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Conserved domains on  [gi|1720371462|ref|XP_030102531|]
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ras and Rab interactor 3 isoform X2 [Mus musculus]

Protein Classification

VPS9 and Ubl1_cv_Nsp3_N-like domain-containing protein( domain architecture ID 13672345)

VPS9 and Ubl1_cv_Nsp3_N-like domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ubl1_cv_Nsp3_N-like super family cl28922
first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV ...
 544-631 4.66e-40

first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV non-structural protein 3 (Nsp3) and related proteins; This ubiquitin-like (Ubl) domain (Ubl1) is found at the N-terminus of coronavirus Nsp3, a large multi-functional multi-domain protein which is an essential component of the replication/transcription complex (RTC). The functions of Ubl1 in CoVs are related to single-stranded RNA (ssRNA) binding and to interacting with the nucleocapsid (N) protein. SARS-CoV Ubl1 has been shown to bind ssRNA having AUA patterns, and since the 5'-UTR of the SARS-CoV genome has a number of AUA repeats, it may bind there. In mouse hepatitis virus (MHV), this Ubl1 domain binds the cognate N protein. Adjacent to Ubl1 is a Glu-rich acidic region (also referred to as hypervariable region, HVR); Ubl1 together with HVR has been called Nsp3a. Currently, the function of HVR in CoVs is unknown. This model corresponds to one of two Ubl domains in Nsp3; the other is located N-terminal to the papain-like protease (PLpro) and is not represented by this model.


The actual alignment was detected with superfamily member cd16130:

Pssm-ID: 475130  Cd Length: 88  Bit Score: 141.40  E-value: 4.66e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720371462 544 QDFICVSYLKPEQQSRTLASRADTAAQALCAQCAEKFEVSQPQDYRLFVLVDGRCFQLADEALPHRIKGYLLRSEPKRDF 623
Cdd:cd16130     1 QDFISVSFLEPGSNTRTLAIRPDTTAEDLCKQCAEKFEVLDPENYGLFVLVDGRCLQLADDALPHHIKSDLLKSEPRKDF 80


                  ....*...
gi 1720371462 624 HFVYRPQD 631
Cdd:cd16130    81 HFLYKQLS 88
VPS9 pfam02204
Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). ...
 406-509 1.24e-35

Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). It activates Rab GTPases by stimulating the release of GDP and allowing GTP to bind.


:

Pssm-ID: 460489  Cd Length: 104  Bit Score: 129.64  E-value: 1.24e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720371462 406 MEKILQKLTSMHKAYSPGKKISILLKTCKLIYDSMALGNPGKPYGADDFLPVLMYVLARSNLTEMLLNVEYMMELMDPAL 485
Cdd:pfam02204   1 WEQAQQELKKLNEAKSPREKLKCLLRTCKLITEALSKSNRDESLGADDLLPILIYVLIRANPPNLYSNLQFISEFRDPDL 80

                          90       100
                  ....*....|....*....|....
gi 1720371462 486 QLGEGSYYLTTTYGALEHIKNYDK 509
Cdd:pfam02204  81 LSGEEGYYLTTLEAALEFIESLDP 104
 
Name Accession Description Interval E-value
RA_Rin3 cd16130
Ras-associating (RA) domain found in Ras and Rab interactor 3 (Rin3); Rin3, also termed Ras ...
 544-631 4.66e-40

Ras-associating (RA) domain found in Ras and Rab interactor 3 (Rin3); Rin3, also termed Ras interaction/interference protein 3, is a RAS effector and a RAB5-activating guanine nucleotide exchange factor (GEF) specifically for GTPase Rab31. It functions as a negative regulator of mast cell responses to Stem Cell Factor (SCF). Rin3 contains the Vps9p-like guanine nucleotide exchange factor and Ras-association (RA) domains.


Pssm-ID: 340547  Cd Length: 88  Bit Score: 141.40  E-value: 4.66e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720371462 544 QDFICVSYLKPEQQSRTLASRADTAAQALCAQCAEKFEVSQPQDYRLFVLVDGRCFQLADEALPHRIKGYLLRSEPKRDF 623
Cdd:cd16130     1 QDFISVSFLEPGSNTRTLAIRPDTTAEDLCKQCAEKFEVLDPENYGLFVLVDGRCLQLADDALPHHIKSDLLKSEPRKDF 80


                  ....*...
gi 1720371462 624 HFVYRPQD 631
Cdd:cd16130    81 HFLYKQLS 88
VPS9 pfam02204
Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). ...
 406-509 1.24e-35

Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). It activates Rab GTPases by stimulating the release of GDP and allowing GTP to bind.


Pssm-ID: 460489  Cd Length: 104  Bit Score: 129.64  E-value: 1.24e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720371462 406 MEKILQKLTSMHKAYSPGKKISILLKTCKLIYDSMALGNPGKPYGADDFLPVLMYVLARSNLTEMLLNVEYMMELMDPAL 485
Cdd:pfam02204   1 WEQAQQELKKLNEAKSPREKLKCLLRTCKLITEALSKSNRDESLGADDLLPILIYVLIRANPPNLYSNLQFISEFRDPDL 80

                          90       100
                  ....*....|....*....|....
gi 1720371462 486 QLGEGSYYLTTTYGALEHIKNYDK 509
Cdd:pfam02204  81 LSGEEGYYLTTLEAALEFIESLDP 104
VPS9 smart00167
Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
 406-522 1.23e-27

Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.


Pssm-ID: 128469  Cd Length: 117  Bit Score: 107.54  E-value: 1.23e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720371462  406 MEKILQKLTSMHKaySPGKKISILLKTCKLIYDSMALgNPGKPYGADDFLPVLMYVLARSNLTEMLLNVEYMMELMDPAL 485
Cdd:smart00167   4 IEQIELKFLQLYK--SPSDKIKCLLRACKLIYTLLET-QSGEVAGADDFLPVLIYVIIKCDPRDLLLNAEYMEEFLEPSL 80

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1720371462  486 QLGEGSYYLTTTYGALEHIKNYDKITVTRQLSVEVQD 522
Cdd:smart00167  81 LTGEGGYYLTSLSAALALIKGLTEAHALPLSPEQELE 117
 
Name Accession Description Interval E-value
RA_Rin3 cd16130
Ras-associating (RA) domain found in Ras and Rab interactor 3 (Rin3); Rin3, also termed Ras ...
 544-631 4.66e-40

Ras-associating (RA) domain found in Ras and Rab interactor 3 (Rin3); Rin3, also termed Ras interaction/interference protein 3, is a RAS effector and a RAB5-activating guanine nucleotide exchange factor (GEF) specifically for GTPase Rab31. It functions as a negative regulator of mast cell responses to Stem Cell Factor (SCF). Rin3 contains the Vps9p-like guanine nucleotide exchange factor and Ras-association (RA) domains.


Pssm-ID: 340547  Cd Length: 88  Bit Score: 141.40  E-value: 4.66e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720371462 544 QDFICVSYLKPEQQSRTLASRADTAAQALCAQCAEKFEVSQPQDYRLFVLVDGRCFQLADEALPHRIKGYLLRSEPKRDF 623
Cdd:cd16130     1 QDFISVSFLEPGSNTRTLAIRPDTTAEDLCKQCAEKFEVLDPENYGLFVLVDGRCLQLADDALPHHIKSDLLKSEPRKDF 80


                  ....*...
gi 1720371462 624 HFVYRPQD 631
Cdd:cd16130    81 HFLYKQLS 88
VPS9 pfam02204
Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). ...
 406-509 1.24e-35

Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). It activates Rab GTPases by stimulating the release of GDP and allowing GTP to bind.


Pssm-ID: 460489  Cd Length: 104  Bit Score: 129.64  E-value: 1.24e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720371462 406 MEKILQKLTSMHKAYSPGKKISILLKTCKLIYDSMALGNPGKPYGADDFLPVLMYVLARSNLTEMLLNVEYMMELMDPAL 485
Cdd:pfam02204   1 WEQAQQELKKLNEAKSPREKLKCLLRTCKLITEALSKSNRDESLGADDLLPILIYVLIRANPPNLYSNLQFISEFRDPDL 80

                          90       100
                  ....*....|....*....|....
gi 1720371462 486 QLGEGSYYLTTTYGALEHIKNYDK 509
Cdd:pfam02204  81 LSGEEGYYLTTLEAALEFIESLDP 104
VPS9 smart00167
Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
 406-522 1.23e-27

Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.


Pssm-ID: 128469  Cd Length: 117  Bit Score: 107.54  E-value: 1.23e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720371462  406 MEKILQKLTSMHKaySPGKKISILLKTCKLIYDSMALgNPGKPYGADDFLPVLMYVLARSNLTEMLLNVEYMMELMDPAL 485
Cdd:smart00167   4 IEQIELKFLQLYK--SPSDKIKCLLRACKLIYTLLET-QSGEVAGADDFLPVLIYVIIKCDPRDLLLNAEYMEEFLEPSL 80

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1720371462  486 QLGEGSYYLTTTYGALEHIKNYDKITVTRQLSVEVQD 522
Cdd:smart00167  81 LTGEGGYYLTSLSAALALIKGLTEAHALPLSPEQELE 117
RA_Rin cd01776
Ras-associating (RA) domain of Ras and Rab interactor (Rin) protein family; Family of ...
 544-631 5.80e-23

Ras-associating (RA) domain of Ras and Rab interactor (Rin) protein family; Family of Ras-interaction/interference (Rin) proteins, also known as Ras and Rab interactors, is composed of Rin1, Rin2, and Rin3, which have multifunctional domains, including SH2 and proline-rich domains in the N-terminal region, and RH, VPS9, and RA domains in the C-terminal region. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. The RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin; ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. The RA domains of Rin1, Rin2, and Rin3 are well conserved and they all have Ras binding characteristics.


Pssm-ID: 340474  Cd Length: 90  Bit Score: 93.13  E-value: 5.80e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720371462 544 QDFICVSYLKPEQ---QSRTLASRADTAAQALCAQCAEKFEVSQPQDYRLFVLVDGRCFQLADEALPHRIKGYLLRsEPK 620
Cdd:cd01776     1 QGFLRVAVPDENNgsiVSKTLPVRPSMTAREVCKMIAHKFRVTNPQDYGLFLLVDGEEIQLEDNECPQLIKGELLA-TSK 79

                          90
                  ....*....|.
gi 1720371462 621 RDFHFVYRPQD 631
Cdd:cd01776    80 KPCYFAYKRID 90
RA_Rin1 cd17215
Ras-associating (RA) domain found in Ras and Rab interactor 1 (Rin1); Rin1, also termed Ras ...
 544-631 1.71e-07

Ras-associating (RA) domain found in Ras and Rab interactor 1 (Rin1); Rin1, also termed Ras inhibitor JC99, or Ras interaction/interference protein 1, is a downstream Ras effector that represents a unique class of Ras effector connected to two independent signaling pathways. The first effector pathway is the direct activation of RAB5-mediated endocytosis and the second pathway involves direct activation of ABL tyrosine kinase activity. Rin1 functions as a guanine nucleotide exchange factor (GEF) for RAB5 GTPases. The RAB5 GEF activity of Rin1 promotes early endosome fusion, an early event in transit to the lysosome. Rin1 binds the SH3 and SH2 domains of ABL proteins, ABL1 and ABL2, and activates their tyrosine kinase activity. Rin1 contains SH2 and proline-rich domains in the N-terminal region, and RH, VPS9, and RA domains in the C-terminal region. The RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin; ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair.


Pssm-ID: 340735  Cd Length: 88  Bit Score: 49.21  E-value: 1.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720371462 544 QDFICVSYLKPEQ--QSRTLASRADTAAQALCAQCAEKFEVSQPQDYRLFVLVDGRCFQLADEALPHRIKGYLlrSEPKR 621
Cdd:cd17215     1 QNFLRVAYQDPSSgcTSKTLAVPPSATVADLNQLCATKFKVTQPETYGIFLYKEQGYQRLPPDALPQRIKAQL--KEKGS 78

                          90
                  ....*....|
gi 1720371462 622 DFHFVYRPQD 631
Cdd:cd17215    79 TFYFVYQRAE 88
RA_Rin2 cd16131
Ras-associating (RA) domain found in Ras and Rab interactor 2 (Rin2); Rin2, also termed Ras ...
 558-628 5.62e-07

Ras-associating (RA) domain found in Ras and Rab interactor 2 (Rin2); Rin2, also termed Ras association domain family 4, or Ras inhibitor JC265, or Ras interaction/interference protein 2, is a Rab5 GDP/GTP exchange factor with the Vps9p-like guanine nucleotide exchange factor and Ras-association (RA) domains. Rin2 connects three GTPases, R-Ras, Rab5 and Rac1, to promote endothelial cell adhesion through the regulation of integrin internalization and Rac1 activation. Rin2 is involved in the regulation of Rab5-mediated early endocytosis. The deficiency of Rin2 can cause the RIN2 syndrome, an autosomal recessive connective tissue disorder.


Pssm-ID: 340548  Cd Length: 91  Bit Score: 47.93  E-value: 5.62e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720371462 558 SRTLASRADTAAQALCAQCAEKFEVSQPQDYRLFVLVDGRCFQLADEALPHRIKGYlLRSEPK-RDFHFVYR 628
Cdd:cd16131    18 AKTLLVRPYTTTEEVCQLCAQKFKVQDPENYSLFLLIDDTWQQLAEDTYPQKIKAE-LHSRPQpQIFHFVYK 88
 
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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