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Conserved domains on  [gi|149944486|ref|NP_001010906|]
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nuclear GTPase SLIP-GC [Homo sapiens]

Protein Classification

P-loop NTPase family protein( domain architecture ID 1562424)

P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Dynamin_N super family cl47533
Dynamin family;
103-182 2.04e-09

Dynamin family;


The actual alignment was detected with superfamily member pfam00350:

Pssm-ID: 459775 [Multi-domain]  Cd Length: 168  Bit Score: 57.24  E-value: 2.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149944486  103 IALFGSTGAGKSSLINAIIQQAmFLPvSGESICTSCIVQVSSGccvQYEAKIHLLSDQEWREELKNLTKLLHRTEELSRE 182
Cdd:pfam00350   1 IAVVGDQSSGKSSVLNALLGRD-ILP-RGPGPTTRRPTVLRLG---ESPGASEGAVKVEYKDGEKKFEDFSELREEIEKE 75
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 284-450 4.49e-05

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd09912:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 180  Bit Score: 44.84  E-value: 4.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149944486 284 EGVVLVDIPGTGDFNSKRDEMWKKTIDKCSVIWVISDIERVsggQAHEDLlnESIKACQRGFCRDVALVVTKMDKLhlpe 363
Cdd:cd09912   46 KGVVLVDTPGLNSTIEHHTEITESFLPRADAVIFVLSADQP---LTESER--EFLKEILKWSGKKIFFVLNKIDLL---- 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149944486 364 ylrerkagnqaiqSQREavlERNEMIKLQRTRILKEKLKRKLPadfkvleasdlVYTVSAQ---EYWQQ-ALLTEEETEI 439
Cdd:cd09912  117 -------------SEEE---LEEVLEYSREELGVLELGGGEPR-----------IFPVSAKealEARLQgDEELLEQSGF 169

                        170
                 ....*....|.
gi 149944486 440 PKLREYIRKSL 450
Cdd:cd09912  170 EELEEHLEEFL 180
YlqF_related_GTPase super family cl49605
Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, ...
 52-123 6.14e-03

Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea. They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases.


The actual alignment was detected with superfamily member cd01855:

Pssm-ID: 483945 [Multi-domain]  Cd Length: 191  Bit Score: 38.78  E-value: 6.14e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149944486  52 KLESRTRRVLSNTYQKlIQSVFLDDSiPNGvkYLINRLLALIEKPTVDPIYIALFGSTGAGKSSLINAIIQQ 123
Cdd:cd01855   81 RLKQWVKKRLKIGGLK-IKDVILVSA-KKG--WGVEELIEEIKKLAKYRGDVYVVGATNVGKSTLINALLKS 148
 
Name Accession Description Interval E-value
Dynamin_N pfam00350
Dynamin family;
103-182 2.04e-09

Dynamin family;


Pssm-ID: 459775 [Multi-domain]  Cd Length: 168  Bit Score: 57.24  E-value: 2.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149944486  103 IALFGSTGAGKSSLINAIIQQAmFLPvSGESICTSCIVQVSSGccvQYEAKIHLLSDQEWREELKNLTKLLHRTEELSRE 182
Cdd:pfam00350   1 IAVVGDQSSGKSSVLNALLGRD-ILP-RGPGPTTRRPTVLRLG---ESPGASEGAVKVEYKDGEKKFEDFSELREEIEKE 75
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 104-143 3.91e-05

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


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 44.75  E-value: 3.91e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 149944486 104 ALFGSTGAGKSSLINAIIQQaMFLPVSGESICTSCIVQVS 143
Cdd:cd00882    1 VVVGRGGVGKSSLLNALLGG-EVGEVSDVPGTTRDPDVYV 39
DLP_2 cd09912
Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ...
 284-450 4.49e-05

Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. This family also includes bacterial DLPs. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) involved in self-assembly and oligomerization, a pleckstrin homology (PH) domain responsible for interactions with the plasma membrane, GED, which is also involved in self-assembly, and a proline arginine rich domain (PRD) that interacts with SH3 domains on accessory proteins. To date, three vertebrate dynamin genes have been identified; dynamin 1, which is brain specific, mediates uptake of synaptic vesicles in presynaptic terminals; dynamin-2 is expressed ubiquitously and similarly participates in membrane fission; mutations in the MD, PH and GED domains of dynamin 2 have been linked to human diseases such as Charcot-Marie-Tooth peripheral neuropathy and rare forms of centronuclear myopathy. Dynamin 3 participates in megakaryocyte progenitor amplification, and is also involved in cytoplasmic enlargement and the formation of the demarcation membrane system. This family also includes mitofusins (MFN1 and MFN2 in mammals) that are involved in mitochondrial fusion. Dynamin oligomerizes into helical structures around the neck of budding vesicles in a GTP hydrolysis-dependent manner.


Pssm-ID: 206739 [Multi-domain]  Cd Length: 180  Bit Score: 44.84  E-value: 4.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149944486 284 EGVVLVDIPGTGDFNSKRDEMWKKTIDKCSVIWVISDIERVsggQAHEDLlnESIKACQRGFCRDVALVVTKMDKLhlpe 363
Cdd:cd09912   46 KGVVLVDTPGLNSTIEHHTEITESFLPRADAVIFVLSADQP---LTESER--EFLKEILKWSGKKIFFVLNKIDLL---- 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149944486 364 ylrerkagnqaiqSQREavlERNEMIKLQRTRILKEKLKRKLPadfkvleasdlVYTVSAQ---EYWQQ-ALLTEEETEI 439
Cdd:cd09912  117 -------------SEEE---LEEVLEYSREELGVLELGGGEPR-----------IFPVSAKealEARLQgDEELLEQSGF 169

                        170
                 ....*....|.
gi 149944486 440 PKLREYIRKSL 450
Cdd:cd09912  170 EELEEHLEEFL 180
YeeP COG3596
Predicted GTPase [General function prediction only];
87-123 1.36e-03

Predicted GTPase [General function prediction only];


Pssm-ID: 442815 [Multi-domain]  Cd Length: 318  Bit Score: 41.68  E-value: 1.36e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 149944486  87 NRLLALIEKPTV--DPIYIALFGSTGAGKSSLINAIIQQ 123
Cdd:COG3596   24 ELLAEALERLLVelPPPVIALVGKTGAGKSSLINALFGA 62
YqeH cd01855
Circularly permuted YqeH GTPase; YqeH is an essential GTP-binding protein. Depletion of YqeH ...
 52-123 6.14e-03

Circularly permuted YqeH GTPase; YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases.


Pssm-ID: 206748 [Multi-domain]  Cd Length: 191  Bit Score: 38.78  E-value: 6.14e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149944486  52 KLESRTRRVLSNTYQKlIQSVFLDDSiPNGvkYLINRLLALIEKPTVDPIYIALFGSTGAGKSSLINAIIQQ 123
Cdd:cd01855   81 RLKQWVKKRLKIGGLK-IKDVILVSA-KKG--WGVEELIEEIKKLAKYRGDVYVVGATNVGKSTLINALLKS 148
 
Name Accession Description Interval E-value
Dynamin_N pfam00350
Dynamin family;
103-182 2.04e-09

Dynamin family;


Pssm-ID: 459775 [Multi-domain]  Cd Length: 168  Bit Score: 57.24  E-value: 2.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149944486  103 IALFGSTGAGKSSLINAIIQQAmFLPvSGESICTSCIVQVSSGccvQYEAKIHLLSDQEWREELKNLTKLLHRTEELSRE 182
Cdd:pfam00350   1 IAVVGDQSSGKSSVLNALLGRD-ILP-RGPGPTTRRPTVLRLG---ESPGASEGAVKVEYKDGEKKFEDFSELREEIEKE 75
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 104-143 3.91e-05

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


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 44.75  E-value: 3.91e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 149944486 104 ALFGSTGAGKSSLINAIIQQaMFLPVSGESICTSCIVQVS 143
Cdd:cd00882    1 VVVGRGGVGKSSLLNALLGG-EVGEVSDVPGTTRDPDVYV 39
DLP_2 cd09912
Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ...
 284-450 4.49e-05

Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. This family also includes bacterial DLPs. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) involved in self-assembly and oligomerization, a pleckstrin homology (PH) domain responsible for interactions with the plasma membrane, GED, which is also involved in self-assembly, and a proline arginine rich domain (PRD) that interacts with SH3 domains on accessory proteins. To date, three vertebrate dynamin genes have been identified; dynamin 1, which is brain specific, mediates uptake of synaptic vesicles in presynaptic terminals; dynamin-2 is expressed ubiquitously and similarly participates in membrane fission; mutations in the MD, PH and GED domains of dynamin 2 have been linked to human diseases such as Charcot-Marie-Tooth peripheral neuropathy and rare forms of centronuclear myopathy. Dynamin 3 participates in megakaryocyte progenitor amplification, and is also involved in cytoplasmic enlargement and the formation of the demarcation membrane system. This family also includes mitofusins (MFN1 and MFN2 in mammals) that are involved in mitochondrial fusion. Dynamin oligomerizes into helical structures around the neck of budding vesicles in a GTP hydrolysis-dependent manner.


Pssm-ID: 206739 [Multi-domain]  Cd Length: 180  Bit Score: 44.84  E-value: 4.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149944486 284 EGVVLVDIPGTGDFNSKRDEMWKKTIDKCSVIWVISDIERVsggQAHEDLlnESIKACQRGFCRDVALVVTKMDKLhlpe 363
Cdd:cd09912   46 KGVVLVDTPGLNSTIEHHTEITESFLPRADAVIFVLSADQP---LTESER--EFLKEILKWSGKKIFFVLNKIDLL---- 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149944486 364 ylrerkagnqaiqSQREavlERNEMIKLQRTRILKEKLKRKLPadfkvleasdlVYTVSAQ---EYWQQ-ALLTEEETEI 439
Cdd:cd09912  117 -------------SEEE---LEEVLEYSREELGVLELGGGEPR-----------IFPVSAKealEARLQgDEELLEQSGF 169

                        170
                 ....*....|.
gi 149944486 440 PKLREYIRKSL 450
Cdd:cd09912  170 EELEEHLEEFL 180
YeeP COG3596
Predicted GTPase [General function prediction only];
87-123 1.36e-03

Predicted GTPase [General function prediction only];


Pssm-ID: 442815 [Multi-domain]  Cd Length: 318  Bit Score: 41.68  E-value: 1.36e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 149944486  87 NRLLALIEKPTV--DPIYIALFGSTGAGKSSLINAIIQQ 123
Cdd:COG3596   24 ELLAEALERLLVelPPPVIALVGKTGAGKSSLINALFGA 62
YfjP cd11383
YfjP GTPase; The Era (E. coli Ras-like protein)-like YfjP subfamily includes several ...
 104-137 1.44e-03

YfjP GTPase; The Era (E. coli Ras-like protein)-like YfjP subfamily includes several uncharacterized bacterial GTPases that are similar to Era. They generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain.


Pssm-ID: 206743 [Multi-domain]  Cd Length: 140  Bit Score: 39.63  E-value: 1.44e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 149944486 104 ALFGSTGAGKSSLINAIIQQAMfLPVSGESICTS 137
Cdd:cd11383    1 GLMGKTGAGKSSLCNALFGTEV-AAVGDRRPTTR 33
YqeH cd01855
Circularly permuted YqeH GTPase; YqeH is an essential GTP-binding protein. Depletion of YqeH ...
 52-123 6.14e-03

Circularly permuted YqeH GTPase; YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases.


Pssm-ID: 206748 [Multi-domain]  Cd Length: 191  Bit Score: 38.78  E-value: 6.14e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149944486  52 KLESRTRRVLSNTYQKlIQSVFLDDSiPNGvkYLINRLLALIEKPTVDPIYIALFGSTGAGKSSLINAIIQQ 123
Cdd:cd01855   81 RLKQWVKKRLKIGGLK-IKDVILVSA-KKG--WGVEELIEEIKKLAKYRGDVYVVGATNVGKSTLINALLKS 148
ABCG_EPDR cd03213
Eye pigment and drug resistance transporter subfamily G of the ATP-binding cassette ...
 103-132 6.17e-03

Eye pigment and drug resistance transporter subfamily G of the ATP-binding cassette superfamily; ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR). DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.


Pssm-ID: 213180 [Multi-domain]  Cd Length: 194  Bit Score: 38.69  E-value: 6.17e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 149944486 103 IALFGSTGAGKSSLINAIIQQAMFLPVSGE 132
Cdd:cd03213   38 TAIMGPSGAGKSTLLNALAGRRTGLGVSGE 67
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 103-123 6.46e-03

50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide.


Pssm-ID: 460387 [Multi-domain]  Cd Length: 113  Bit Score: 37.21  E-value: 6.46e-03
                          10        20
                  ....*....|....*....|.
gi 149944486  103 IALFGSTGAGKSSLINAIIQQ 123
Cdd:pfam01926   2 VALVGRPNVGKSTLINALTGA 22
 
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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