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Conserved domains on  [gi|530382255|ref|XP_005249289|]
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ATPase WRNIP1 isoform X2 [Homo sapiens]

Protein Classification

replication-associated recombination protein A( domain architecture ID 13924005)

replication-associated recombination protein A is a DNA-dependent ATPase that plays important roles in cellular responses to stalled DNA replication processes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RarA super family cl34445
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 225-394 2.96e-93

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG2256:

Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 287.34  E-value: 2.96e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 225 KPLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTND 304
Cdd:COG2256   13 APLAERMRPRTLDEVVGQEHLLGPGKPLRRAIEAGRLSSMILWGPPGTGKTTLARLIANATDAE---FVALSAVTSGVKD 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 305 VRDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKLPVEA 384
Cdd:COG2256   90 IREVIEEARERRAY-GRRTILFVDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNSALLSRCRVFVLKPLSEED 168

                        170
                 ....*....|
gi 530382255 385 MVTILMRAIN 394
Cdd:COG2256  169 LEQLLERALA 178
ZnF_Rad18 smart00734
Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative ...
 17-40 1.73e-09

Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.


:

Pssm-ID: 128973 [Multi-domain]  Cd Length: 24  Bit Score: 52.61  E-value: 1.73e-09
                           10        20
                   ....*....|....*....|....
gi 530382255    17 QVQCPVCQQMMPAAHINSHLDRCL 40
Cdd:smart00734   1 LVQCPVCFREVPENLINSHLDSCL 24
RAD18 super family cl35000
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
18-83 9.63e-04

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];


The actual alignment was detected with superfamily member COG5432:

Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 41.23  E-value: 9.63e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530382255  18 VQCPVCQQMMPAAHINSHLDRCLLLH--PAGHAEP---AAGSH-RAGERAKGPSPPGAKRRRLSESSALKQP 83
Cdd:COG5432  161 VHCPACSNLVPHNQINQHLDSCLNSPssPSSSSSPyknKDNSKsNSLLSFKTDDDSITKRRLRSFNSADELP 232
 
Name Accession Description Interval E-value
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 225-394 2.96e-93

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, recombination and repair];


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 287.34  E-value: 2.96e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 225 KPLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTND 304
Cdd:COG2256   13 APLAERMRPRTLDEVVGQEHLLGPGKPLRRAIEAGRLSSMILWGPPGTGKTTLARLIANATDAE---FVALSAVTSGVKD 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 305 VRDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKLPVEA 384
Cdd:COG2256   90 IREVIEEARERRAY-GRRTILFVDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNSALLSRCRVFVLKPLSEED 168

                        170
                 ....*....|
gi 530382255 385 MVTILMRAIN 394
Cdd:COG2256  169 LEQLLERALA 178
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 226-397 1.39e-91

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 282.36  E-value: 1.39e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 226 PLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTNDV 305
Cdd:PRK13342   1 PLAERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAP---FEALSAVTSGVKDL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 306 RDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKLPVEAM 385
Cdd:PRK13342  78 REVIEEARQRRSA-GRRTILFIDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDI 156

                        170
                 ....*....|..
gi 530382255 386 VTILMRAINSLG 397
Cdd:PRK13342 157 EQLLKRALEDKE 168
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 246-376 1.75e-20

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: 87.20  E-value: 1.75e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 246 VGQD---TLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFFKRK 322
Cdd:cd00009    1 VGQEeaiEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 530382255 323 -----TILFIDEIHRFNKSQQDTFLP--------HVECGTITLIGATTENPSFQVNAALLSRCRVIV 376
Cdd:cd00009   81 ekakpGVLFIDEIDSLSRGAQNALLRvletlndlRIDRENVRVIGATNRPLLGDLDRALYDRLDIRI 147
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 264-377 3.00e-19

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 83.03  E-value: 3.00e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  264 LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATN-------AKTNDVRDVIKQAQNeksffKRKTILFIDEIHRFNKS 336
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELG---APFIEISGSElvskyvgESEKRLRELFEAAKK-----LAPCVIFIDEIDALAGS 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 530382255  337 Q-----------QDTFLPHVE-----CGTITLIGATTEnpSFQVNAALLSRCRVIVL 377
Cdd:pfam00004  73 RgsggdsesrrvVNQLLTELDgftssNSKVIVIAATNR--PDKLDPALLGRFDRIIE 127
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 235-398 2.77e-12

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: 66.94  E-value: 2.77e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  235 TLQDYFGQSKAVGQ-DTLLRSLLETNEIPS-LILWGPPGCGKTTLAHIIASNSKKhSIRfVTLSATNAKTNDVRDVIkqa 312
Cdd:TIGR00635   2 LLAEFIGQEKVKEQlQLFIEAAKMRQEALDhLLLYGPPGLGKTTLAHIIANEMGV-NLK-ITSGPALEKPGDLAAIL--- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  313 qnekSFFKRKTILFIDEIHRFNKSQQDTFLPHVE-------------CGTI-------TLIGATTEnpSFQVNAALLSRC 372
Cdd:TIGR00635  77 ----TNLEEGDVLFIDEIHRLSPAVEELLYPAMEdfrldivigkgpsARSVrldlppfTLVGATTR--AGMLTSPLRDRF 150

                         170       180
                  ....*....|....*....|....*..
gi 530382255  373 RVIV-LEKLPVEAMVTILMRAINSLGI 398
Cdd:TIGR00635 151 GIILrLEFYTVEELAEIVSRSAGLLNV 177
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 263-380 3.87e-12

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 63.55  E-value: 3.87e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255   263 SLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFF----------------KRKTILF 326
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASgsgelrlrlalalarkLKPDVLI 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 530382255   327 IDEIHRFNKSQQD----------TFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKL 380
Cdd:smart00382  84 LDEITSLLDAEQEallllleelrLLLLLKSEKNLTVILTTNDEKDLGPALLRRRFDRRIVLLLI 147
ZnF_Rad18 smart00734
Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative ...
 17-40 1.73e-09

Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.


Pssm-ID: 128973 [Multi-domain]  Cd Length: 24  Bit Score: 52.61  E-value: 1.73e-09
                           10        20
                   ....*....|....*....|....
gi 530382255    17 QVQCPVCQQMMPAAHINSHLDRCL 40
Cdd:smart00734   1 LVQCPVCFREVPENLINSHLDSCL 24
zf-WRNIP1_ubi pfam18279
Werner helicase-interacting protein 1 ubiquitin-binding domain; This domain is found in the ...
 16-36 3.80e-09

Werner helicase-interacting protein 1 ubiquitin-binding domain; This domain is found in the Werner helicase-interacting protein 1 present in Homo sapiens. The domain is a zinc finger responsible and has a zinc-coordinating B-B-A fold. WRNIP1 UBZ binds ubiquitin in a similar manner to Rad18 UBZ.


Pssm-ID: 375706  Cd Length: 21  Bit Score: 51.75  E-value: 3.80e-09
                          10        20
                  ....*....|....*....|.
gi 530382255   16 HQVQCPVCQQMMPAAHINSHL 36
Cdd:pfam18279   1 HQVQCPVCQQMMPAAHINSHL 21
cell_div_CdvC NF041006
cell division protein CdvC;
264-330 1.91e-04

cell division protein CdvC;


Pssm-ID: 468935 [Multi-domain]  Cd Length: 371  Bit Score: 43.18  E-value: 1.91e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530382255 264 LILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATN--------AKTNdVRDVIKQAQNEKSFFKRKTILFIDEI 330
Cdd:NF041006 137 ILLYGPPGCGKTMLAAAVANEIDSE---FIHVDAASimskwlgeAEKN-VAKIFKKAREKSKEEGKPAIIFIDEI 207
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
18-83 9.63e-04

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 41.23  E-value: 9.63e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530382255  18 VQCPVCQQMMPAAHINSHLDRCLLLH--PAGHAEP---AAGSH-RAGERAKGPSPPGAKRRRLSESSALKQP 83
Cdd:COG5432  161 VHCPACSNLVPHNQINQHLDSCLNSPssPSSSSSPyknKDNSKsNSLLSFKTDDDSITKRRLRSFNSADELP 232
 
Name Accession Description Interval E-value
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 225-394 2.96e-93

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, recombination and repair];


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 287.34  E-value: 2.96e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 225 KPLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTND 304
Cdd:COG2256   13 APLAERMRPRTLDEVVGQEHLLGPGKPLRRAIEAGRLSSMILWGPPGTGKTTLARLIANATDAE---FVALSAVTSGVKD 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 305 VRDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKLPVEA 384
Cdd:COG2256   90 IREVIEEARERRAY-GRRTILFVDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNSALLSRCRVFVLKPLSEED 168

                        170
                 ....*....|
gi 530382255 385 MVTILMRAIN 394
Cdd:COG2256  169 LEQLLERALA 178
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 226-397 1.39e-91

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 282.36  E-value: 1.39e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 226 PLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTNDV 305
Cdd:PRK13342   1 PLAERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAP---FEALSAVTSGVKDL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 306 RDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKLPVEAM 385
Cdd:PRK13342  78 REVIEEARQRRSA-GRRTILFIDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDI 156

                        170
                 ....*....|..
gi 530382255 386 VTILMRAINSLG 397
Cdd:PRK13342 157 EQLLKRALEDKE 168
PRK13341 PRK13341
AAA family ATPase;
220-394 2.12e-63

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 216.46  E-value: 2.12e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 220 QMLQG-KPLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSAT 298
Cdd:PRK13341  10 QMSQSeAPLADRLRPRTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHTRAH---FSSLNAV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 299 NAKTNDVRDVIKQAQNEKSFFKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLE 378
Cdd:PRK13341  87 LAGVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWVENGTITLIGATTENPYFEVNKALVSRSRLFRLK 166

                        170
                 ....*....|....*.
gi 530382255 379 KLPVEAMVTILMRAIN 394
Cdd:PRK13341 167 SLSDEDLHQLLKRALQ 182
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 246-376 1.75e-20

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: 87.20  E-value: 1.75e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 246 VGQD---TLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFFKRK 322
Cdd:cd00009    1 VGQEeaiEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 530382255 323 -----TILFIDEIHRFNKSQQDTFLP--------HVECGTITLIGATTENPSFQVNAALLSRCRVIV 376
Cdd:cd00009   81 ekakpGVLFIDEIDSLSRGAQNALLRvletlndlRIDRENVRVIGATNRPLLGDLDRALYDRLDIRI 147
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 264-377 3.00e-19

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 83.03  E-value: 3.00e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  264 LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATN-------AKTNDVRDVIKQAQNeksffKRKTILFIDEIHRFNKS 336
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELG---APFIEISGSElvskyvgESEKRLRELFEAAKK-----LAPCVIFIDEIDALAGS 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 530382255  337 Q-----------QDTFLPHVE-----CGTITLIGATTEnpSFQVNAALLSRCRVIVL 377
Cdd:pfam00004  73 RgsggdsesrrvVNQLLTELDgftssNSKVIVIAATNR--PDKLDPALLGRFDRIIE 127
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
230-398 4.08e-16

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 78.63  E-value: 4.08e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 230 TMRPDTLQDYFGQSKAVGQ-DTLLRSLLETNEIPS-LILWGPPGCGKTTLAHIIAsNSKKHSIRFVT---------LSA- 297
Cdd:PRK00080  18 SLRPKSLDEFIGQEKVKENlKIFIEAAKKRGEALDhVLLYGPPGLGKTTLANIIA-NEMGVNIRITSgpalekpgdLAAi 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 298 -TNAKTNDVrdvikqaqneksffkrktiLFIDEIHRFNKSQQDTFLPHVECGTI--------------------TLIGAT 356
Cdd:PRK00080  97 lTNLEEGDV-------------------LFIDEIHRLSPVVEEILYPAMEDFRLdimigkgpaarsirldlppfTLIGAT 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 530382255 357 TEnpsfqvnAALLS---RCR---VIVLEKLPVEAMVTILMRAINSLGI 398
Cdd:PRK00080 158 TR-------AGLLTsplRDRfgiVQRLEFYTVEELEKIVKRSARILGV 198
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 230-398 1.67e-15

Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, recombination and repair];


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 77.04  E-value: 1.67e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 230 TMRPDTLQDYFGQSKAVGQ-DTLLRSLLETNE-IPSLILWGPPGCGKTTLAHIIAsNSKKHSIRfVT----------LSA 297
Cdd:COG2255   21 SLRPKRLDEYIGQEKVKENlKIFIEAAKKRGEaLDHVLLYGPPGLGKTTLAHIIA-NEMGVNIR-ITsgpaiekpgdLAA 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 298 --TNAKTNDVrdvikqaqneksffkrktiLFIDEIHRFNKSQQDTFLPHVECGTI--------------------TLIGA 355
Cdd:COG2255   99 ilTNLEEGDV-------------------LFIDEIHRLSRVVEEILYPAMEDFRLdivigkgpaarsirldlppfTLVGA 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 530382255 356 TTenpsfqvNAALLS---RCRVIVLEKL---PVEAMVTILMRAINSLGI 398
Cdd:COG2255  160 TT-------RAGLLTsplRDRFGIVLRLefyTVEELAEIVKRSARILGV 201
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 231-357 5.90e-14

Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.


Pssm-ID: 398900 [Multi-domain]  Cd Length: 159  Bit Score: 69.07  E-value: 5.90e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  231 MRPDTLQDYFGQSKAVGQ-DTLLRSLLETNEIPS-LILWGPPGCGKTTLAHIIAsNSKKHSIRfVT----------LSA- 297
Cdd:pfam05496   1 LRPRTLDEYIGQEKVKENlKIFIEAAKQRGEALDhVLLYGPPGLGKTTLANIIA-NEMGVNIR-ITsgpaierpgdLAAi 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  298 -TNAKTNDVrdvikqaqneksffkrktiLFIDEIHRFNKSQQDTFLPHVECGTI--------------------TLIGAT 356
Cdd:pfam05496  79 lTNLEPGDV-------------------LFIDEIHRLNRAVEEILYPAMEDFRLdivigkgpsarsirldlppfTLVGAT 139


                  .
gi 530382255  357 T 357
Cdd:pfam05496 140 T 140
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 235-398 2.77e-12

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: 66.94  E-value: 2.77e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  235 TLQDYFGQSKAVGQ-DTLLRSLLETNEIPS-LILWGPPGCGKTTLAHIIASNSKKhSIRfVTLSATNAKTNDVRDVIkqa 312
Cdd:TIGR00635   2 LLAEFIGQEKVKEQlQLFIEAAKMRQEALDhLLLYGPPGLGKTTLAHIIANEMGV-NLK-ITSGPALEKPGDLAAIL--- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  313 qnekSFFKRKTILFIDEIHRFNKSQQDTFLPHVE-------------CGTI-------TLIGATTEnpSFQVNAALLSRC 372
Cdd:TIGR00635  77 ----TNLEEGDVLFIDEIHRLSPAVEELLYPAMEdfrldivigkgpsARSVrldlppfTLVGATTR--AGMLTSPLRDRF 150

                         170       180
                  ....*....|....*....|....*..
gi 530382255  373 RVIV-LEKLPVEAMVTILMRAINSLGI 398
Cdd:TIGR00635 151 GIILrLEFYTVEELAEIVSRSAGLLNV 177
PRK04195 PRK04195
replication factor C large subunit; Provisional
 226-331 3.60e-12

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 67.64  E-value: 3.60e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 226 PLADTMRPDTLQDYFGQSKAVGQdtlLRSLLET--NEIPS--LILWGPPGCGKTTLAHIIAsnskkHSIRF--VTLSATN 299
Cdd:PRK04195   3 PWVEKYRPKTLSDVVGNEKAKEQ---LREWIESwlKGKPKkaLLLYGPPGVGKTSLAHALA-----NDYGWevIELNASD 74

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 530382255 300 AKTNDV-RDVIKQAQNEKSFF-KRKTILFIDE---IH 331
Cdd:PRK04195  75 QRTADViERVAGEAATSGSLFgARRKLILLDEvdgIH 111
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 263-380 3.87e-12

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 63.55  E-value: 3.87e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255   263 SLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFF----------------KRKTILF 326
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASgsgelrlrlalalarkLKPDVLI 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 530382255   327 IDEIHRFNKSQQD----------TFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKL 380
Cdd:smart00382  84 LDEITSLLDAEQEallllleelrLLLLLKSEKNLTVILTTNDEKDLGPALLRRRFDRRIVLLLI 147
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
233-400 6.47e-12

DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 66.37  E-value: 6.47e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 233 PDTLQDYFGQSKAVgqdTLLRSLLETNEIP-SLILWGPPGCGKTTLAHIIA-----------------SNSKKHS----- 289
Cdd:COG2812    6 PQTFDDVVGQEHVV---RTLKNALASGRLAhAYLFTGPRGVGKTTLARILAkalncengptgepcgecESCRAIAagshp 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 290 -IRFVTLSATNAKTNDVRDVIKQAQNeKSFFKRKTILFIDEIHRFNKSQQDTFL-------PHVecgtiTLIGATTEnPS 361
Cdd:COG2812   83 dVIEIDAEASNIGVDDIRELIEKVSY-APVEGRYKVYIIDEAHMLTTEAFNALLktleeppPHV-----VFILATTE-PQ 155

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 530382255 362 fQVNAALLSRCRVIVLEKLPVEAMVTILMRAINSLGIHV 400
Cdd:COG2812  156 -KLLPTILSRCQRFDFRRLPPEEIAEHLAKIAEREGIEI 193
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 264-389 1.14e-10

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 63.01  E-value: 1.14e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 264 LILWGPPGCGKTTLAHIIASNSKKHSIRfVTLSA--------TNAKtndVRDVIKQAQNEKsffkrKTILFIDEI----- 330
Cdd:COG0464  194 LLLYGPPGTGKTLLARALAGELGLPLIE-VDLSDlvskyvgeTEKN---LREVFDKARGLA-----PCVLFIDEAdalag 264

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 530382255 331 ------HRFNKSQQDTFLPHVECGT--ITLIGATteNPSFQVNAALLSRCRVIVLEKLP-VEAMVTIL 389
Cdd:COG0464  265 krgevgDGVGRRVVNTLLTEMEELRsdVVVIAAT--NRPDLLDPALLRRFDEIIFFPLPdAEERLEIF 330
44 PHA02544
clamp loader, small subunit; Provisional
 250-375 1.46e-10

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 61.93  E-value: 1.46e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 250 TLLRSLLETNEIPSLILWGP-PGCGKTTLAHIIASNSkkhSIRFVTLSATNAKTNDVRDVIKQAQNEKSFFKRKTILFID 328
Cdd:PHA02544  31 ETFKSIVKKGRIPNMLLHSPsPGTGKTTVAKALCNEV---GAEVLFVNGSDCRIDFVRNRLTRFASTVSLTGGGKVIIID 107

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 530382255 329 EIHRfnksqqdTFLPHVECGTITLIGATTENPSF--------QVNAALLSRCRVI 375
Cdd:PHA02544 108 EFDR-------LGLADAQRHLRSFMEAYSKNCSFiitannknGIIEPLRSRCRVI 155
PRK08691 PRK08691
DNA polymerase III subunits gamma and tau; Validated
 227-399 2.83e-10

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236333 [Multi-domain]  Cd Length: 709  Bit Score: 62.42  E-value: 2.83e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 227 LADTMRPDTLQDYFGQSKAVgqDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIA------------------SNSKKH 288
Cdd:PRK08691   6 LARKWRPKTFADLVGQEHVV--KALQNALDEGRLHHAYLLTGTRGVGKTTIARILAkslncenaqhgepcgvcqSCTQID 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 289 SIRFVTL----SATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNKSQQDTFLPHVE--CGTITLIGATTEnpSF 362
Cdd:PRK08691  84 AGRYVDLleidAASNTGIDNIREVLENAQYAPTAGKYK-VYIIDEVHMLSKSAFNAMLKTLEepPEHVKFILATTD--PH 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 530382255 363 QVNAALLSRCRVIVLEKLPVEAMVTILMRAINSLGIH 399
Cdd:PRK08691 161 KVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIA 197
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 228-383 8.61e-10

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 59.89  E-value: 8.61e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 228 ADTMRPDTLQDYFGQSKAVgqDTLLRSLlETNEIPSLILW-GPPGCGKTTLAHIIASNSKKHSIR----------FVTLS 296
Cdd:PRK14970   8 ARKYRPQTFDDVVGQSHIT--NTLLNAI-ENNHLAQALLFcGPRGVGKTTCARILARKINQPGYDdpnedfsfniFELDA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 297 ATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNKSQQDTFLPHVE--CGTITLIGATTENpsFQVNAALLSRCRV 374
Cdd:PRK14970  85 ASNNSVDDIRNLIDQVRIPPQTGKYK-IYIIDEVHMLSSAAFNAFLKTLEepPAHAIFILATTEK--HKIIPTILSRCQI 161


                 ....*....
gi 530382255 375 IVLEKLPVE 383
Cdd:PRK14970 162 FDFKRITIK 170
ZnF_Rad18 smart00734
Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative ...
 17-40 1.73e-09

Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.


Pssm-ID: 128973 [Multi-domain]  Cd Length: 24  Bit Score: 52.61  E-value: 1.73e-09
                           10        20
                   ....*....|....*....|....
gi 530382255    17 QVQCPVCQQMMPAAHINSHLDRCL 40
Cdd:smart00734   1 LVQCPVCFREVPENLINSHLDSCL 24
zf-WRNIP1_ubi pfam18279
Werner helicase-interacting protein 1 ubiquitin-binding domain; This domain is found in the ...
 16-36 3.80e-09

Werner helicase-interacting protein 1 ubiquitin-binding domain; This domain is found in the Werner helicase-interacting protein 1 present in Homo sapiens. The domain is a zinc finger responsible and has a zinc-coordinating B-B-A fold. WRNIP1 UBZ binds ubiquitin in a similar manner to Rad18 UBZ.


Pssm-ID: 375706  Cd Length: 21  Bit Score: 51.75  E-value: 3.80e-09
                          10        20
                  ....*....|....*....|.
gi 530382255   16 HQVQCPVCQQMMPAAHINSHL 36
Cdd:pfam18279   1 HQVQCPVCQQMMPAAHINSHL 21
PLN03025 PLN03025
replication factor C subunit; Provisional
 226-391 4.10e-09

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 57.43  E-value: 4.10e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 226 PLADTMRPDTLQDYFGQSKAVGQdtlLRSLLETNEIPSLILWGPPGCGKTT----LAHIIASNSKKHSIrfVTLSATNAK 301
Cdd:PLN03025   2 PWVEKYRPTKLDDIVGNEDAVSR---LQVIARDGNMPNLILSGPPGTGKTTsilaLAHELLGPNYKEAV--LELNASDDR 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 302 TND-VRDVIKQ-AQNEKSFFK-RKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLE 378
Cdd:PLN03025  77 GIDvVRNKIKMfAQKKVTLPPgRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFS 156

                        170
                 ....*....|...
gi 530382255 379 KLPVEAMVTILMR 391
Cdd:PLN03025 157 RLSDQEILGRLMK 169
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 232-330 2.26e-08

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 55.40  E-value: 2.26e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 232 RPDTLQDYFGqskavGQDTLLRSLLETNEIP----------------SLILWGPPGCGKTTLAHIIASNSKKHSIR---- 291
Cdd:COG1222   72 SPDVTFDDIG-----GLDEQIEEIREAVELPlknpelfrkygieppkGVLLYGPPGTGKTLLAKAVAGELGAPFIRvrgs 146

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 530382255 292 -----FVTLSATNaktndVRDVIKQAQNeksffKRKTILFIDEI 330
Cdd:COG1222  147 elvskYIGEGARN-----VREVFELARE-----KAPSIIFIDEI 180
PRK14700 PRK14700
recombination factor protein RarA; Provisional
 342-394 3.15e-08

recombination factor protein RarA; Provisional


Pssm-ID: 173163 [Multi-domain]  Cd Length: 300  Bit Score: 54.63  E-value: 3.15e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 530382255 342 LPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKLPVEAMVTILMRAIN 394
Cdd:PRK14700   1 MPYVESGKIILIGATTENPTYYLNDALVSRLFILRLKRLSLVATQKLIEKALS 53
PRK05896 PRK05896
DNA polymerase III subunits gamma and tau; Validated
 232-380 6.29e-08

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235638 [Multi-domain]  Cd Length: 605  Bit Score: 54.85  E-value: 6.29e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 232 RPDTLQDYFGQSKAvgQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIAS-----NSKK----------------HSI 290
Cdd:PRK05896  11 RPHNFKQIIGQELI--KKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKainclNPKDgdccnscsvcesintnQSV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 291 RFVTL-SATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNKSQQDTFLPHVE--CGTITLIGATTEnpSFQVNAA 367
Cdd:PRK05896  89 DIVELdAASNNGVDEIRNIIDNINYLPTTFKYK-VYIIDEAHMLSTSAWNALLKTLEepPKHVVFIFATTE--FQKIPLT 165

                        170
                 ....*....|...
gi 530382255 368 LLSRCRVIVLEKL 380
Cdd:PRK05896 166 IISRCQRYNFKKL 178
COG1373 COG1373
Predicted ATPase, AAA+ superfamily [General function prediction only];
249-335 1.25e-07

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440984 [Multi-domain]  Cd Length: 405  Bit Score: 53.41  E-value: 1.25e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 249 DTLLRSLLETNEIpsLILWGPPGCGKTTLA-HIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAqneKSFFKRKTILFI 327
Cdd:COG1373   10 LDKLLKLLDNRKA--VVITGPRQVGKTTLLkQLAKELENILYINLDDPRLRALAEEDPDDLLEAL---KELYPGKTYLFL 84


                 ....*...
gi 530382255 328 DEIHRFNK 335
Cdd:COG1373   85 DEIQRVPE 92
rfc PRK00440
replication factor C small subunit; Reviewed
 232-329 1.35e-07

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 52.95  E-value: 1.35e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 232 RPDTLQDYFGQSKAVGQdtlLRSLLETNEIPSLILWGPPGCGKTTLAHIIAsnskkHSI-------RFVTLSATNAKTND 304
Cdd:PRK00440  12 RPRTLDEIVGQEEIVER---LKSYVKEKNMPHLLFAGPPGTGKTTAALALA-----RELygedwreNFLELNASDERGID 83

                         90       100       110
                 ....*....|....*....|....*....|
gi 530382255 305 V-RDVIKQAQNEKSF----FKrktILFIDE 329
Cdd:PRK00440  84 ViRNKIKEFARTAPVggapFK---IIFLDE 110
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 262-374 1.59e-07

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 50.74  E-value: 1.59e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 262 PSLILWGPPGCGKTTLAHIIASNSKKHSIRfVTLSATNAKTND-----VRDVIKQAQNeksffKRKTILFIDEIH----- 331
Cdd:cd19481   27 KGILLYGPPGTGKTLLAKALAGELGLPLIV-VKLSSLLSKYVGeseknLRKIFERARR-----LAPCILFIDEIDaigrk 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 530382255 332 RFNKSQQDTFLPHV-----------ECGTITLIGATteNPSFQVNAALLSRCRV 374
Cdd:cd19481  101 RDSSGESGELRRVLnqllteldgvnSRSKVLVIAAT--NRPDLLDPALLRPGRF 152
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
232-386 4.80e-07

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 52.09  E-value: 4.80e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 232 RPDTLQDYFGQSKAVgqdTLLRSLLETNEIPSLILW-GPPGCGKTTLAHIIA----------------------SNSKKH 288
Cdd:PRK14971  12 RPSTFESVVGQEALT---TTLKNAIATNKLAHAYLFcGPRGVGKTTCARIFAktincqnltadgeacnecescvAFNEQR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 289 SIRFVTL-SATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNKSQQDTFL------PHvecgTITLIGATTENps 361
Cdd:PRK14971  89 SYNIHELdAASNNSVDDIRNLIEQVRIPPQIGKYK-IYIIDEVHMLSQAAFNAFLktleepPS----YAIFILATTEK-- 161

                        170       180
                 ....*....|....*....|....*
gi 530382255 362 FQVNAALLSRCRVIVLEKLPVEAMV 386
Cdd:PRK14971 162 HKILPTILSRCQIFDFNRIQVADIV 186
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
242-392 5.33e-07

DNA polymerase III, delta prime subunit [Replication, recombination and repair];


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 50.74  E-value: 5.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 242 QSKAVGQdtlLRSLLETNEIP-SLILWGPPGCGKTTLAHIIA------------SNSKKHSIR--------FVTLSATNA 300
Cdd:COG0470    1 QEEAWEQ---LLAAAESGRLPhALLLHGPPGIGKTTLALALArdllcenpeggkACGQCHSRLmaagnhpdLLELNPEEK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 301 KT----NDVRDVIKQAQNeKSFFKRKTILFIDEIHRFNKSQQDTFL-----PHVECgTITLIgatTENPSfQVNAALLSR 371
Cdd:COG0470   78 SDqigiDQIRELGEFLSL-TPLEGGRKVVIIDEADAMNEAAANALLktleePPKNT-PFILI---ANDPS-RLLPTIRSR 151

                        170       180
                 ....*....|....*....|.
gi 530382255 372 CRVIVLEKLPVEAMVTILMRA 392
Cdd:COG0470  152 CQVIRFRPPSEEEALAWLREE 172
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
264-400 1.89e-06

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 48.73  E-value: 1.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 264 LILWGPPGCGKTTLAHIIASNSKKHSI---------RFVTLSATNaktndVRDVIKQAQNeksffkRKTILFIDEIH--- 331
Cdd:COG1223   38 ILFYGPPGTGKTMLAEALAGELKLPLLtvrldsligSYLGETARN-----LRKLFDFARR------APCVIFFDEFDaia 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 332 --RFNKS-------------QQDTFLPhvecGTITLIGATteNPSFQVNAALLSRCRVIVLEKLP-VEAMVTILMRAINS 395
Cdd:COG1223  107 kdRGDQNdvgevkrvvnallQELDGLP----SGSVVIAAT--NHPELLDSALWRRFDEVIEFPLPdKEERKEILELNLKK 180


                 ....*
gi 530382255 396 LGIHV 400
Cdd:COG1223  181 FPLPF 185
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 229-391 5.67e-06

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 48.06  E-value: 5.67e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 229 DTMRPDTLQDYFGQSKAVGQdtlLRSLLETNEIPSLILWGPPGCGKTT----LAHIIASNSKKHSI-------------- 290
Cdd:PRK12402   7 EKYRPALLEDILGQDEVVER---LSRAVDSPNLPHLLVQGPPGSGKTAavraLARELYGDPWENNFtefnvadffdqgkk 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 291 ------RFVTLSATNAKTN-DVRDVIKQAQNEKSFFKR-----KTILFiDEIHRFNKSQQDTFLPHVE--CGTITLIGAT 356
Cdd:PRK12402  84 ylvedpRFAHFLGTDKRIRsSKIDNFKHVLKEYASYRPlsadyKTILL-DNAEALREDAQQALRRIMEqySRTCRFIIAT 162

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 530382255 357 TeNPSfQVNAALLSRCRVIVLEKLPVEAMVTILMR 391
Cdd:PRK12402 163 R-QPS-KLIPPIRSRCLPLFFRAPTDDELVDVLES 195
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 263-372 6.50e-06

AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.


Pssm-ID: 400191 [Multi-domain]  Cd Length: 135  Bit Score: 45.36  E-value: 6.50e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  263 SLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSAtNAKTNDVRDVIKQAQNEKSF--------FKRKTILFIDEIHRFN 334
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAAALSNRPVFYVQLTR-DTTEEDLFGRRNIDPGGASWvdgplvraAREGEIAVLDEINRAN 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 530382255  335 KSQQDTFLP-------HVECGT---------ITLIgATTENPSFQVN---AALLSRC 372
Cdd:pfam07728  80 PDVLNSLLSllderrlLLPDGGelvkaapdgFRLI-ATMNPLDRGLNelsPALRSRF 135
PRK14964 PRK14964
DNA polymerase III subunits gamma and tau; Provisional
 227-389 1.01e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237870 [Multi-domain]  Cd Length: 491  Bit Score: 47.47  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 227 LADTMRPDTLQDYfgqskaVGQDTLLRSL---LETNEIP-SLILWGPPGCGKTTLAHIIA-------------SNSKKHS 289
Cdd:PRK14964   3 LALKYRPSSFKDL------VGQDVLVRILrnaFTLNKIPqSILLVGASGVGKTTCARIISlclncsngptsdpCGTCHNC 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 290 IRFVTLS---------ATNAKTNDVRdVIKQAQNEKSFFKRKTILFIDEIHRFNKSQQDTFL-------PHVEcgtitLI 353
Cdd:PRK14964  77 ISIKNSNhpdvieidaASNTSVDDIK-VILENSCYLPISSKFKVYIIDEVHMLSNSAFNALLktleepaPHVK-----FI 150

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 530382255 354 GATTENPSFQVNAAllSRCRVIVLEKLPVEAMVTIL 389
Cdd:PRK14964 151 LATTEVKKIPVTII--SRCQRFDLQKIPTDKLVEHL 184
DnaA COG0593
Chromosomal replication initiation ATPase DnaA [Replication, recombination and repair];
264-341 1.01e-05

Chromosomal replication initiation ATPase DnaA [Replication, recombination and repair];


Pssm-ID: 440358 [Multi-domain]  Cd Length: 303  Bit Score: 47.11  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 264 LILWGPPGCGKTTLAHIIA----SNSKKHSIRFVTLSA-TNAKTNDVRDviKQAQNEKSFFKRKTILFIDEIHRF--NKS 336
Cdd:COG0593   37 LFLYGGVGLGKTHLLHAIGnealENNPGARVVYLTAEEfTNDFINAIRN--NTIEEFKEKYRSVDVLLIDDIQFLagKEA 114


                 ....*
gi 530382255 337 QQDTF 341
Cdd:COG0593  115 TQEEF 119
DNA_pol3_delta2 pfam13177
DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required ...
 241-381 1.17e-05

DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalyzed reaction. The delta subunit is also known as HolA.


Pssm-ID: 433013 [Multi-domain]  Cd Length: 161  Bit Score: 45.28  E-value: 1.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  241 GQSKAVgqdTLLRSLLETNEIPSLILW-GPPGCGKTTLAHIIAS----------------------NSKKHS-IRFVTLS 296
Cdd:pfam13177   1 GQPEAI---QLLQNSLENGRLSHAYLFsGPEGVGKLELALAFAKalfceepgddlpcgqcrscrriESGNHPdLVIIEPE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  297 ATNAKTNDVRDVIKQAQnEKSFFKRKTILFIDEIHRFNKSQQDTFL-----PHVEcgtiTLIGATTENPSfQVNAALLSR 371
Cdd:pfam13177  78 GQSIKIDQIRELQKEFS-KSPYEGKKKVYIIEDAEKMTASAANSLLkfleePPGN----TVIILLTENPS-RLLPTIRSR 151

                         170
                  ....*....|
gi 530382255  372 CRVIVLEKLP 381
Cdd:pfam13177 152 CQIIRFKPLS 161
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 264-330 1.76e-05

first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410926 [Multi-domain]  Cd Length: 169  Bit Score: 44.70  E-value: 1.76e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 530382255 264 LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATN-------AKTNDVRDVIKQAQNEKSffkrkTILFIDEI 330
Cdd:cd19518   37 VLLHGPPGCGKTMLANAIAGELK---VPFLKISATEivsgvsgESEEKIRELFDQAISNAP-----CIVFIDEI 102
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 264-329 2.80e-05

second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as Peroxin-1)/PEX6 is a protein unfoldase; PEX1 and PEX6 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. PEX-1 is required for stability of PEX5. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410934 [Multi-domain]  Cd Length: 158  Bit Score: 43.96  E-value: 2.80e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530382255 264 LILWGPPGCGKTTLAHIIASNSkkhSIRFVTLSA-------TNAKTNDVRDVIKQAQNEKSffkrkTILFIDE 329
Cdd:cd19526   30 ILLYGPPGCGKTLLASAIASEC---GLNFISVKGpellnkyIGASEQNVRDLFSRAQSAKP-----CILFFDE 94
AAA_14 pfam13173
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 264-332 3.41e-05

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.


Pssm-ID: 463799 [Multi-domain]  Cd Length: 128  Bit Score: 43.35  E-value: 3.41e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530382255  264 LILWGPPGCGKTTLA-HIIASNSKKHSIRFVTL---SATNAKTNDVRDVIkqaqnEKSFFKRKTILFIDEIHR 332
Cdd:pfam13173   5 LVITGPRQVGKTTLLlQLIKELLPPENILYINLddpRLLKLADFELLELF-----LELLYPGKTYLFLDEIQR 72
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 265-330 3.56e-05

second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase domains; This subfamily includes the second of two ATPase domains of the molecular chaperone CDC48 in yeast and p97 or VCP in metazoans, Peroxisomal biogenesis factor 1 (PEX1) and -6 (PEX6), Valosin-containing protein-like ATPase (VAT), and nuclear VCP-like protein (NVL). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 43.81  E-value: 3.56e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530382255 265 ILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATNAKT-------NDVRDVIKQAQNEKSffkrkTILFIDEI 330
Cdd:cd19511   31 LLYGPPGCGKTLLAKALASEAG---LNFISVKGPELFSkyvgeseRAVREIFQKARQAAP-----CIIFFDEI 95
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 264-340 5.63e-05

ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase) is an ATPase that plays a critical role in regulating the surface expression of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, thereby regulating synaptic plasticity, learning and memory. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410928 [Multi-domain]  Cd Length: 166  Bit Score: 43.18  E-value: 5.63e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 530382255 264 LILWGPPGCGKTTLAHIIAsnsKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFFKR--KTILFIDEIHRFNKSQQDT 340
Cdd:cd19520   38 VLLYGPPGCGKTMLAKATA---KEAGARFINLQVSSLTDKWYGESQKLVAAVFSLASKlqPSIIFIDEIDSFLRQRSST 113
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 266-330 5.68e-05

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 44.82  E-value: 5.68e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530382255 266 LWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATN------AKTndVRDVIKQAQnEKSffkrKTILFIDEI 330
Cdd:PRK03992 170 LYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQkfigegARL--VRELFELAR-EKA----PSIIFIDEI 233
ftsH CHL00176
cell division protein; Validated
 253-330 6.81e-05

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 45.04  E-value: 6.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 253 RSLLETNEIPS-LILWGPPGCGKTTLAHIIASNSKK--HSI-------RFVTLSATNaktndVRDVIKQAQNeksffKRK 322
Cdd:CHL00176 207 RFTAVGAKIPKgVLLVGPPGTGKTLLAKAIAGEAEVpfFSIsgsefveMFVGVGAAR-----VRDLFKKAKE-----NSP 276


                 ....*...
gi 530382255 323 TILFIDEI 330
Cdd:CHL00176 277 CIVFIDEI 284
cell_div_CdvC NF041006
cell division protein CdvC;
264-330 1.91e-04

cell division protein CdvC;


Pssm-ID: 468935 [Multi-domain]  Cd Length: 371  Bit Score: 43.18  E-value: 1.91e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530382255 264 LILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATN--------AKTNdVRDVIKQAQNEKSFFKRKTILFIDEI 330
Cdd:NF041006 137 ILLYGPPGCGKTMLAAAVANEIDSE---FIHVDAASimskwlgeAEKN-VAKIFKKAREKSKEEGKPAIIFIDEI 207
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 265-330 2.14e-04

proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily contains ATPase subunits of the eukaryotic 26S proteasome, and of the archaeal proteasome which carry out ATP-dependent degradation of substrates of the ubiquitin-proteasome pathway. The eukaryotic 26S proteasome consists of a proteolytic 20S core particle (CP), and a 19S regulatory particle (RP) which provides the ATP-dependence and the specificity for ubiquitinated proteins. In the archaea the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). This subfamily also includes various eukaryotic 26S subunits including, proteasome 26S subunit, ATPase 2 (PSMC2, also known as S7 and MSS1) which is a member of the 19S RP and has a chaperone like activity; and proteasome 20S subunit alpha 6 (PSMA6, also known as IOTA, p27K, and PROS27) which is a member of the 20S CP. This RecA-like_PAN subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410910 [Multi-domain]  Cd Length: 171  Bit Score: 41.55  E-value: 2.14e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 265 ILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTND----VRDVIKQAQNeksffKRKTILFIDEI 330
Cdd:cd19502   41 LLYGPPGTGKTLLAKAVANHTDATFIRVVGSELVQKYIGEgarlVRELFEMARE-----KAPSIIFIDEI 105
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 263-371 2.83e-04

ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This subfamily includes the ATPase domains of vacuolar protein sorting-associated protein 4 (VPS4), ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase), Katanin p60 ATPase-containing subunit A1 (KTNA1), Spastin, and Fidgetin-Like 1 (FIGL-1). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410917 [Multi-domain]  Cd Length: 163  Bit Score: 41.18  E-value: 2.83e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 263 SLILWGPPGCGKTTLAHIIASNSkkhSIRFVTLSATN-------AKTNDVRDVIKQAQneksfFKRKTILFIDEIHRFNK 335
Cdd:cd19509   34 GILLYGPPGTGKTLLARAVASES---GSTFFSISASSlvskwvgESEKIVRALFALAR-----ELQPSIIFIDEIDSLLS 105

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 530382255 336 SQQDT-----------FL------PHVECGTITLIGATteNPSFQVNAALLSR 371
Cdd:cd19509  106 ERGSGeheasrrvkteFLvqmdgvLNKPEDRVLVLGAT--NRPWELDEAFLRR 156
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 216-290 2.92e-04

second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410938 [Multi-domain]  Cd Length: 161  Bit Score: 41.32  E-value: 2.92e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 530382255 216 EEIRQMLQGKPLADTMRPDtlqdyfgQSKAVGQDTllrslletneiPS-LILWGPPGCGKTTLAHIIASNSKKHSI 290
Cdd:cd19530    2 DHVREELTMSILRPIKRPD-------IYKALGIDL-----------PTgVLLYGPPGCGKTLLAKAVANESGANFI 59
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 260-330 3.13e-04

ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. It is anchored to the cytoplasmic membrane such that the amino- and carboxy-termini are exposed to the cytoplasm. It presents a membrane-bound hexameric structure that is able to unfold and degrade protein substrates. It is comprised of an N-terminal transmembrane region and the larger C-terminal cytoplasmic region, which consists of an ATPase domain and a protease domain. This RecA-Like FTsH subfamily represents the ATPase domain, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410909 [Multi-domain]  Cd Length: 171  Bit Score: 41.06  E-value: 3.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 260 EIP-SLILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATN---------AKTndVRDVIKQAqneksffKRKT--ILFI 327
Cdd:cd19501   35 KIPkGVLLVGPPGTGKTLLAKAVAGEAG---VPFFSISGSDfvemfvgvgASR--VRDLFEQA-------KKNApcIVFI 102


                 ...
gi 530382255 328 DEI 330
Cdd:cd19501  103 DEI 105
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 205-401 3.22e-04

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 42.66  E-value: 3.22e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 205 GGRPHPRALAAEE-----IRQmLQGKPLADTMRPDTLQDYFGQSKAV---GQDTLLRSLLETNEIpsLILWGPPGCGKTT 276
Cdd:COG0507   79 GRRYLTRLLEAEQrlarrLRR-LARPALDEADVEAALAALEPRAGITlsdEQREAVALALTTRRV--SVLTGGAGTGKTT 155

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 277 LAHIIASNSKKHSIRFVTLSATNaktndvrdviKQAQN--EKSFFKRKTilfideIHRfnksqqdtflphvecgtitLIG 354
Cdd:COG0507  156 TLRALLAALEALGLRVALAAPTG----------KAAKRlsESTGIEART------IHR-------------------LLG 200

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 530382255 355 ATTENPSFQVNA-ALLSRCRVIVLEklpvEA-MVTI-----LMRAINSLGIHVL 401
Cdd:COG0507  201 LRPDSGRFRHNRdNPLTPADLLVVD----EAsMVDTrlmaaLLEALPRAGARLI 250
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 264-330 4.34e-04

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 40.74  E-value: 4.34e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 530382255 264 LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSA----------TNAKtndVRDVIKQAQNEKsffkrKTILFIDEI 330
Cdd:cd19503   37 VLLHGPPGTGKTLLARAVANEAG---ANFLSISGpsivskylgeSEKN---LREIFEEARSHA-----PSIIFIDEI 102
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 264-337 4.75e-04

second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP in metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the second of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r2-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410936 [Multi-domain]  Cd Length: 161  Bit Score: 40.57  E-value: 4.75e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 530382255 264 LILWGPPGCGKTTLAHIIASNSKKHSI-----RFVTLSATNAKTNdVRDVIKQAQNEKSffkrkTILFIDEIHRFNKSQ 337
Cdd:cd19528   30 VLFYGPPGCGKTLLAKAIANECQANFIsvkgpELLTMWFGESEAN-VRDIFDKARAAAP-----CVLFFDELDSIAKAR 102
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
260-330 5.52e-04

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 42.33  E-value: 5.52e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 530382255 260 EIPSLILW-GPPGCGKTTLAHIIASNSKkhsIRFVTLSATN-------AKTNDVRDVIKQAQNEKSffkrkTILFIDEI 330
Cdd:PRK10733 183 KIPKGVLMvGPPGTGKTLLAKAIAGEAK---VPFFTISGSDfvemfvgVGASRVRDMFEQAKKAAP-----CIIFIDEI 253
clpC CHL00095
Clp protease ATP binding subunit
 265-389 5.83e-04

Clp protease ATP binding subunit


Pssm-ID: 214361 [Multi-domain]  Cd Length: 821  Bit Score: 42.35  E-value: 5.83e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 265 ILWGPPGCGKTT----LAHIIASNSKK---HSIRFVTLSATN--AKTND-------VRDVIKQAQNEKsffkrKTILFID 328
Cdd:CHL00095 204 ILIGEPGVGKTAiaegLAQRIVNRDVPdilEDKLVITLDIGLllAGTKYrgefeerLKRIFDEIQENN-----NIILVID 278

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530382255 329 EIHR-FNKSQQDT-------FLPHVECGTITLIGATTEN---PSFQVNAALLSRCRVIVLEKLPVEAMVTIL 389
Cdd:CHL00095 279 EVHTlIGAGAAEGaidaaniLKPALARGELQCIGATTLDeyrKHIEKDPALERRFQPVYVGEPSVEETIEIL 350
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 224-396 6.33e-04

checkpoint protein rad24; All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129690 [Multi-domain]  Cd Length: 637  Bit Score: 41.87  E-value: 6.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  224 GKPLADTMRPDTLQDYFGQSKAVG--QDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIA--------SNSKKHSIRF- 292
Cdd:TIGR00602  71 NEPWVEKYKPETQHELAVHKKKIEevETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSkelgiqvqEWSNPTLPDFq 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  293 -----VTLSATNAKTNDV------RDVIKQAQNE-----KSFFKRKTILFIDEI----HRFNKSQQDTF-LPHVECGTIT 351
Cdd:TIGR00602 151 kndhkVTLSLESCFSNFQsqievfSEFLLRATNKlqmlgDDLMTDKKIILVEDLpnqfYRDTRALHEILrWKYVSIGRCP 230

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 530382255  352 LIGATTEN------------PSFQV-NAALLSRCRVIVLEKLPVEAmvTILMRAINSL 396
Cdd:TIGR00602 231 LVFIITESlegdnnqrrllfPAETImNKEILEEPRVSNISFNPIAP--TIMKKFLNRI 286
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
18-83 9.63e-04

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 41.23  E-value: 9.63e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530382255  18 VQCPVCQQMMPAAHINSHLDRCLLLH--PAGHAEP---AAGSH-RAGERAKGPSPPGAKRRRLSESSALKQP 83
Cdd:COG5432  161 VHCPACSNLVPHNQINQHLDSCLNSPssPSSSSSPyknKDNSKsNSLLSFKTDDDSITKRRLRSFNSADELP 232
AAA_7 pfam12775
P-loop containing dynein motor region; This domain is found in human cytoplasmic dynein-2 ...
 251-331 9.99e-04

P-loop containing dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the third nucleotide binding sites in the dynein motor. However, AAA3 has lost the catalytic residues necessary for ATP hydrolysis (the Walker B glutamate, the arginine finger, sensor-I and sensor-II motifs).


Pssm-ID: 463698 [Multi-domain]  Cd Length: 179  Bit Score: 39.68  E-value: 9.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  251 LLRSLLeTNEIPSLiLWGPPGCGKTTLAH--IIASNSKKHSIRFVTLSA-TNAktNDVRDVIkqaqnEKSFFKR------ 321
Cdd:pfam12775  23 LLDLLL-KNGKPVL-LVGPTGTGKTVIIQnlLRKLDKEKYLPLFINFSAqTTS--NQTQDII-----ESKLEKRrkgvyg 93

                          90
                  ....*....|....*
gi 530382255  322 -----KTILFIDEIH 331
Cdd:pfam12775  94 ppggkKLVVFIDDLN 108
Rad17 pfam03215
Rad17 P-loop domain;
223-381 1.03e-03

Rad17 P-loop domain;


Pssm-ID: 367398 [Multi-domain]  Cd Length: 186  Bit Score: 39.94  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  223 QGKPLADTMRPDTLQDYFGQSKAVG--QDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIasnSKKHSIRFVT-LSATN 299
Cdd:pfam03215   5 GGEQWYEKYKPNCLEQLAVHKRKIKdvQEWLDAMFLENAKHRILLISGPSGCGKSTVIKEL---SKELGPKYREwSNPTS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  300 AKTNDvrdvikqaqNEKSFFKRKTILFideihrfnksqqDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEK 379
Cdd:pfam03215  82 FRSPP---------NQVTDFRGDCIVN------------SRFLSQMESFSEFELKGARYLVMQKRGKNAQGNKKLILIED 140


                  ..
gi 530382255  380 LP 381
Cdd:pfam03215 141 LP 142
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 264-330 1.06e-03

26S protease regulatory subunit 6B-like protein; Provisional


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 40.90  E-value: 1.06e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530382255 264 LILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTND----VRDVIKQAQnEKSffkrKTILFIDEI 330
Cdd:PTZ00454 182 VLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKYLGEgprmVRDVFRLAR-ENA----PSIIFIDEV 247
IstB_IS21 pfam01695
IstB-like ATP binding protein; This protein contains an ATP/GTP binding P-loop motif. It is ...
 235-330 1.08e-03

IstB-like ATP binding protein; This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function.


Pssm-ID: 426385 [Multi-domain]  Cd Length: 238  Bit Score: 40.51  E-value: 1.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  235 TLQDY-FGQSKAVGQDTL--LRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKH--SIRFVTlsatnakTNDVRDVI 309
Cdd:pfam01695  63 TLEDFdFTFAPGLDQRIVaeLASLSFIDRAQNVVLLGPPGVGKTHLAIALGVEACRAgySVRFTS-------AADLVNQL 135

                          90       100
                  ....*....|....*....|....*..
gi 530382255  310 KQAQNEKSF------FKRKTILFIDEI 330
Cdd:pfam01695 136 KRAHGDGKLtrklqqLLKPDVLILDEW 162
PRK04132 PRK04132
replication factor C small subunit; Provisional
 225-274 1.46e-03

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 40.98  E-value: 1.46e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 530382255 225 KPLADTMRPDTLQDYFGQSKAVGQdtlLRSLLETNEIPSLILWGPPGCGK 274
Cdd:PRK04132   7 KPWVEKYRPQRLDDIVGQEHIVKR---LKHYVKTGSMPHLLFAGPPGVGK 53
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 246-330 2.06e-03

ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in microtubule dynamics; it specifically recognizes and cuts microtubules that are polyglutamylated. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410932 [Multi-domain]  Cd Length: 164  Bit Score: 38.68  E-value: 2.06e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 246 VGQDTLLRSLLETNEIPS---------------LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATNAKTNDVRDVIK 310
Cdd:cd19524    3 AGQDLAKQALQEMVILPSlrpelftglrapargLLLFGPPGNGKTMLAKAVAAESN---ATFFNISAASLTSKYVGEGEK 79

                         90       100
                 ....*....|....*....|....*
gi 530382255 311 QAqneKSFFK-----RKTILFIDEI 330
Cdd:cd19524   80 LV---RALFAvarelQPSIIFIDEV 101
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 264-283 2.22e-03

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.


Pssm-ID: 459992  Cd Length: 102  Bit Score: 37.20  E-value: 2.22e-03
                          10        20
                  ....*....|....*....|
gi 530382255  264 LILWGPPGCGKTTLAHIIAS 283
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLAR 20
AAA_22 pfam13401
AAA domain;
263-333 2.73e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 37.71  E-value: 2.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  263 SLILWGPPGCGKTTLAHIIASNSKKHSIR--FVTLSATNAKTNDVRDVIKQAQNEKSFFKRKTILF-------------- 326
Cdd:pfam13401   7 ILVLTGESGTGKTTLLRRLLEQLPEVRDSvvFVDLPSGTSPKDLLRALLRALGLPLSGRLSKEELLaalqqlllalavav 86

                          90
                  ....*....|
gi 530382255  327 ---IDEIHRF 333
Cdd:pfam13401  87 vliIDEAQHL 96
PRK08451 PRK08451
DNA polymerase III subunits gamma and tau; Validated
 227-335 2.75e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236267 [Multi-domain]  Cd Length: 535  Bit Score: 40.02  E-value: 2.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 227 LADTMRPDTLqdyfgqSKAVGQDTLLRSL---LETNEIPSLILW-GPPGCGKTTLAHI---------------------- 280
Cdd:PRK08451   4 LALKYRPKHF------DELIGQESVSKTLslaLDNNRLAHAYLFsGLRGSGKTSSARIfaralvceqgpsstpcdtciqc 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 530382255 281 IASNSKKHsIRFVTL-SATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNK 335
Cdd:PRK08451  78 QSALENRH-IDIIEMdAASNRGIDDIRELIEQTKYKPSMARFK-IFIIDEVHMLTK 131
Bac_DnaA pfam00308
Bacterial dnaA protein;
264-338 3.50e-03

Bacterial dnaA protein;


Pssm-ID: 278724 [Multi-domain]  Cd Length: 219  Bit Score: 38.85  E-value: 3.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255  264 LILWGPPGCGKTTLAHIIASN--SKKHSIRFVTLSATNAkTNDVRDVIKqaQNEKSFFKRK----TILFIDEIHRFNKSQ 337
Cdd:pfam00308  37 LFIYGGVGLGKTHLLHAIGNYalQNAPNLRVVYLTAEEF-LNDFVDAIR--DNKTNQFKEKyrnvDVLLIDDIQFLAGKE 113


                  .
gi 530382255  338 Q 338
Cdd:pfam00308 114 G 114
PRK08903 PRK08903
DnaA regulatory inactivator Hda; Validated
 233-338 7.34e-03

DnaA regulatory inactivator Hda; Validated


Pssm-ID: 236347 [Multi-domain]  Cd Length: 227  Bit Score: 37.65  E-value: 7.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530382255 233 PDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSAtnaktndvrdviKQA 312
Cdd:PRK08903  14 PPTFDNFVAGENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDA------------ASP 81

                         90       100
                 ....*....|....*....|....*.
gi 530382255 313 QNEKSFFKRKTILFIDEIHRFNKSQQ 338
Cdd:PRK08903  82 LLAFDFDPEAELYAVDDVERLDDAQQ 107
PRK04182 PRK04182
cytidylate kinase; Provisional
 268-293 7.70e-03

cytidylate kinase; Provisional


Pssm-ID: 235244 [Multi-domain]  Cd Length: 180  Bit Score: 37.09  E-value: 7.70e-03
                         10        20
                 ....*....|....*....|....*.
gi 530382255 268 GPPGCGKTTLAHIIAsnsKKHSIRFV 293
Cdd:PRK04182   7 GPPGSGKTTVARLLA---EKLGLKHV 29
ABC_Carb_Solutes_like cd03259
ATP-binding cassette domain of the carbohydrate and solute transporters-like; This family is ...
 243-282 8.43e-03

ATP-binding cassette domain of the carbohydrate and solute transporters-like; This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213226 [Multi-domain]  Cd Length: 213  Bit Score: 37.50  E-value: 8.43e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 530382255 243 SKAVGQDTLLRSL---LETNEIPSLIlwGPPGCGKTTLAHIIA 282
Cdd:cd03259    7 SKTYGSVRALDDLsltVEPGEFLALL--GPSGCGKTTLLRLIA 47
 
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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