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Conserved domains on  [gi|1734335954|ref|NP_001360530|]
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Rap-GAP domain-containing protein [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rap_GAP pfam02145
Rap/ran-GAP;
384-564 9.93e-85

Rap/ran-GAP;


:

Pssm-ID: 460463  Cd Length: 179  Bit Score: 269.77  E-value: 9.93e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734335954 384 YNNEFSTPSFDEFLDFLGQRVTLKGFEAYKGGLDTRGDTTGTHSIYSEYQAHEIMFHVSTLLPFTPSNRQQLSRKRHIGN 463
Cdd:pfam02145   1 LSNEEGSPAYEEFLNLLGWLVELKGFKGYRGGLDTKNNTTGEYSYYWADRGTEIMFHVSTLMPTTENDPQQLEKKRHIGN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734335954 464 DMVTIVFQEPGaLPFSPITVRSHFQHVFIIVRVHNECSENVTYSVAVSRSKDVPAFGPPVPKGACFSK--CAEFHDWLLt 541
Cdd:pfam02145  81 DIVNIVFNESG-GPFDPSTIKSQFNHVFIVVQPNLPDTDNTLYRVSVVRKDDVPPFGPLLPDPKIFSKdnLPEFVRFLA- 158

                         170       180
                  ....*....|....*....|...
gi 1734335954 542 kiINAENAVHRSKKFATMAARTR 564
Cdd:pfam02145 159 --INAERAALKSSSFAERLRRIR 179
PDZ_SIPA1-like cd06745
PDZ domain of signal-induced proliferation-associated protein 1 (SIPA1), and related domains; ...
 712-785 2.49e-31

PDZ domain of signal-induced proliferation-associated protein 1 (SIPA1), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SIPA1, and related domains. The Rap-GTPase activating protein SIPA1 (also known as GTPase-activating protein Spa-1, p130 SPA1) is a metastasis promoter; a polymorphism in a region of the Sipa1 gene encoding the PDZ domain is associated with metastasis. The SIPA1 PDZ domain binds ribosomal RNA processing 1 homolog B (Rrp1b). SIPA1 also forms a complex with water channel aquaporin-2 (AQP2) and plays a role in trafficking of AQP2, targeted positioning of which strictly regulates body water homeostasis; the SIPA1 PDZ domain binds AQP2. Rrp1b or AQP2 binding inhibits the RapGAP activity of SIPA1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SIPA1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F.


:

Pssm-ID: 467227 [Multi-domain]  Cd Length: 73  Bit Score: 117.00  E-value: 2.49e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1734335954 712 EVVLRRLKTtDNWGFHVQDEGVVTDVEMYQLAWKAGIRQGSRIVEMDSMPISTLSFDKICDQLAVSECVRLLMI 785
Cdd:cd06745     1 ELTLRRNGL-GQLGFHVNYEGFVTEVERFGFAWQAGLRQGSRLVEICKVPVATLTHEQMIDLLRTSVKVKVTVI 73
COG2433 super family cl43687
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
874-955 2.32e-03

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


The actual alignment was detected with superfamily member COG2433:

Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 41.77  E-value: 2.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734335954 874 EQLRSpLMDELNRKapLSARESTNERESSELVRIQTHLERTVQEKRALEML---AQQLKKQLIQERQSHDNTKREMERLK 950
Cdd:COG2433   423 ERLEA-EVEELEAE--LEEKDERIERLERELSEARSEERREIRKDREISRLdreIERLERELEEERERIEELKRKLERLK 499


                  ....*
gi 1734335954 951 KMYEK 955
Cdd:COG2433   500 ELWKL 504
 
Name Accession Description Interval E-value
Rap_GAP pfam02145
Rap/ran-GAP;
384-564 9.93e-85

Rap/ran-GAP;


Pssm-ID: 460463  Cd Length: 179  Bit Score: 269.77  E-value: 9.93e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734335954 384 YNNEFSTPSFDEFLDFLGQRVTLKGFEAYKGGLDTRGDTTGTHSIYSEYQAHEIMFHVSTLLPFTPSNRQQLSRKRHIGN 463
Cdd:pfam02145   1 LSNEEGSPAYEEFLNLLGWLVELKGFKGYRGGLDTKNNTTGEYSYYWADRGTEIMFHVSTLMPTTENDPQQLEKKRHIGN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734335954 464 DMVTIVFQEPGaLPFSPITVRSHFQHVFIIVRVHNECSENVTYSVAVSRSKDVPAFGPPVPKGACFSK--CAEFHDWLLt 541
Cdd:pfam02145  81 DIVNIVFNESG-GPFDPSTIKSQFNHVFIVVQPNLPDTDNTLYRVSVVRKDDVPPFGPLLPDPKIFSKdnLPEFVRFLA- 158

                         170       180
                  ....*....|....*....|...
gi 1734335954 542 kiINAENAVHRSKKFATMAARTR 564
Cdd:pfam02145 159 --INAERAALKSSSFAERLRRIR 179
PDZ_SIPA1-like cd06745
PDZ domain of signal-induced proliferation-associated protein 1 (SIPA1), and related domains; ...
 712-785 2.49e-31

PDZ domain of signal-induced proliferation-associated protein 1 (SIPA1), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SIPA1, and related domains. The Rap-GTPase activating protein SIPA1 (also known as GTPase-activating protein Spa-1, p130 SPA1) is a metastasis promoter; a polymorphism in a region of the Sipa1 gene encoding the PDZ domain is associated with metastasis. The SIPA1 PDZ domain binds ribosomal RNA processing 1 homolog B (Rrp1b). SIPA1 also forms a complex with water channel aquaporin-2 (AQP2) and plays a role in trafficking of AQP2, targeted positioning of which strictly regulates body water homeostasis; the SIPA1 PDZ domain binds AQP2. Rrp1b or AQP2 binding inhibits the RapGAP activity of SIPA1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SIPA1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F.


Pssm-ID: 467227 [Multi-domain]  Cd Length: 73  Bit Score: 117.00  E-value: 2.49e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1734335954 712 EVVLRRLKTtDNWGFHVQDEGVVTDVEMYQLAWKAGIRQGSRIVEMDSMPISTLSFDKICDQLAVSECVRLLMI 785
Cdd:cd06745     1 ELTLRRNGL-GQLGFHVNYEGFVTEVERFGFAWQAGLRQGSRLVEICKVPVATLTHEQMIDLLRTSVKVKVTVI 73
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 709-788 2.62e-06

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.


Pssm-ID: 214570 [Multi-domain]  Cd Length: 85  Bit Score: 46.22  E-value: 2.62e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734335954  709 EAKEVVLRrlKTTDNWGFHVQDEG------VVTDVEMYQLAWKAGIRQGSRIVEMDSMPISTLSFDKICDQL-AVSECVR 781
Cdd:smart00228   1 EPRLVELE--KGGGGLGFSLVGGKdegggvVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLkKAGGKVT 78


                   ....*..
gi 1734335954  782 LLMISPS 788
Cdd:smart00228  79 LTVLRGG 85
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
874-955 2.32e-03

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 41.77  E-value: 2.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734335954 874 EQLRSpLMDELNRKapLSARESTNERESSELVRIQTHLERTVQEKRALEML---AQQLKKQLIQERQSHDNTKREMERLK 950
Cdd:COG2433   423 ERLEA-EVEELEAE--LEEKDERIERLERELSEARSEERREIRKDREISRLdreIERLERELEEERERIEELKRKLERLK 499


                  ....*
gi 1734335954 951 KMYEK 955
Cdd:COG2433   500 ELWKL 504
Nuf2_DHR10-like pfam18595
Nuf2, DHR10-like domain; This domain is found at the C-terminal region of Nuf2 proteins. This ...
 898-956 5.63e-03

Nuf2, DHR10-like domain; This domain is found at the C-terminal region of Nuf2 proteins. This domain was identified as MazG related domain also designated as Designed helical repeat protein 10 (DHR10) that actually adopts a coiled-coil structure. Nuf2 is part of the Ndc80 complex, which binds to the spindle and is required for chromosome segregation and spindle checkpoint activity.


Pssm-ID: 465814 [Multi-domain]  Cd Length: 117  Bit Score: 37.56  E-value: 5.63e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1734335954 898 ERESSELVRIQTHLERTVQEKRALEMLAQQLKKQLiqerqshDNTKREMERLKKMYEKK 956
Cdd:pfam18595  53 EEAKKKLKELRDALEEKEIELRELERREERLQRQL-------ENAQEKLERLREQAEEK 104
 
Name Accession Description Interval E-value
Rap_GAP pfam02145
Rap/ran-GAP;
384-564 9.93e-85

Rap/ran-GAP;


Pssm-ID: 460463  Cd Length: 179  Bit Score: 269.77  E-value: 9.93e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734335954 384 YNNEFSTPSFDEFLDFLGQRVTLKGFEAYKGGLDTRGDTTGTHSIYSEYQAHEIMFHVSTLLPFTPSNRQQLSRKRHIGN 463
Cdd:pfam02145   1 LSNEEGSPAYEEFLNLLGWLVELKGFKGYRGGLDTKNNTTGEYSYYWADRGTEIMFHVSTLMPTTENDPQQLEKKRHIGN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734335954 464 DMVTIVFQEPGaLPFSPITVRSHFQHVFIIVRVHNECSENVTYSVAVSRSKDVPAFGPPVPKGACFSK--CAEFHDWLLt 541
Cdd:pfam02145  81 DIVNIVFNESG-GPFDPSTIKSQFNHVFIVVQPNLPDTDNTLYRVSVVRKDDVPPFGPLLPDPKIFSKdnLPEFVRFLA- 158

                         170       180
                  ....*....|....*....|...
gi 1734335954 542 kiINAENAVHRSKKFATMAARTR 564
Cdd:pfam02145 159 --INAERAALKSSSFAERLRRIR 179
PDZ_SIPA1-like cd06745
PDZ domain of signal-induced proliferation-associated protein 1 (SIPA1), and related domains; ...
 712-785 2.49e-31

PDZ domain of signal-induced proliferation-associated protein 1 (SIPA1), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SIPA1, and related domains. The Rap-GTPase activating protein SIPA1 (also known as GTPase-activating protein Spa-1, p130 SPA1) is a metastasis promoter; a polymorphism in a region of the Sipa1 gene encoding the PDZ domain is associated with metastasis. The SIPA1 PDZ domain binds ribosomal RNA processing 1 homolog B (Rrp1b). SIPA1 also forms a complex with water channel aquaporin-2 (AQP2) and plays a role in trafficking of AQP2, targeted positioning of which strictly regulates body water homeostasis; the SIPA1 PDZ domain binds AQP2. Rrp1b or AQP2 binding inhibits the RapGAP activity of SIPA1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SIPA1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F.


Pssm-ID: 467227 [Multi-domain]  Cd Length: 73  Bit Score: 117.00  E-value: 2.49e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1734335954 712 EVVLRRLKTtDNWGFHVQDEGVVTDVEMYQLAWKAGIRQGSRIVEMDSMPISTLSFDKICDQLAVSECVRLLMI 785
Cdd:cd06745     1 ELTLRRNGL-GQLGFHVNYEGFVTEVERFGFAWQAGLRQGSRLVEICKVPVATLTHEQMIDLLRTSVKVKVTVI 73
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 709-788 2.62e-06

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.


Pssm-ID: 214570 [Multi-domain]  Cd Length: 85  Bit Score: 46.22  E-value: 2.62e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734335954  709 EAKEVVLRrlKTTDNWGFHVQDEG------VVTDVEMYQLAWKAGIRQGSRIVEMDSMPISTLSFDKICDQL-AVSECVR 781
Cdd:smart00228   1 EPRLVELE--KGGGGLGFSLVGGKdegggvVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLkKAGGKVT 78


                   ....*..
gi 1734335954  782 LLMISPS 788
Cdd:smart00228  79 LTVLRGG 85
PDZ2_APBA1_3-like cd06793
PDZ domain 2 of amyloid-beta A4 precursor protein-binding family A member 1 (APBA1), APBA2, ...
 712-777 3.12e-06

PDZ domain 2 of amyloid-beta A4 precursor protein-binding family A member 1 (APBA1), APBA2, APBA3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of APBA1, APBA2, APBA3, and related domains. The APBA/X11/Mint protein family includes three members: neuron specific APBA1 (also known as X11alpha and Mint1) and APBA2 (also known as X11beta and Mint2), and the ubiquitously expressed APBA3 (also known as X12gamma and Mint3). They are involved in regulating neuronal signaling, trafficking, and plasticity. They contain two PDZ domains (PDZ1 and PDZ2) which bind a variety of proteins: Arf GTPases (APBA1 and APBA2 PDZ2) and neurexin (APBA1 and APBA2 PDZ1 and 2) which are involved in vesicle docking and exocytosis; alpha1B subunit of N-type Ca2+ channel (APBA1 PDZ1) that is involved in ion channels; KIF17 (APBA1 PDZ1) that is involved in transport and traffic; and Alzheimer's disease related proteins, APP (APBA3 PDZ2), CCS (APBA1 PDZ2), NF-kappa-B/p65 (APBA2 PDZ2), presenilin-1 (APBA1 and APBA2 PDZ1 and PDZ2). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This APBA1,3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467255 [Multi-domain]  Cd Length: 78  Bit Score: 45.85  E-value: 3.12e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1734335954 712 EVVLRRLKTTDNWGFHVQDeGVVTDVEMYQLAWKAGIRQGSRIVEMDSMPISTLSFDKICDQLAVS 777
Cdd:cd06793     4 TVLIRRPDLKYQLGFSVQN-GIICSLLRGGIAERGGVRVGHRIIEINGQSVVATPHEKIVQLLSNS 68
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
874-955 2.32e-03

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 41.77  E-value: 2.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734335954 874 EQLRSpLMDELNRKapLSARESTNERESSELVRIQTHLERTVQEKRALEML---AQQLKKQLIQERQSHDNTKREMERLK 950
Cdd:COG2433   423 ERLEA-EVEELEAE--LEEKDERIERLERELSEARSEERREIRKDREISRLdreIERLERELEEERERIEELKRKLERLK 499


                  ....*
gi 1734335954 951 KMYEK 955
Cdd:COG2433   500 ELWKL 504
Nuf2_DHR10-like pfam18595
Nuf2, DHR10-like domain; This domain is found at the C-terminal region of Nuf2 proteins. This ...
 898-956 5.63e-03

Nuf2, DHR10-like domain; This domain is found at the C-terminal region of Nuf2 proteins. This domain was identified as MazG related domain also designated as Designed helical repeat protein 10 (DHR10) that actually adopts a coiled-coil structure. Nuf2 is part of the Ndc80 complex, which binds to the spindle and is required for chromosome segregation and spindle checkpoint activity.


Pssm-ID: 465814 [Multi-domain]  Cd Length: 117  Bit Score: 37.56  E-value: 5.63e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1734335954 898 ERESSELVRIQTHLERTVQEKRALEMLAQQLKKQLiqerqshDNTKREMERLKKMYEKK 956
Cdd:pfam18595  53 EEAKKKLKELRDALEEKEIELRELERREERLQRQL-------ENAQEKLERLREQAEEK 104
 
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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