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Conserved domains on  [gi|224028271|ref|NP_001138886|]
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rab proteins geranylgeranyltransferase component A 1 isoform b [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NADB_Rossmann super family cl21454
Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a ...
 5-61 5.01e-13

Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction.


The actual alignment was detected with superfamily member PTZ00363:

Pssm-ID: 473865  Cd Length: 443  Bit Score: 63.47  E-value: 5.01e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 224028271   5 LPSEFDVIVIGTGLPESIIAAACSRSGRRVLHVDSRSYYGGNWASFSFSGLLSWLKE 61
Cdd:PTZ00363   1 MDETYDVIVCGTGLKECILSGLLSVNGKKVLHMDRNPYYGGESASLNLTQLYKKFKP 57
 
Name Accession Description Interval E-value
PTZ00363 PTZ00363
rab-GDP dissociation inhibitor; Provisional
 5-61 5.01e-13

rab-GDP dissociation inhibitor; Provisional


Pssm-ID: 185577  Cd Length: 443  Bit Score: 63.47  E-value: 5.01e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 224028271   5 LPSEFDVIVIGTGLPESIIAAACSRSGRRVLHVDSRSYYGGNWASFSFSGLLSWLKE 61
Cdd:PTZ00363   1 MDETYDVIVCGTGLKECILSGLLSVNGKKVLHMDRNPYYGGESASLNLTQLYKKFKP 57
MRS6 COG5044
RAB proteins geranylgeranyltransferase component A (RAB escort protein) [Posttranslational ...
 6-61 5.18e-13

RAB proteins geranylgeranyltransferase component A (RAB escort protein) [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227377  Cd Length: 434  Bit Score: 63.27  E-value: 5.18e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 224028271   6 PSEFDVIVIGTGLPESIIAAACSRSGRRVLHVDSRSYYGGNWASFSFSGLLSWLKE 61
Cdd:COG5044    4 ETLYDVIILGTGLRESILSAALSWDGKNVLHIDKNDYYGSTSASLTLTQLEKYFDE 59
GDI pfam00996
GDP dissociation inhibitor;
8-55 1.43e-11

GDP dissociation inhibitor;


Pssm-ID: 395792  Cd Length: 436  Bit Score: 59.36  E-value: 1.43e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 224028271    8 EFDVIVIGTGLPESIIAAACSRSGRRVLHVDSRSYYGGNWASFSFSGL 55
Cdd:pfam00996   4 EYDVIVLGTGLKECILSGLLSVDGKKVLHIDRNDYYGGESASLNLTQL 51
 
Name Accession Description Interval E-value
PTZ00363 PTZ00363
rab-GDP dissociation inhibitor; Provisional
 5-61 5.01e-13

rab-GDP dissociation inhibitor; Provisional


Pssm-ID: 185577  Cd Length: 443  Bit Score: 63.47  E-value: 5.01e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 224028271   5 LPSEFDVIVIGTGLPESIIAAACSRSGRRVLHVDSRSYYGGNWASFSFSGLLSWLKE 61
Cdd:PTZ00363   1 MDETYDVIVCGTGLKECILSGLLSVNGKKVLHMDRNPYYGGESASLNLTQLYKKFKP 57
MRS6 COG5044
RAB proteins geranylgeranyltransferase component A (RAB escort protein) [Posttranslational ...
 6-61 5.18e-13

RAB proteins geranylgeranyltransferase component A (RAB escort protein) [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227377  Cd Length: 434  Bit Score: 63.27  E-value: 5.18e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 224028271   6 PSEFDVIVIGTGLPESIIAAACSRSGRRVLHVDSRSYYGGNWASFSFSGLLSWLKE 61
Cdd:COG5044    4 ETLYDVIILGTGLRESILSAALSWDGKNVLHIDKNDYYGSTSASLTLTQLEKYFDE 59
GDI pfam00996
GDP dissociation inhibitor;
8-55 1.43e-11

GDP dissociation inhibitor;


Pssm-ID: 395792  Cd Length: 436  Bit Score: 59.36  E-value: 1.43e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 224028271    8 EFDVIVIGTGLPESIIAAACSRSGRRVLHVDSRSYYGGNWASFSFSGL 55
Cdd:pfam00996   4 EYDVIVLGTGLKECILSGLLSVDGKKVLHIDRNDYYGGESASLNLTQL 51
NAD_binding_8 pfam13450
NAD(P)-binding Rossmann-like domain;
13-54 2.76e-05

NAD(P)-binding Rossmann-like domain;


Pssm-ID: 433218 [Multi-domain]  Cd Length: 67  Bit Score: 39.05  E-value: 2.76e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 224028271   13 VIGTGLPESIIAAACSRSGRRVLHVDSRSYYGGNWASFSFSG 54
Cdd:pfam13450   1 IVGAGLAGLVAAALLAKRGFRVLVLEKRDRLGGNAYSYRVPG 42
FAD_oxidored pfam12831
FAD dependent oxidoreductase; This family of proteins contains FAD dependent oxidoreductases ...
 10-59 1.28e-04

FAD dependent oxidoreductase; This family of proteins contains FAD dependent oxidoreductases and related proteins.


Pssm-ID: 432816 [Multi-domain]  Cd Length: 420  Bit Score: 39.51  E-value: 1.28e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 224028271   10 DVIVIGTGlPESIIAA-ACSRSGRRVLHVDSRSYYGGNWAsfsfSGLLSWL 59
Cdd:pfam12831   1 DVVVVGGG-PAGVAAAiAAARAGAKVLLVERRGFLGGMLT----SGLVGPD 46
PRK12834 PRK12834
putative FAD-binding dehydrogenase; Reviewed
 8-55 2.62e-04

putative FAD-binding dehydrogenase; Reviewed


Pssm-ID: 183782 [Multi-domain]  Cd Length: 549  Bit Score: 38.73  E-value: 2.62e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 224028271   8 EFDVIVIGTGLPESIIAAACSRSGRRVLHVD--SRSYYGGNwASFSFSGL 55
Cdd:PRK12834   4 DADVIVVGAGLAGLVAAAELADAGKRVLLLDqeNEANLGGQ-AFWSLGGL 52
COG3573 COG3573
Predicted oxidoreductase [General function prediction only];
10-55 8.11e-04

Predicted oxidoreductase [General function prediction only];


Pssm-ID: 442794 [Multi-domain]  Cd Length: 551  Bit Score: 37.08  E-value: 8.11e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 224028271  10 DVIVIGTGLpESIIAAA-CSRSGRRVLHVD--SRSYYGGNwASFSFSGL 55
Cdd:COG3573    7 DVIVVGAGL-AGLVAAAeLADAGRRVLLLDqePEANLGGQ-AFWSFGGL 53
PRK08274 PRK08274
FAD-dependent tricarballylate dehydrogenase TcuA;
6-46 1.80e-03

FAD-dependent tricarballylate dehydrogenase TcuA;


Pssm-ID: 236214 [Multi-domain]  Cd Length: 466  Bit Score: 36.01  E-value: 1.80e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 224028271   6 PSEFDVIVIGTGlpesiIAAACS-----RSGRRVLHVDS--RSYYGGN 46
Cdd:PRK08274   2 ASMVDVLVIGGG-----NAALCAalaarEAGASVLLLEAapREWRGGN 44
PLN02576 PLN02576
protoporphyrinogen oxidase
 7-85 3.86e-03

protoporphyrinogen oxidase


Pssm-ID: 215314 [Multi-domain]  Cd Length: 496  Bit Score: 35.37  E-value: 3.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224028271   7 SEFDVIVIGTGLPESIIAAAC-SRSGRRVLHVDSRSYYGGNWASFSFSGLLsWLK---EYQENSDIVS---DSPVWQDQI 79
Cdd:PLN02576  11 SSKDVAVVGAGVSGLAAAYALaSKHGVNVLVTEARDRVGGNITSVSEDGFI-WEEgpnSFQPSDPELTsavDSGLRDDLV 89


                 ....*.
gi 224028271  80 LENEEA 85
Cdd:PLN02576  90 FPDPQA 95
CzcO COG2072
Predicted flavoprotein CzcO associated with the cation diffusion facilitator CzcD [Inorganic ...
 4-78 5.38e-03

Predicted flavoprotein CzcO associated with the cation diffusion facilitator CzcD [Inorganic ion transport and metabolism];


Pssm-ID: 441675 [Multi-domain]  Cd Length: 414  Bit Score: 34.84  E-value: 5.38e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 224028271   4 TLPSEFDVIVIGTGLpeSIIAAAC--SRSGRRVLHVDSRSYYGGNWASFSFSGLlswlkeyqensdiVSDSPVWQDQ 78
Cdd:COG2072    2 AATEHVDVVVIGAGQ--AGLAAAYhlRRAGIDFVVLEKADDVGGTWRDNRYPGL-------------RLDTPSHLYS 63
PRK07608 PRK07608
UbiH/UbiF family hydroxylase;
6-40 6.63e-03

UbiH/UbiF family hydroxylase;


Pssm-ID: 181057 [Multi-domain]  Cd Length: 388  Bit Score: 34.54  E-value: 6.63e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 224028271   6 PSEFDVIVIGTGLPESIIAAACSRSGRRVLHVDSR 40
Cdd:PRK07608   3 HMKFDVVVVGGGLVGASLALALAQSGLRVALLAPR 37
COG1233 COG1233
Phytoene dehydrogenase-related protein [Secondary metabolites biosynthesis, transport and ...
 7-54 7.08e-03

Phytoene dehydrogenase-related protein [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 440846 [Multi-domain]  Cd Length: 491  Bit Score: 34.44  E-value: 7.08e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 224028271   7 SEFDVIVIGTGLpeSIIAAAC--SRSGRRVLHVDSRSYYGGNWASFSFSG 54
Cdd:COG1233    2 MMYDVVVIGAGI--GGLAAAAllARAGYRVTVLEKNDTPGGRARTFERPG 49
PRK05249 PRK05249
Si-specific NAD(P)(+) transhydrogenase;
6-46 8.49e-03

Si-specific NAD(P)(+) transhydrogenase;


Pssm-ID: 235373 [Multi-domain]  Cd Length: 461  Bit Score: 34.36  E-value: 8.49e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 224028271   6 PSEFDVIVIGTGlP---ESIIAAAcsRSGRRVLHVDSRSYYGGN 46
Cdd:PRK05249   3 MYDYDLVVIGSG-PageGAAMQAA--KLGKRVAVIERYRNVGGG 43
PRK07494 PRK07494
UbiH/UbiF family hydroxylase;
9-46 9.92e-03

UbiH/UbiF family hydroxylase;


Pssm-ID: 181001 [Multi-domain]  Cd Length: 388  Bit Score: 34.11  E-value: 9.92e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 224028271   9 FDVIVIGTGLPESIIAAACSRSGRRVLHVDSRSYYGGN 46
Cdd:PRK07494   8 TDIAVIGGGPAGLAAAIALARAGASVALVAPEPPYADL 45
 
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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