NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1907189702|ref|XP_036009985|]
View 

NACHT domain- and WD repeat-containing protein 1 isoform X9 [Mus musculus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
858-910 7.01e-07

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 52.61  E-value: 7.01e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907189702 858 GPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:COG2319   194 GKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHS 246
ExeA super family cl30749
Type II secretory pathway ATPase component GspA/ExeA/MshM [Intracellular trafficking, ...
 315-421 3.85e-04

Type II secretory pathway ATPase component GspA/ExeA/MshM [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


The actual alignment was detected with superfamily member COG3267:

Pssm-ID: 442498 [Multi-domain]  Cd Length: 261  Bit Score: 43.24  E-value: 3.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907189702 315 GHQELLAQLRQQLRQDESrthtPLVLFGPPGIGKTSLMCKLAQQVPEllghkTVVVLRLLGTsklSLDARSLLRslsfQV 394
Cdd:COG3267    27 SHREALARLEYALAQGGG----FVVLTGEVGTGKTTLLRRLLERLPD-----DVKVAYIPNP---QLSPAELLR----AI 90

                          90       100
                  ....*....|....*....|....*..
gi 1907189702 395 CLAYGLPLPPAQVLEAHSRVGHFFHTL 421
Cdd:COG3267    91 ADELGLEPKGASKADLLRQLQEFLLEL 117
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
858-910 7.01e-07

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 52.61  E-value: 7.01e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907189702 858 GPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:COG2319   194 GKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHS 246
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 860-910 1.59e-06

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 50.80  E-value: 1.59e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907189702 860 LRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:cd00200     1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHT 51
ExeA COG3267
Type II secretory pathway ATPase component GspA/ExeA/MshM [Intracellular trafficking, ...
 315-421 3.85e-04

Type II secretory pathway ATPase component GspA/ExeA/MshM [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 442498 [Multi-domain]  Cd Length: 261  Bit Score: 43.24  E-value: 3.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907189702 315 GHQELLAQLRQQLRQDESrthtPLVLFGPPGIGKTSLMCKLAQQVPEllghkTVVVLRLLGTsklSLDARSLLRslsfQV 394
Cdd:COG3267    27 SHREALARLEYALAQGGG----FVVLTGEVGTGKTTLLRRLLERLPD-----DVKVAYIPNP---QLSPAELLR----AI 90

                          90       100
                  ....*....|....*....|....*..
gi 1907189702 395 CLAYGLPLPPAQVLEAHSRVGHFFHTL 421
Cdd:COG3267    91 ADELGLEPKGASKADLLRQLQEFLLEL 117
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 315-361 5.39e-04

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 41.36  E-value: 5.39e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1907189702 315 GHQELLAQLRQQLRQDESRthtPLVLFGPPGIGKTSLMCKLAQQVPE 361
Cdd:cd00009     2 GQEEAIEALREALELPPPK---NLLLYGPPGTGKTTLARAIANELFR 45
FxSxx_TPR NF040586
FxSxx-COOH system tetratricopeptide repeat protein; Members of this family are typically about ...
 313-351 1.01e-03

FxSxx-COOH system tetratricopeptide repeat protein; Members of this family are typically about 850 amino acids long, or 1300 long because of an additional N-terminal domain. Proteins have a P-loop motif, GxGGxGKT, near the N-terminus of the region covered by this HMM, and a region over 400 residues long of tetratricopeptide repeat sequence. The family is found regularly next to other components of FxSxx-COOH systems, which feature an FxsB family radical SAM protein and a protein modified by it, FxsA. Members of this FxsA family typically have an FxSxx motif as the final five amino acids.


Pssm-ID: 468560 [Multi-domain]  Cd Length: 836  Bit Score: 42.98  E-value: 1.01e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907189702 313 FCGHQELLAQLRQQLRQdESRTHTPLVLFGPPGIGKTSL 351
Cdd:NF040586    8 FTGREELLERLRDQLRS-GGAAVVPQALHGLGGVGKTQL 45
WD40 pfam00400
WD domain, G-beta repeat;
858-896 1.09e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 37.32  E-value: 1.09e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907189702 858 GPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWD 896
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 858-896 1.80e-03

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 36.91  E-value: 1.80e-03
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1907189702  858 GPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWD 896
Cdd:smart00320   2 GELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
NACHT pfam05729
NACHT domain; This NTPase domain is found in apoptosis proteins as well as those involved in ...
 337-504 4.40e-03

NACHT domain; This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.


Pssm-ID: 428606 [Multi-domain]  Cd Length: 166  Bit Score: 38.83  E-value: 4.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907189702 337 PLVLFGPPGIGKTSLMCKLAQ--QVPELLGHKTVVVLRLLGTSKLSLDARSlLRSLSFQVCLAYGLPLPP--AQVLEAHS 412
Cdd:pfam05729   2 TVILQGEAGSGKTTLLQKLALlwAQGKLPQGFDFVFFLPCRELSRSGNARS-LADLLFSQWPEPAAPVSEvwAVILELPE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907189702 413 RVGHFFHTLLHTVSQRNFESLVLLLDSVDDldsichsprvSWLPLKCPPRVHLILSTCSGQqvLHNLQQTLKDPsTYWEV 492
Cdd:pfam05729  81 RLLLILDGLDELVSDLGQLDGPCPVLTLLS----------SLLRKKLLPGASLLLTVRPDA--LRDLRRGLEEP-RYLEV 147

                         170
                  ....*....|..
gi 1907189702 493 KALSGSQGQEFI 504
Cdd:pfam05729 148 RGFSESDRKQYV 159
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 313-351 4.71e-03

Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129721 [Multi-domain]  Cd Length: 305  Bit Score: 39.98  E-value: 4.71e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1907189702 313 FCGHQELLAQLRQQLRQDESRTHTP--LVLFGPPGIGKTSL 351
Cdd:TIGR00635   6 FIGQEKVKEQLQLFIEAAKMRQEALdhLLLYGPPGLGKTTL 46
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
858-910 7.01e-07

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 52.61  E-value: 7.01e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907189702 858 GPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:COG2319   194 GKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHS 246
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 860-910 1.59e-06

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 50.80  E-value: 1.59e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907189702 860 LRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:cd00200     1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHT 51
WD40 COG2319
WD40 repeat [General function prediction only];
857-910 1.60e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 51.45  E-value: 1.60e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907189702 857 GGPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:COG2319   277 TGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHT 330
WD40 COG2319
WD40 repeat [General function prediction only];
857-910 2.75e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 50.68  E-value: 2.75e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907189702 857 GGPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:COG2319   235 TGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHS 288
WD40 COG2319
WD40 repeat [General function prediction only];
858-910 4.98e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 49.91  E-value: 4.98e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907189702 858 GPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:COG2319   320 GKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHT 372
WD40 COG2319
WD40 repeat [General function prediction only];
858-910 5.33e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 49.91  E-value: 5.33e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907189702 858 GPLRATLTGcHKG-ITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:COG2319   152 GKLLRTLTG-HSGaVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHT 204
WD40 COG2319
WD40 repeat [General function prediction only];
854-910 1.02e-05

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 48.75  E-value: 1.02e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907189702 854 QPPGGPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:COG2319   106 DLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHS 162
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 855-910 1.35e-05

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 48.10  E-value: 1.35e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907189702 855 PPGGPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:cd00200   206 LSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHT 261
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 858-910 2.11e-05

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 47.33  E-value: 2.11e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907189702 858 GPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:cd00200   125 GKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHT 177
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 858-910 1.08e-04

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 45.02  E-value: 1.08e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907189702 858 GPLRATLTGcHKG-ITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:cd00200   167 GKCVATLTG-HTGeVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHE 219
ExeA COG3267
Type II secretory pathway ATPase component GspA/ExeA/MshM [Intracellular trafficking, ...
 315-421 3.85e-04

Type II secretory pathway ATPase component GspA/ExeA/MshM [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 442498 [Multi-domain]  Cd Length: 261  Bit Score: 43.24  E-value: 3.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907189702 315 GHQELLAQLRQQLRQDESrthtPLVLFGPPGIGKTSLMCKLAQQVPEllghkTVVVLRLLGTsklSLDARSLLRslsfQV 394
Cdd:COG3267    27 SHREALARLEYALAQGGG----FVVLTGEVGTGKTTLLRRLLERLPD-----DVKVAYIPNP---QLSPAELLR----AI 90

                          90       100
                  ....*....|....*....|....*..
gi 1907189702 395 CLAYGLPLPPAQVLEAHSRVGHFFHTL 421
Cdd:COG3267    91 ADELGLEPKGASKADLLRQLQEFLLEL 117
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 315-361 5.39e-04

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 41.36  E-value: 5.39e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1907189702 315 GHQELLAQLRQQLRQDESRthtPLVLFGPPGIGKTSLMCKLAQQVPE 361
Cdd:cd00009     2 GQEEAIEALREALELPPPK---NLLLYGPPGTGKTTLARAIANELFR 45
FxSxx_TPR NF040586
FxSxx-COOH system tetratricopeptide repeat protein; Members of this family are typically about ...
 313-351 1.01e-03

FxSxx-COOH system tetratricopeptide repeat protein; Members of this family are typically about 850 amino acids long, or 1300 long because of an additional N-terminal domain. Proteins have a P-loop motif, GxGGxGKT, near the N-terminus of the region covered by this HMM, and a region over 400 residues long of tetratricopeptide repeat sequence. The family is found regularly next to other components of FxSxx-COOH systems, which feature an FxsB family radical SAM protein and a protein modified by it, FxsA. Members of this FxsA family typically have an FxSxx motif as the final five amino acids.


Pssm-ID: 468560 [Multi-domain]  Cd Length: 836  Bit Score: 42.98  E-value: 1.01e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907189702 313 FCGHQELLAQLRQQLRQdESRTHTPLVLFGPPGIGKTSL 351
Cdd:NF040586    8 FTGREELLERLRDQLRS-GGAAVVPQALHGLGGVGKTQL 45
WD40 pfam00400
WD domain, G-beta repeat;
858-896 1.09e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 37.32  E-value: 1.09e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907189702 858 GPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWD 896
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 858-896 1.80e-03

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 36.91  E-value: 1.80e-03
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1907189702  858 GPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWD 896
Cdd:smart00320   2 GELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
NACHT pfam05729
NACHT domain; This NTPase domain is found in apoptosis proteins as well as those involved in ...
 337-504 4.40e-03

NACHT domain; This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.


Pssm-ID: 428606 [Multi-domain]  Cd Length: 166  Bit Score: 38.83  E-value: 4.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907189702 337 PLVLFGPPGIGKTSLMCKLAQ--QVPELLGHKTVVVLRLLGTSKLSLDARSlLRSLSFQVCLAYGLPLPP--AQVLEAHS 412
Cdd:pfam05729   2 TVILQGEAGSGKTTLLQKLALlwAQGKLPQGFDFVFFLPCRELSRSGNARS-LADLLFSQWPEPAAPVSEvwAVILELPE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907189702 413 RVGHFFHTLLHTVSQRNFESLVLLLDSVDDldsichsprvSWLPLKCPPRVHLILSTCSGQqvLHNLQQTLKDPsTYWEV 492
Cdd:pfam05729  81 RLLLILDGLDELVSDLGQLDGPCPVLTLLS----------SLLRKKLLPGASLLLTVRPDA--LRDLRRGLEEP-RYLEV 147

                         170
                  ....*....|..
gi 1907189702 493 KALSGSQGQEFI 504
Cdd:pfam05729 148 RGFSESDRKQYV 159
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 313-351 4.71e-03

Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129721 [Multi-domain]  Cd Length: 305  Bit Score: 39.98  E-value: 4.71e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1907189702 313 FCGHQELLAQLRQQLRQDESRTHTP--LVLFGPPGIGKTSL 351
Cdd:TIGR00635   6 FIGQEKVKEQLQLFIEAAKMRQEALdhLLLYGPPGLGKTTL 46
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 871-906 6.02e-03

Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped WD40 domain.The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC,


Pssm-ID: 403945 [Multi-domain]  Cd Length: 91  Bit Score: 36.87  E-value: 6.02e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1907189702 871 ITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVL 906
Cdd:pfam12894  41 VTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHF 76
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 857-910 6.60e-03

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 39.63  E-value: 6.60e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907189702 857 GGPLRATLTGcHKG-ITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:cd00200    82 TGECVRTLTG-HTSyVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHT 135
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 857-910 7.15e-03

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 39.63  E-value: 7.15e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907189702 857 GGPLRATLTGCHKGITAIAWSLEEKLLVVGTQDGAMVVWDVEEQQVVHVLMGHT 910
Cdd:cd00200    40 TGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHT 93
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH