH and double SH3 domains 2 (FCHSD2) contains an N-terminal F-BAR domain and two SH3 domains at the C-terminus. It has been characterized only in silico, and its biological function is still unknown. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.


Pssm-ID: 153361 [Multi-domain]  Cd Length: 260  Bit Score: 38.96  E-value: 6.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 418 WTGVTSGTMQEDGSEVPL---QQEVIKDPGYGLQLAKEQ--AQCQEQLRAQEAELQALQEQLSRCQKE----RALLQVKL 488
Cdd:cd07677   72 WKSFLEGTMQVAQSRINIcenYKNLISEPARTVRLYKEQqlKRCVDQLTKIQAELQETVKDLAKGKKKyfetEQMAHAVR 151

                         90       100       110
                 ....*....|....*....|....*....|.
gi 568906665 489 EQKQQEAERRDAMYQTELEGQRDLVQAMKRR 519
Cdd:cd07677  152 EKADIEAKSKLSLFQSRISLQKASVKLKARR 182
CwlO1 COG3883
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ...
 448-536 6.55e-03

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];


Pssm-ID: 443091 [Multi-domain]  Cd Length: 379  Bit Score: 39.04  E-value: 6.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAMYQTELEGQRDLVQAMKRRVLELIHEK 527
Cdd:COG3883  126 KIADADADLLEELKADKAELEAKKAELEAKLAELEALKAELEAAKAELEAQQAEQEALLAQLSAEEAAAEAQLAELEAEL 205


                 ....*....
gi 568906665 528 DLQWQRLQQ 536
Cdd:COG3883  206 AAAEAAAAA 214
FYVE_endofin cd15729
FYVE domain found in endofin and similar proteins; Endofin, also termed zinc finger FYVE ...
 545-588 6.65e-03

FYVE domain found in endofin and similar proteins; Endofin, also termed zinc finger FYVE domain-containing protein 16 (ZFY16), or endosome-associated FYVE domain protein, is a FYVE domain-containing protein that is localized to EEA1-containing endosomes. It is regulated by phosphoinositol lipid and engaged in endosome-mediated receptor modulation. Endofin is involved in Bone morphogenetic protein (BMP) signaling through interacting with Smad1 preferentially and enhancing Smad1 phosphorylation and nuclear localization upon BMP stimulation. It also functions as a scaffold protein that brings Smad4 to the proximity of the receptor complex in Transforming growth factor (TGF)-beta signaling. Moreover, endofin is a novel tyrosine phosphorylation target downstream of epidermal growth factor receptor (EGFR) in EGF-signaling. In addition, endofin plays a role in endosomal trafficking by recruiting cytosolic TOM1, an important molecule for membrane recruitment of clathrin, onto endosomal membranes.


Pssm-ID: 277268 [Multi-domain]  Cd Length: 68  Bit Score: 35.41  E-value: 6.65e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 568906665 545 CIGCNKVFRRLSRRYPCRLCGGLVCHAC-----SVDY--KKRERCCPTCAQ 588
Cdd:cd15729   16 CMQCEVKFTFTKRRHHCRACGKVLCSACcslkaRLEYldNKEARVCVPCYQ 66
FYVE_PIKfyve_Fab1 cd15725
FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins; PIKfyve, ...
 545-588 6.65e-03

FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins; PIKfyve, also termed FYVE finger-containing phosphoinositide kinase, or 1-phosphatidylinositol 3-phosphate 5-kinase, or phosphatidylinositol 3-phosphate 5-kinase (PIP5K3), or phosphatidylinositol 3-phosphate 5-kinase type III (PIPkin-III or type III PIP kinase), is a phosphoinositide 5-kinase that forms a complex with its regulators, the scaffolding protein Vac14 and the lipid phosphatase Fig4. The complex is responsible for synthesizing phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P2] from phosphatidylinositol 3-phosphate (PtdIns3P or PI3P). Then phosphatidylinositol-5-phosphate (PtdIns5P) is generated directly from PtdIns(3,5)P2. PtdIns(3,5)P2 and PtdIns5P regulate endosomal trafficking and responses to extracellular stimuli. At this point, PIKfyve is vital in early embryonic development. Moreover, PIKfyve forms a complex with ArPIKfyve (associated regulator of PIKfyve) and SAC3 at the endomembranes, which plays a role in receptor tyrosine kinase (RTK) degradation. The phosphorylation of PIKfyve by AKT can facilitate Epidermal growth factor receptor (EGFR) degradation. In addition, PIKfyve may participate in the regulation of the glutamate transporters EAAT2, EAAT3 and EAAT4, and the cystic fibrosis transmembrane conductance regulator (CFTR). It is also essential for systemic glucose homeostasis and insulin-regulated glucose uptake/GLUT4 translocation in skeletal muscle. It can be activated by protein kinase B (PKB/Akt) and further up-regulates human ether-a-go-go (hERG) channels. This family also includes the yeast and plant orthologs of human PIKfyve, Fab1. PIKfyve and its orthologs share a similar architecture. They contain an N-terminal FYVE domain, a middle region related to the CCT/TCP-1/Cpn60 chaperonins that are involved in productive folding of actin and tubulin, a second middle domain that contains a number of conserved cysteine residues (CCR) unique to this family, and a C-terminal lipid kinase domain related to PtdInsP kinases.


Pssm-ID: 277264 [Multi-domain]  Cd Length: 62  Bit Score: 35.38  E-value: 6.65e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 568906665 545 CIGCNKVFRRLSRRYPCRLCGGLVCHACS--------VDYKKRERCCPTCAQ 588
Cdd:cd15725   11 CYECSEKFTTFRRRHHCRLCGQIFCSRCCnqeipgkfIGYPGDLRVCTYCCK 62
FYVE_LST2 cd15731
FYVE domain found in lateral signaling target protein 2 homolog (Lst2) and similar proteins; ...
 544-573 6.86e-03

FYVE domain found in lateral signaling target protein 2 homolog (Lst2) and similar proteins; Lst2, also termed zinc finger FYVE domain-containing protein 28, is a monoubiquitinylated phosphoprotein that functions as a negative regulator of epidermal growth factor receptor (EGFR) signaling. Unlike other FYVE domain-containing proteins, Lst2 displays primarily non-endosomal localization. Its endosomal localization is regulated by monoubiquitinylation. Lst2 physically binds Trim3, also known as BERP or RNF22, which is a coordinator of endosomal trafficking and interacts with Hrs and a complex that biases cargo recycling.


Pssm-ID: 277270 [Multi-domain]  Cd Length: 65  Bit Score: 35.40  E-value: 6.86e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 568906665 544 HCIGCNKVFRRLSRRYPCRLCGGLVCHACS 573
Cdd:cd15731   13 QCMACSAPFTVLRRRHHCRNCGKIFCSRCS 42
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
457-536 7.13e-03

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 39.51  E-value: 7.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  457 QEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQE----AERRDAMYQTELEGQRDLVQAMKRRVLELIHEKDLQwQ 532
Cdd:COG4913   691 EEQLEELEAELEELEEELDELKGEIGRLEKELEQAEEEldelQDRLEAAEDLARLELRALLEERFAAALGDAVERELR-E 769


                  ....
gi 568906665  533 RLQQ 536
Cdd:COG4913   770 NLEE 773
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 448-523 7.24e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 38.98  E-value: 7.24e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQEAERRDAMYQTELEGQRDLVQAMKRRVLEL 523
Cdd:COG4942  150 EQAEELRADLAELAALRAELEAERAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQEAEEL 225
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 448-537 7.59e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 39.53  E-value: 7.59e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQ----------KQQEAERRDAMYQTELEGQRDLVQAMK 517
Cdd:COG1196  257 ELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARleqdiarleeRRRELEERLEELEEELAELEEELEELE 336

                         90       100
                 ....*....|....*....|
gi 568906665 518 RRVLELIHEKDLQWQRLQQL 537
Cdd:COG1196  337 EELEELEEELEEAEEELEEA 356
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 448-521 8.25e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 38.98  E-value: 8.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665 448 QLAKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVKLEQKQQE-AERRDAMYQTE-------LEGQRDLVQAMKRR 519
Cdd:COG4942   59 ALERRIAALARRIRALEQELAALEAELAELEKEIAELRAELEAQKEElAELLRALYRLGrqpplalLLSPEDFLDAVRRL 138


                 ..
gi 568906665 520 VL 521
Cdd:COG4942  139 QY 140
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
450-537 9.85e-03

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 39.13  E-value: 9.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906665  450 AKEQAQCQEQLRAQEAELQALQEQLSRCQKERALLQVkleqkqQEAERRDAMYQTELEGQRDLVQAMKRRVLELIHEKDL 529
Cdd:COG4913   247 AREQIELLEPIRELAERYAAARERLAELEYLRAALRL------WFAQRRLELLEAELEELRAELARLEAELERLEARLDA 320


                  ....*...
gi 568906665  530 QWQRLQQL 537
Cdd:COG4913   321 LREELDEL 328
 
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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