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Conserved domains on  [gi|18426902|ref|NP_064520|]
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ATPase WRNIP1 isoform 1 [Homo sapiens]

Protein Classification

replication-associated recombination protein A( domain architecture ID 12219000)

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 COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 225-661 0e+00

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


:

Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 612.83  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 225 KPLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTND 304
Cdd:COG2256  13 APLAERMRPRTLDEVVGQEHLLGPGKPLRRAIEAGRLSSMILWGPPGTGKTTLARLIANATDAE---FVALSAVTSGVKD 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 305 VRDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKLPVEA 384
Cdd:COG2256  90 IREVIEEARERRAY-GRRTILFVDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNSALLSRCRVFVLKPLSEED 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 385 MVTILMRAINSLGIHVLDSSRPtdplshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLAVLARLSSrkmfckk 464
Cdd:COG2256 169 LEQLLERALADDERGLGGYKLE-----------------LDDEALEALARLADGDARRALNALELAVLSAPPD------- 224

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 465 sgqsyspSRVLITENDVKEGLQRSHILYDRAGEEHYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYVARRLVRFAS 544
Cdd:COG2256 225 -------GVIEITLELVEEALQRRALRYDKDGDEHYDLISAFIKSIRGSDPDAALYWLARMLEAGEDPRFIARRLVIMAS 297

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 545 EDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYSAYNNVKACLRnhQGPLPPVPLHLRNAPTR 624
Cdd:COG2256 298 EDIGLADPQALQIAVAAAQAVERLGMPEGRIALAQAVIYLATAPKSNAAYLAINAALADVR--EGGSLPVPLHLRNAPTK 375

                       410       420       430       440
                ....*....|....*....|....*....|....*....|
gi 18426902 625 LMKDLGYGKGYKYnpMYSEP---VDQEYLPEELRGVDFFK 661
Cdd:COG2256 376 LMKELGYGKGYKY--PHDYPggyVGQQYLPDELKGRRYYE 413
ZnF_Rad18 smart00734
Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative ...
 17-40 3.77e-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: 52.22  E-value: 3.77e-09
                           10        20
                   ....*....|....*....|....
gi 18426902     17 QVQCPVCQQMMPAAHINSHLDRCL 40
Cdd:smart00734   1 LVQCPVCFREVPENLINSHLDSCL 24
RAD18 super family cl35000
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
18-83 7.48e-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: 42.38  E-value: 7.48e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18426902  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, ...
 225-661 0e+00

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 612.83  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 225 KPLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTND 304
Cdd:COG2256  13 APLAERMRPRTLDEVVGQEHLLGPGKPLRRAIEAGRLSSMILWGPPGTGKTTLARLIANATDAE---FVALSAVTSGVKD 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 305 VRDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKLPVEA 384
Cdd:COG2256  90 IREVIEEARERRAY-GRRTILFVDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNSALLSRCRVFVLKPLSEED 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 385 MVTILMRAINSLGIHVLDSSRPtdplshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLAVLARLSSrkmfckk 464
Cdd:COG2256 169 LEQLLERALADDERGLGGYKLE-----------------LDDEALEALARLADGDARRALNALELAVLSAPPD------- 224

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 465 sgqsyspSRVLITENDVKEGLQRSHILYDRAGEEHYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYVARRLVRFAS 544
Cdd:COG2256 225 -------GVIEITLELVEEALQRRALRYDKDGDEHYDLISAFIKSIRGSDPDAALYWLARMLEAGEDPRFIARRLVIMAS 297

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 545 EDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYSAYNNVKACLRnhQGPLPPVPLHLRNAPTR 624
Cdd:COG2256 298 EDIGLADPQALQIAVAAAQAVERLGMPEGRIALAQAVIYLATAPKSNAAYLAINAALADVR--EGGSLPVPLHLRNAPTK 375

                       410       420       430       440
                ....*....|....*....|....*....|....*....|
gi 18426902 625 LMKDLGYGKGYKYnpMYSEP---VDQEYLPEELRGVDFFK 661
Cdd:COG2256 376 LMKELGYGKGYKY--PHDYPggyVGQQYLPDELKGRRYYE 413
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 226-661 0e+00

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 604.77  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  226 PLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTNDV 305
Cdd:PRK13342   1 PLAERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAP---FEALSAVTSGVKDL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  306 RDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKLPVEAM 385
Cdd:PRK13342  78 REVIEEARQRRSA-GRRTILFIDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDI 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  386 VTILMRAINslgihvlDSSRPTDPlshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLAVLarlssrkmfckks 465
Cdd:PRK13342 157 EQLLKRALE-------DKERGLVE--------------LDDEALDALARLANGDARRALNLLELAAL------------- 202

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  466 gqsyspSRVLITENDVKEGLQRSHILYDRAGEEHYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYVARRLVRFASE 545
Cdd:PRK13342 203 ------GVDSITLELLEEALQKRAARYDKDGDEHYDLISALHKSIRGSDPDAALYYLARMLEAGEDPLFIARRLVIIASE 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  546 DIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYSAYNNVKACLRNhqGPLPPVPLHLRNAPTRL 625
Cdd:PRK13342 277 DIGLADPNALQVAVAAADAVERIGMPEGRIALAQAVIYLALAPKSNAAYTAINAALADVRE--GGSLPVPLHLRNAPTKL 354

                        410       420       430
                 ....*....|....*....|....*....|....*....
gi 18426902  626 MKDLGYGKGYKYnpMYSEP---VDQEYLPEELRGVDFFK 661
Cdd:PRK13342 355 MKELGYGKGYKY--PHDYPngyVGQQYLPDELKGKRYYE 391
MgsA_C pfam12002
MgsA AAA+ ATPase C terminal; The MgsA protein possesses DNA-dependent ATPase and ssDNA ...
 512-661 2.81e-81

MgsA AAA+ ATPase C terminal; The MgsA protein possesses DNA-dependent ATPase and ssDNA annealing activities. MgsA contributes to the recovery of stalled replication forks and therefore prevents genomic instability caused by aberrant DNA replication. Additionally, MgsA may play a role in chromosomal segregation. This is consistent with a report that MgsA co-localizes with the replisome and affects chromosome segregation. This domain represents the C terminal region of MgsA.


Pssm-ID: 463426 [Multi-domain]  Cd Length: 158  Bit Score: 253.81  E-value: 2.81e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   512 GSDQNASLYWLARMLEGGEDPLYVARRLVRFASEDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSI 591
Cdd:pfam12002   1 GSDPDAALYWLARMLEAGEDPLFIARRLVIIASEDIGLADPQALVVAVAAAQAVERIGMPEARIPLAQAVIYLALAPKSN 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18426902   592 EVYSAYNNVKACLRNhqGPLPPVPLHLRNAPTRLMKDLGYGKGYKYNPMYSE-PVDQEYLPEELRGVDFFK 661
Cdd:pfam12002  81 SAYLAIDAALADVRE--GGSLPVPLHLRNAPTKLMKKLGYGKGYKYPHDYPNgYVKQQYLPDELKGRRYYE 149
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 246-376 4.08e-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: 4.08e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 246 VGQD---TLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFFKRK 322
Cdd:cd00009   1 VGQEeaiEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELA 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18426902 323 -----TILFIDEIHRFNKSQQDTFLP--------HVECGTITLIGATTENPSFQVNAALLSRCRVIV 376
Cdd:cd00009  81 ekakpGVLFIDEIDSLSRGAQNALLRvletlndlRIDRENVRVIGATNRPLLGDLDRALYDRLDIRI 147
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 235-398 3.49e-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: 67.71  E-value: 3.49e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   235 TLQDYFGQSKAVGQ-DTLLRSLLETNEIPS-LILWGPPGCGKTTLAHIIASNSKKhSIRfVTLSATNAKTNDVRDVIkqa 312
Cdd:TIGR00635   2 LLAEFIGQEKVKEQlQLFIEAAKMRQEALDhLLLYGPPGLGKTTLAHIIANEMGV-NLK-ITSGPALEKPGDLAAIL--- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   313 qnekSFFKRKTILFIDEIHRFNKSQQDTFLPHVE-------------CGTI-------TLIGATTEnpSFQVNAALLSRC 372
Cdd:TIGR00635  77 ----TNLEEGDVLFIDEIHRLSPAVEELLYPAMEdfrldivigkgpsARSVrldlppfTLVGATTR--AGMLTSPLRDRF 150

                         170       180
                  ....*....|....*....|....*..
gi 18426902   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 4.75e-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: 64.32  E-value: 4.75e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902    263 SLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFF----------------KRKTILF 326
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASgsgelrlrlalalarkLKPDVLI 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18426902    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 3.77e-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: 52.22  E-value: 3.77e-09
                           10        20
                   ....*....|....*....|....
gi 18426902     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 5.07e-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: 5.07e-09
                          10        20
                  ....*....|....*....|.
gi 18426902    16 HQVQCPVCQQMMPAAHINSHL 36
Cdd:pfam18279   1 HQVQCPVCQQMMPAAHINSHL 21
cell_div_CdvC NF041006
cell division protein CdvC;
264-330 3.66e-04

cell division protein CdvC;


Pssm-ID: 468935 [Multi-domain]  Cd Length: 371  Bit Score: 43.18  E-value: 3.66e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18426902  264 LILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATN--------AKTNdVRDVIKQAQNEKSFFKRKTILFIDEI 330
Cdd:NF041006 137 ILLYGPPGCGKTMLAAAVANEIDSE---FIHVDAASimskwlgeAEKN-VAKIFKKAREKSKEEGKPAIIFIDEI 207
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
18-83 7.48e-04

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


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 42.38  E-value: 7.48e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18426902  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, ...
 225-661 0e+00

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 612.83  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 225 KPLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTND 304
Cdd:COG2256  13 APLAERMRPRTLDEVVGQEHLLGPGKPLRRAIEAGRLSSMILWGPPGTGKTTLARLIANATDAE---FVALSAVTSGVKD 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 305 VRDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKLPVEA 384
Cdd:COG2256  90 IREVIEEARERRAY-GRRTILFVDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNSALLSRCRVFVLKPLSEED 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 385 MVTILMRAINSLGIHVLDSSRPtdplshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLAVLARLSSrkmfckk 464
Cdd:COG2256 169 LEQLLERALADDERGLGGYKLE-----------------LDDEALEALARLADGDARRALNALELAVLSAPPD------- 224

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 465 sgqsyspSRVLITENDVKEGLQRSHILYDRAGEEHYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYVARRLVRFAS 544
Cdd:COG2256 225 -------GVIEITLELVEEALQRRALRYDKDGDEHYDLISAFIKSIRGSDPDAALYWLARMLEAGEDPRFIARRLVIMAS 297

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 545 EDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYSAYNNVKACLRnhQGPLPPVPLHLRNAPTR 624
Cdd:COG2256 298 EDIGLADPQALQIAVAAAQAVERLGMPEGRIALAQAVIYLATAPKSNAAYLAINAALADVR--EGGSLPVPLHLRNAPTK 375

                       410       420       430       440
                ....*....|....*....|....*....|....*....|
gi 18426902 625 LMKDLGYGKGYKYnpMYSEP---VDQEYLPEELRGVDFFK 661
Cdd:COG2256 376 LMKELGYGKGYKY--PHDYPggyVGQQYLPDELKGRRYYE 413
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 226-661 0e+00

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 604.77  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  226 PLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTNDV 305
Cdd:PRK13342   1 PLAERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAP---FEALSAVTSGVKDL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  306 RDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKLPVEAM 385
Cdd:PRK13342  78 REVIEEARQRRSA-GRRTILFIDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDI 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  386 VTILMRAINslgihvlDSSRPTDPlshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLAVLarlssrkmfckks 465
Cdd:PRK13342 157 EQLLKRALE-------DKERGLVE--------------LDDEALDALARLANGDARRALNLLELAAL------------- 202

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  466 gqsyspSRVLITENDVKEGLQRSHILYDRAGEEHYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYVARRLVRFASE 545
Cdd:PRK13342 203 ------GVDSITLELLEEALQKRAARYDKDGDEHYDLISALHKSIRGSDPDAALYYLARMLEAGEDPLFIARRLVIIASE 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  546 DIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYSAYNNVKACLRNhqGPLPPVPLHLRNAPTRL 625
Cdd:PRK13342 277 DIGLADPNALQVAVAAADAVERIGMPEGRIALAQAVIYLALAPKSNAAYTAINAALADVRE--GGSLPVPLHLRNAPTKL 354

                        410       420       430
                 ....*....|....*....|....*....|....*....
gi 18426902  626 MKDLGYGKGYKYnpMYSEP---VDQEYLPEELRGVDFFK 661
Cdd:PRK13342 355 MKELGYGKGYKY--PHDYPngyVGQQYLPDELKGKRYYE 391
PRK13341 PRK13341
AAA family ATPase;
220-660 4.23e-134

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 410.60  E-value: 4.23e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  220 QMLQG-KPLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSAT 298
Cdd:PRK13341  10 QMSQSeAPLADRLRPRTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHTRAH---FSSLNAV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  299 NAKTNDVRDVIKQAQNEKSFFKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLE 378
Cdd:PRK13341  87 LAGVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWVENGTITLIGATTENPYFEVNKALVSRSRLFRLK 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  379 KLPVEAMVTILMRAINslgihvlDSSRPTDPLshssnsssepAMFIEDKAVDTLAYLSDGDARAGLNGLQLAVlarlssr 458
Cdd:PRK13341 167 SLSDEDLHQLLKRALQ-------DKERGYGDR----------KVDLEPEAEKHLVDVANGDARSLLNALELAV------- 222

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  459 kmfckksgQSYSP---SRVLITENDVKEGLQRSHILYDRAGEEHYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYV 535
Cdd:PRK13341 223 --------ESTPPdedGLIDITLAIAEESIQQRAVLYDKEGDAHFDTISAFIKSLRGSDPDAALYWLARMVEAGEDPRFI 294

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  536 ARRLVRFASEDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYSAYNNVKAClrnHQGPLPPVP 615
Cdd:PRK13341 295 FRRMLIAASEDVGLADPQALVVVEACAAAFERVGLPEGLYPLAQAALYLATAPKSNSVLGFFDALKKV---REEQVQDVP 371

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....*.
gi 18426902  616 LHLRNaPTRLMKDLGYGKGYKYNPMYSEP-VDQEYLPEELRGVDFF 660
Cdd:PRK13341 372 NHLRD-ANRDGKAFGDGVGYRYPHAFRDHwVAQQYLPEALQGEVFW 416
MgsA_C pfam12002
MgsA AAA+ ATPase C terminal; The MgsA protein possesses DNA-dependent ATPase and ssDNA ...
 512-661 2.81e-81

MgsA AAA+ ATPase C terminal; The MgsA protein possesses DNA-dependent ATPase and ssDNA annealing activities. MgsA contributes to the recovery of stalled replication forks and therefore prevents genomic instability caused by aberrant DNA replication. Additionally, MgsA may play a role in chromosomal segregation. This is consistent with a report that MgsA co-localizes with the replisome and affects chromosome segregation. This domain represents the C terminal region of MgsA.


Pssm-ID: 463426 [Multi-domain]  Cd Length: 158  Bit Score: 253.81  E-value: 2.81e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   512 GSDQNASLYWLARMLEGGEDPLYVARRLVRFASEDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSI 591
Cdd:pfam12002   1 GSDPDAALYWLARMLEAGEDPLFIARRLVIIASEDIGLADPQALVVAVAAAQAVERIGMPEARIPLAQAVIYLALAPKSN 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18426902   592 EVYSAYNNVKACLRNhqGPLPPVPLHLRNAPTRLMKDLGYGKGYKYNPMYSE-PVDQEYLPEELRGVDFFK 661
Cdd:pfam12002  81 SAYLAIDAALADVRE--GGSLPVPLHLRNAPTKLMKKLGYGKGYKYPHDYPNgYVKQQYLPDELKGRRYYE 149
PRK14700 PRK14700
recombination factor protein RarA; Provisional
 342-655 1.96e-45

recombination factor protein RarA; Provisional


Pssm-ID: 173163 [Multi-domain]  Cd Length: 300  Bit Score: 163.65  E-value: 1.96e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  342 LPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKLPVEAMVTILMRAINS---LGIHVLDssrptdplshssnsss 418
Cdd:PRK14700   1 MPYVESGKIILIGATTENPTYYLNDALVSRLFILRLKRLSLVATQKLIEKALSQdevLAKHKFK---------------- 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  419 epamfIEDKAVDTLAYLSDGDARAGLNGLQLAVLARLSSRKMFCKKSgqsyspsrvlITENDVKEGLQRSHilydRAGEE 498
Cdd:PRK14700  65 -----IDDGLYNAMHNYNEGDCRKILNLLERMFLISTRGDEIYLNKE----------LFDQAVGETSRDFH----REGKE 125

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  499 HYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYVARRLVRFASEDIGLADPSALTQAVAAYQGCHFIGMPECEVLLA 578
Cdd:PRK14700 126 FYEQLSAFHKSVRGTDPDAAIFWLSVMLDNGVDPLVIARRMLCIASEDIGNADPQALRVAMDAWNAYEKLGMPEGRLVLA 205

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18426902  579 QCVVYFARAPKSIEVYSAYNNVKACLRNhQGPLpPVPLHLRNaptrlMKDLGYGKGYKYNPMYsepVDQEYLPEELR 655
Cdd:PRK14700 206 QAAIYLAVAPKSNACYKALAQAQQLVKS-LGNI-DVPQHLKN-----YKDSNYLYPHNYPNSY---VIQQYLPDNII 272
AAA_assoc_2 pfam16193
AAA C-terminal domain; AAA_assoc_2 is found at the C-terminus of a relatively small set of AAA ...
 424-511 1.70e-29

AAA C-terminal domain; AAA_assoc_2 is found at the C-terminus of a relatively small set of AAA domains in proteins ranging from archaeal to fungi, plants and mammals.


Pssm-ID: 465057  Cd Length: 81  Bit Score: 111.41  E-value: 1.70e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   424 IEDKAVDTLAYLSDGDARAGLNGLQLAVLARLSSRKmfckksgqsyspsRVLITENDVKEGLQRSHILYDRAGEEHYNCI 503
Cdd:pfam16193   7 LDDEALEALAELADGDARRALNALELAVLSTPPDDG-------------GIHITLEILEEALQRKALRYDKDGDEHYDLI 73


                  ....*...
gi 18426902   504 SALHKSMR 511
Cdd:pfam16193  74 SAFHKSIR 81
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 246-376 4.08e-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: 4.08e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 246 VGQD---TLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFFKRK 322
Cdd:cd00009   1 VGQEeaiEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELA 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18426902 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 3.06e-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: 84.18  E-value: 3.06e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   264 LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATN-------AKTNDVRDVIKQAQNeksffKRKTILFIDEIHRFNKS 336
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELG---APFIEISGSElvskyvgESEKRLRELFEAAKK-----LAPCVIFIDEIDALAGS 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 18426902   337 Q-----------QDTFLPHVE-----CGTITLIGATTEnpSFQVNAALLSRCRVIVL 377
Cdd:pfam00004  73 RgsggdsesrrvVNQLLTELDgftssNSKVIVIAATNR--PDKLDPALLGRFDRIIE 127
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
230-398 9.41e-16

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 79.02  E-value: 9.41e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  230 TMRPDTLQDYFGQSKAVGQ-DTLLRSLLETNEIPS-LILWGPPGCGKTTLAHIIAsNSKKHSIRFVT---------LSA- 297
Cdd:PRK00080  18 SLRPKSLDEFIGQEKVKENlKIFIEAAKKRGEALDhVLLYGPPGLGKTTLANIIA-NEMGVNIRITSgpalekpgdLAAi 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  298 -TNAKTNDVrdvikqaqneksffkrktiLFIDEIHRFNKSQQDTFLPHVECGTI--------------------TLIGAT 356
Cdd:PRK00080  97 lTNLEEGDV-------------------LFIDEIHRLSPVVEEILYPAMEDFRLdimigkgpaarsirldlppfTLIGAT 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 18426902  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 2.53e-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: 77.81  E-value: 2.53e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 230 TMRPDTLQDYFGQSKAVGQ-DTLLRSLLETNE-IPSLILWGPPGCGKTTLAHIIAsNSKKHSIRfVT----------LSA 297
Cdd:COG2255  21 SLRPKRLDEYIGQEKVKENlKIFIEAAKKRGEaLDHVLLYGPPGLGKTTLAHIIA-NEMGVNIR-ITsgpaiekpgdLAA 98

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 298 --TNAKTNDVrdvikqaqneksffkrktiLFIDEIHRFNKSQQDTFLPHVECGTI--------------------TLIGA 355
Cdd:COG2255  99 ilTNLEEGDV-------------------LFIDEIHRLSRVVEEILYPAMEDFRLdivigkgpaarsirldlppfTLVGA 159

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*....
gi 18426902 356 TTenpsfqvNAALLS---RCRVIVLEKL---PVEAMVTILMRAINSLGI 398
Cdd:COG2255 160 TT-------RAGLLTsplRDRFGIVLRLefyTVEELAEIVKRSARILGV 201
PRK04195 PRK04195
replication factor C large subunit; Provisional
 226-487 2.35e-14

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 76.11  E-value: 2.35e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  226 PLADTMRPDTLQDYFGQSKAVGQdtlLRSLLET--NEIPS--LILWGPPGCGKTTLAHIIAsnskkHSIRF--VTLSATN 299
Cdd:PRK04195   3 PWVEKYRPKTLSDVVGNEKAKEQ---LREWIESwlKGKPKkaLLLYGPPGVGKTSLAHALA-----NDYGWevIELNASD 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  300 AKTNDV-RDVIKQAQNEKSFF-KRKTILFIDE---IHrfnkSQQDTflphvecG---TITLIGATTENPSfqVNAA---- 367
Cdd:PRK04195  75 QRTADViERVAGEAATSGSLFgARRKLILLDEvdgIH----GNEDR-------GgarAILELIKKAKQPI--ILTAndpy 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  368 ------LLSRCRVIVLEKLPVEAMVTILMRAINSLGIhvldssrptdplshssnsssepamFIEDKAVDTLAYLSDGDAR 441
Cdd:PRK04195 142 dpslreLRNACLMIEFKRLSTRSIVPVLKRICRKEGI------------------------ECDDEALKEIAERSGGDLR 197

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 18426902  442 AGLNGLQLAVLARLSsrkmfckksgqsyspsrvlITENDVKEGLQR 487
Cdd:PRK04195 198 SAINDLQAIAEGYGK-------------------LTLEDVKTLGRR 224
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 231-357 3.69e-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: 70.61  E-value: 3.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   231 MRPDTLQDYFGQSKAVGQ-DTLLRSLLETNEIPS-LILWGPPGCGKTTLAHIIAsNSKKHSIRfVT----------LSA- 297
Cdd:pfam05496   1 LRPRTLDEYIGQEKVKENlKIFIEAAKQRGEALDhVLLYGPPGLGKTTLANIIA-NEMGVNIR-ITsgpaierpgdLAAi 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   298 -TNAKTNDVrdvikqaqneksffkrktiLFIDEIHRFNKSQQDTFLPHVECGTI--------------------TLIGAT 356
Cdd:pfam05496  79 lTNLEPGDV-------------------LFIDEIHRLNRAVEEILYPAMEDFRLdivigkgpsarsirldlppfTLVGAT 139


                  .
gi 18426902   357 T 357
Cdd:pfam05496 140 T 140
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
233-444 5.24e-13

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 70.61  E-value: 5.24e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 233 PDTLQDYFGQSKAVgqdTLLRSLLETNEIP-SLILWGPPGCGKTTLAHIIA-----------------SNSKKHS----- 289
Cdd:COG2812   6 PQTFDDVVGQEHVV---RTLKNALASGRLAhAYLFTGPRGVGKTTLARILAkalncengptgepcgecESCRAIAagshp 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 290 -IRFVTLSATNAKTNDVRDVIKQAQNeKSFFKRKTILFIDEIHRFNKSQQDTFL-------PHVecgtiTLIGATTEnPS 361
Cdd:COG2812  83 dVIEIDAEASNIGVDDIRELIEKVSY-APVEGRYKVYIIDEAHMLTTEAFNALLktleeppPHV-----VFILATTE-PQ 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 362 fQVNAALLSRCRVIVLEKLPVEAMVTILMRAINSLGIHvldssrptdplshssnsssepamfIEDKAVDTLAYLSDGDAR 441
Cdd:COG2812 156 -KLLPTILSRCQRFDFRRLPPEEIAEHLAKIAEREGIE------------------------IEPEALALIARAADGSMR 210


                ...
gi 18426902 442 AGL 444
Cdd:COG2812 211 DAL 213
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 235-398 3.49e-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: 67.71  E-value: 3.49e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   235 TLQDYFGQSKAVGQ-DTLLRSLLETNEIPS-LILWGPPGCGKTTLAHIIASNSKKhSIRfVTLSATNAKTNDVRDVIkqa 312
Cdd:TIGR00635   2 LLAEFIGQEKVKEQlQLFIEAAKMRQEALDhLLLYGPPGLGKTTLAHIIANEMGV-NLK-ITSGPALEKPGDLAAIL--- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   313 qnekSFFKRKTILFIDEIHRFNKSQQDTFLPHVE-------------CGTI-------TLIGATTEnpSFQVNAALLSRC 372
Cdd:TIGR00635  77 ----TNLEEGDVLFIDEIHRLSPAVEELLYPAMEdfrldivigkgpsARSVrldlppfTLVGATTR--AGMLTSPLRDRF 150

                         170       180
                  ....*....|....*....|....*..
gi 18426902   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 4.75e-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: 64.32  E-value: 4.75e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902    263 SLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFF----------------KRKTILF 326
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASgsgelrlrlalalarkLKPDVLI 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18426902    327 IDEIHRFNKSQQD----------TFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEKL 380
Cdd:smart00382  84 LDEITSLLDAEQEallllleelrLLLLLKSEKNLTVILTTNDEKDLGPALLRRRFDRRIVLLLI 147
PRK05896 PRK05896
DNA polymerase III subunits gamma and tau; Validated
 232-448 1.12e-10

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235638 [Multi-domain]  Cd Length: 605  Bit Score: 64.48  E-value: 1.12e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  232 RPDTLQDYFGQSKAvgQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIAS-----NSKK----------------HSI 290
Cdd:PRK05896  11 RPHNFKQIIGQELI--KKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKainclNPKDgdccnscsvcesintnQSV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  291 RFVTL-SATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNKSQQDTFLPHVE--CGTITLIGATTEnpSFQVNAA 367
Cdd:PRK05896  89 DIVELdAASNNGVDEIRNIIDNINYLPTTFKYK-VYIIDEAHMLSTSAWNALLKTLEepPKHVVFIFATTE--FQKIPLT 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  368 LLSRCRVIVLEKLPveamvtilmraiNSLGIHVLDSSRPTDPLShssnsssepamfIEDKAVDTLAYLSDGDARAGLNGL 447
Cdd:PRK05896 166 IISRCQRYNFKKLN------------NSELQELLKSIAKKEKIK------------IEDNAIDKIADLADGSLRDGLSIL 221


                 .
gi 18426902  448 Q 448
Cdd:PRK05896 222 D 222
PLN03025 PLN03025
replication factor C subunit; Provisional
 226-448 1.62e-10

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 62.82  E-value: 1.62e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  226 PLADTMRPDTLQDYFGQSKAVGQdtlLRSLLETNEIPSLILWGPPGCGKTT----LAHIIASNSKKHSIrfVTLSATNAK 301
Cdd:PLN03025   2 PWVEKYRPTKLDDIVGNEDAVSR---LQVIARDGNMPNLILSGPPGTGKTTsilaLAHELLGPNYKEAV--LELNASDDR 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  302 TND-VRDVIKQ-AQNEKSFFK-RKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLE 378
Cdd:PLN03025  77 GIDvVRNKIKMfAQKKVTLPPgRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFS 156

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  379 KLPVEAMVTILMRAINSLGIhvldssrPTDPlshssnsssepamfiedKAVDTLAYLSDGDARAGLNGLQ 448
Cdd:PLN03025 157 RLSDQEILGRLMKVVEAEKV-------PYVP-----------------EGLEAIIFTADGDMRQALNNLQ 202
PRK08691 PRK08691
DNA polymerase III subunits gamma and tau; Validated
 227-399 1.76e-10

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236333 [Multi-domain]  Cd Length: 709  Bit Score: 63.96  E-value: 1.76e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  227 LADTMRPDTLQDYFGQSKAVgqDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIA------------------SNSKKH 288
Cdd:PRK08691   6 LARKWRPKTFADLVGQEHVV--KALQNALDEGRLHHAYLLTGTRGVGKTTIARILAkslncenaqhgepcgvcqSCTQID 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  289 SIRFVTL----SATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNKSQQDTFLPHVE--CGTITLIGATTEnPSf 362
Cdd:PRK08691  84 AGRYVDLleidAASNTGIDNIREVLENAQYAPTAGKYK-VYIIDEVHMLSKSAFNAMLKTLEepPEHVKFILATTD-PH- 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 18426902  363 QVNAALLSRCRVIVLEKLPVEAMVTILMRAINSLGIH 399
Cdd:PRK08691 161 KVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIA 197
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 264-389 2.57e-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: 2.57e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 264 LILWGPPGCGKTTLAHIIASNSKKHSIRfVTLSA--------TNAKtndVRDVIKQAQNEKsffkrKTILFIDEI----- 330
Cdd:COG0464 194 LLLYGPPGTGKTLLARALAGELGLPLIE-VDLSDlvskyvgeTEKN---LREVFDKARGLA-----PCVLFIDEAdalag 264

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18426902 331 ------HRFNKSQQDTFLPHVECGT--ITLIGATteNPSFQVNAALLSRCRVIVLEKLP-VEAMVTIL 389
Cdd:COG0464 265 krgevgDGVGRRVVNTLLTEMEELRsdVVVIAAT--NRPDLLDPALLRRFDEIIFFPLPdAEERLEIF 330
44 PHA02544
clamp loader, small subunit; Provisional
 250-375 3.05e-10

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 61.93  E-value: 3.05e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  250 TLLRSLLETNEIPSLILWGP-PGCGKTTLAHIIASNSkkhSIRFVTLSATNAKTNDVRDVIKQAQNEKSFFKRKTILFID 328
Cdd:PHA02544  31 ETFKSIVKKGRIPNMLLHSPsPGTGKTTVAKALCNEV---GAEVLFVNGSDCRIDFVRNRLTRFASTVSLTGGGKVIIID 107

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 18426902  329 EIHRfnksqqdTFLPHVECGTITLIGATTENPSF--------QVNAALLSRCRVI 375
Cdd:PHA02544 108 EFDR-------LGLADAQRHLRSFMEAYSKNCSFiitannknGIIEPLRSRCRVI 155
rfc PRK00440
replication factor C small subunit; Reviewed
 232-450 5.23e-10

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 61.43  E-value: 5.23e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  232 RPDTLQDYFGQSKAVGQdtlLRSLLETNEIPSLILWGPPGCGKTTLAHIIAsnskkHSI-------RFVTLSATNAKTND 304
Cdd:PRK00440  12 RPRTLDEIVGQEEIVER---LKSYVKEKNMPHLLFAGPPGTGKTTAALALA-----RELygedwreNFLELNASDERGID 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  305 V-RDVIKQAQNEKSF----FKrktILFIDEIHRFNKSQQdtflpHVECGTITLIGATTE-----NPSFQVNAALLSRCRV 374
Cdd:PRK00440  84 ViRNKIKEFARTAPVggapFK---IIFLDEADNLTSDAQ-----QALRRTMEMYSQNTRfilscNYSSKIIDPIQSRCAV 155

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18426902  375 IVLEKLPVEAMVTILMRAINSLGIHvldssrptdplshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLA 450
Cdd:PRK00440 156 FRFSPLKKEAVAERLRYIAENEGIE------------------------ITDDALEAIYYVSEGDMRKAINALQAA 207
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
242-454 1.76e-09

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 59.22  E-value: 1.76e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 242 QSKAVGQdtlLRSLLETNEIP-SLILWGPPGCGKTTLAHIIA------------SNSKKHSIR--------FVTLSATNA 300
Cdd:COG0470   1 QEEAWEQ---LLAAAESGRLPhALLLHGPPGIGKTTLALALArdllcenpeggkACGQCHSRLmaagnhpdLLELNPEEK 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 301 KT----NDVRDVIKQAQNeKSFFKRKTILFIDEIHRFNKSQQDTFL-----PHVECgTITLIgatTENPSfQVNAALLSR 371
Cdd:COG0470  78 SDqigiDQIRELGEFLSL-TPLEGGRKVVIIDEADAMNEAAANALLktleePPKNT-PFILI---ANDPS-RLLPTIRSR 151

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 372 CRVIVLEKLPVEAMVTILMRAinslgihvldssrptdplshssnsssepamFIEDKAVDTLAYLSDGDARAGLNGLQLAV 451
Cdd:COG0470 152 CQVIRFRPPSEEEALAWLREE------------------------------GVDEDALEAILRLAGGDPRAAINLLQALA 201


                ...
gi 18426902 452 LAR 454
Cdd:COG0470 202 GRK 204
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 228-383 1.86e-09

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 59.89  E-value: 1.86e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  228 ADTMRPDTLQDYFGQSKAVgqDTLLRSLlETNEIPSLILW-GPPGCGKTTLAHIIASNSKKHSIR----------FVTLS 296
Cdd:PRK14970   8 ARKYRPQTFDDVVGQSHIT--NTLLNAI-ENNHLAQALLFcGPRGVGKTTCARILARKINQPGYDdpnedfsfniFELDA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  297 ATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNKSQQDTFLPHVE--CGTITLIGATTENpsFQVNAALLSRCRV 374
Cdd:PRK14970  85 ASNNSVDDIRNLIDQVRIPPQTGKYK-IYIIDEVHMLSSAAFNAFLKTLEepPAHAIFILATTEK--HKIIPTILSRCQI 161


                 ....*....
gi 18426902  375 IVLEKLPVE 383
Cdd:PRK14970 162 FDFKRITIK 170
HLD_clamp_RarA cd18139
helical lid domain of recombination factor protein RarA; Recombination factor RarA ...
 380-486 2.58e-09

helical lid domain of recombination factor protein RarA; Recombination factor RarA (Replication associated recombination gene/protein A, also known as MgsA (Maintenance of genome stability A) or Mgs1 in yeast and WRNIP1 in mammals) is a member of the clamp-loader clade of the AAA+ superfamily. It functions as a tetramer. RarA co-localize with the replication fork throughout the cell cycle and may play a role in the rescue of stalled replication forks.


Pssm-ID: 350841 [Multi-domain]  Cd Length: 75  Bit Score: 54.17  E-value: 2.58e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 380 LPVEAMVTILMRAINSLGIHvldssrptdplshssnssSEPAMFIEDKAVDTLAYLSDGDARAGLNGLQLAVLArlssrk 459
Cdd:cd18139   1 LSEEDLEKLLKRALEDKERG------------------GDRKVTIDDEALELLAEAADGDARSALNLLELAVLS------ 56

                        90       100
                ....*....|....*....|....*..
gi 18426902 460 mfCKKSGqsyspsRVLITENDVKEGLQ 486
Cdd:cd18139  57 --AEEDG------GIVITLEDLEEVLQ 75
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 229-453 3.13e-09

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 59.23  E-value: 3.13e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  229 DTMRPDTLQDYFGQSKAVGQdtlLRSLLETNEIPSLILWGPPGCGKTT----LAHIIASNSKKHSI-------------- 290
Cdd:PRK12402   7 EKYRPALLEDILGQDEVVER---LSRAVDSPNLPHLLVQGPPGSGKTAavraLARELYGDPWENNFtefnvadffdqgkk 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  291 ------RFVTLSATNAKTN-DVRDVIKQAQNEKSFFKR-----KTILFiDEIHRFNKSQQDTFLPHVE--CGTITLIGAT 356
Cdd:PRK12402  84 ylvedpRFAHFLGTDKRIRsSKIDNFKHVLKEYASYRPlsadyKTILL-DNAEALREDAQQALRRIMEqySRTCRFIIAT 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  357 TeNPSfQVNAALLSRCRVIVLEKLPVEAMVTILmrainslgIHVLDSSRPTdplshssnsssepamfIEDKAVDTLAYLS 436
Cdd:PRK12402 163 R-QPS-KLIPPIRSRCLPLFFRAPTDDELVDVL--------ESIAEAEGVD----------------YDDDGLELIAYYA 216

                        250
                 ....*....|....*..
gi 18426902  437 DGDARAGLNGLQLAVLA 453
Cdd:PRK12402 217 GGDLRKAILTLQTAALA 233
ZnF_Rad18 smart00734
Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative ...
 17-40 3.77e-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: 52.22  E-value: 3.77e-09
                           10        20
                   ....*....|....*....|....
gi 18426902     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 5.07e-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: 5.07e-09
                          10        20
                  ....*....|....*....|.
gi 18426902    16 HQVQCPVCQQMMPAAHINSHL 36
Cdd:pfam18279   1 HQVQCPVCQQMMPAAHINSHL 21
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 232-330 3.53e-08

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 55.78  E-value: 3.53e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 232 RPDTLQDYFGqskavGQDTLLRSLLETNEIP----------------SLILWGPPGCGKTTLAHIIASNSKKHSIR---- 291
Cdd:COG1222  72 SPDVTFDDIG-----GLDEQIEEIREAVELPlknpelfrkygieppkGVLLYGPPGTGKTLLAKAVAGELGAPFIRvrgs 146

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 18426902 292 -----FVTLSATNaktndVRDVIKQAQNeksffKRKTILFIDEI 330
Cdd:COG1222 147 elvskYIGEGARN-----VREVFELARE-----KAPSIIFIDEI 180
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 262-374 1.86e-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: 51.13  E-value: 1.86e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 262 PSLILWGPPGCGKTTLAHIIASNSKKHSIRfVTLSATNAKTND-----VRDVIKQAQNeksffKRKTILFIDEIH----- 331
Cdd:cd19481  27 KGILLYGPPGTGKTLLAKALAGELGLPLIV-VKLSSLLSKYVGeseknLRKIFERARR-----LAPCILFIDEIDaigrk 100

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 18426902 332 RFNKSQQDTFLPHV-----------ECGTITLIGATteNPSFQVNAALLSRCRV 374
Cdd:cd19481 101 RDSSGESGELRRVLnqllteldgvnSRSKVLVIAAT--NRPDLLDPALLRPGRF 152
COG1373 COG1373
Predicted ATPase, AAA+ superfamily [General function prediction only];
249-335 2.61e-07

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


Pssm-ID: 440984 [Multi-domain]  Cd Length: 405  Bit Score: 53.41  E-value: 2.61e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 249 DTLLRSLLETNEIpsLILWGPPGCGKTTLA-HIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAqneKSFFKRKTILFI 327
Cdd:COG1373  10 LDKLLKLLDNRKA--VVITGPRQVGKTTLLkQLAKELENILYINLDDPRLRALAEEDPDDLLEAL---KELYPGKTYLFL 84


                ....*...
gi 18426902 328 DEIHRFNK 335
Cdd:COG1373  85 DEIQRVPE 92
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
232-386 7.33e-07

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 52.47  E-value: 7.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  232 RPDTLQDYFGQSKAVgqdTLLRSLLETNEIPSLILW-GPPGCGKTTLAHIIA----------------------SNSKKH 288
Cdd:PRK14971  12 RPSTFESVVGQEALT---TTLKNAIATNKLAHAYLFcGPRGVGKTTCARIFAktincqnltadgeacnecescvAFNEQR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  289 SIRFVTL-SATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNKSQQDTFL------PHvecgTITLIGATTENps 361
Cdd:PRK14971  89 SYNIHELdAASNNSVDDIRNLIEQVRIPPQIGKYK-IYIIDEVHMLSQAAFNAFLktleepPS----YAIFILATTEK-- 161

                        170       180
                 ....*....|....*....|....*
gi 18426902  362 FQVNAALLSRCRVIVLEKLPVEAMV 386
Cdd:PRK14971 162 HKILPTILSRCQIFDFNRIQVADIV 186
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
264-400 3.56e-06

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 48.73  E-value: 3.56e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 264 LILWGPPGCGKTTLAHIIASNSKKHSI---------RFVTLSATNaktndVRDVIKQAQNeksffkRKTILFIDEIH--- 331
Cdd:COG1223  38 ILFYGPPGTGKTMLAEALAGELKLPLLtvrldsligSYLGETARN-----LRKLFDFARR------APCVIFFDEFDaia 106

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 332 --RFNKS-------------QQDTFLPhvecGTITLIGATteNPSFQVNAALLSRCRVIVLEKLP-VEAMVTILMRAINS 395
Cdd:COG1223 107 kdRGDQNdvgevkrvvnallQELDGLP----SGSVVIAAT--NHPELLDSALWRRFDEVIEFPLPdKEERKEILELNLKK 180


                ....*
gi 18426902 396 LGIHV 400
Cdd:COG1223 181 FPLPF 185
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 224-469 9.30e-06

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: 48.80  E-value: 9.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   224 GKPLADTMRPDTLQDYFGQSKAVG--QDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIA--------SNSKKHSIRF- 292
Cdd:TIGR00602  71 NEPWVEKYKPETQHELAVHKKKIEevETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSkelgiqvqEWSNPTLPDFq 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   293 -----VTLSATNAKTNDV------RDVIKQAQNE-----KSFFKRKTILFIDEI----HRFNKSQQDTF-LPHVECGTIT 351
Cdd:TIGR00602 151 kndhkVTLSLESCFSNFQsqievfSEFLLRATNKlqmlgDDLMTDKKIILVEDLpnqfYRDTRALHEILrWKYVSIGRCP 230

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   352 LIGATTEN------------PSFQV-NAALLSRCRVIVLEKLPVEAmvTILMRAINSLgihvldssrptdpLSHSSNSSS 418
Cdd:TIGR00602 231 LVFIITESlegdnnqrrllfPAETImNKEILEEPRVSNISFNPIAP--TIMKKFLNRI-------------VTIEAKKNG 295

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 18426902   419 EPAMFIEDKAVDTLAYLSDGDARAGLNGLQLAVlARLSSRKMFCKKSGQSY 469
Cdd:TIGR00602 296 EKIKVPKKTSVELLCQGCSGDIRSAINSLQFSS-SKSGSLPIKKRMSTKSD 345
DNA_pol3_delta2 pfam13177
DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required ...
 241-381 9.81e-06

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: 46.05  E-value: 9.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   241 GQSKAVgqdTLLRSLLETNEIPSLILW-GPPGCGKTTLAHIIAS----------------------NSKKHS-IRFVTLS 296
Cdd:pfam13177   1 GQPEAI---QLLQNSLENGRLSHAYLFsGPEGVGKLELALAFAKalfceepgddlpcgqcrscrriESGNHPdLVIIEPE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   297 ATNAKTNDVRDVIKQAQnEKSFFKRKTILFIDEIHRFNKSQQDTFL-----PHVEcgtiTLIGATTENPSfQVNAALLSR 371
Cdd:pfam13177  78 GQSIKIDQIRELQKEFS-KSPYEGKKKVYIIEDAEKMTASAANSLLkfleePPGN----TVIILLTENPS-RLLPTIRSR 151

                         170
                  ....*....|
gi 18426902   372 CRVIVLEKLP 381
Cdd:pfam13177 152 CQIIRFKPLS 161
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 263-372 1.11e-05

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: 1.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   263 SLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSAtNAKTNDVRDVIKQAQNEKSF--------FKRKTILFIDEIHRFN 334
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAAALSNRPVFYVQLTR-DTTEEDLFGRRNIDPGGASWvdgplvraAREGEIAVLDEINRAN 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 18426902   335 KSQQDTFLP-------HVECGT---------ITLIgATTENPSFQVN---AALLSRC 372
Cdd:pfam07728  80 PDVLNSLLSllderrlLLPDGGelvkaapdgFRLI-ATMNPLDRGLNelsPALRSRF 135
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 264-330 1.49e-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: 45.86  E-value: 1.49e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18426902 264 LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATN-------AKTNDVRDVIKQAQNEKSffkrkTILFIDEI 330
Cdd:cd19518  37 VLLHGPPGCGKTMLANAIAGELK---VPFLKISATEivsgvsgESEEKIRELFDQAISNAP-----CIVFIDEI 102
DnaA COG0593
Chromosomal replication initiation ATPase DnaA [Replication, recombination and repair];
264-341 2.05e-05

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


Pssm-ID: 440358 [Multi-domain]  Cd Length: 303  Bit Score: 47.11  E-value: 2.05e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 264 LILWGPPGCGKTTLAHIIA----SNSKKHSIRFVTLSA-TNAKTNDVRDviKQAQNEKSFFKRKTILFIDEIHRF--NKS 336
Cdd:COG0593  37 LFLYGGVGLGKTHLLHAIGnealENNPGARVVYLTAEEfTNDFINAIRN--NTIEEFKEKYRSVDVLLIDDIQFLagKEA 114


                ....*
gi 18426902 337 QQDTF 341
Cdd:COG0593 115 TQEEF 119
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 264-329 4.04e-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: 44.34  E-value: 4.04e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18426902 264 LILWGPPGCGKTTLAHIIASNSkkhSIRFVTLSA-------TNAKTNDVRDVIKQAQNEKSffkrkTILFIDE 329
Cdd:cd19526  30 ILLYGPPGCGKTLLASAIASEC---GLNFISVKGpellnkyIGASEQNVRDLFSRAQSAKP-----CILFFDE 94
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 4.80e-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: 44.20  E-value: 4.80e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18426902 265 ILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATNAKT-------NDVRDVIKQAQNEKSffkrkTILFIDEI 330
Cdd:cd19511  31 LLYGPPGCGKTLLAKALASEAG---LNFISVKGPELFSkyvgeseRAVREIFQKARQAAP-----CIIFFDEI 95
AAA_14 pfam13173
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 264-332 5.78e-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: 5.78e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18426902   264 LILWGPPGCGKTTLA-HIIASNSKKHSIRFVTL---SATNAKTNDVRDVIkqaqnEKSFFKRKTILFIDEIHR 332
Cdd:pfam13173   5 LVITGPRQVGKTTLLlQLIKELLPPENILYINLddpRLLKLADFELLELF-----LELLYPGKTYLFLDEIQR 72
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 264-340 6.03e-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: 43.95  E-value: 6.03e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18426902 264 LILWGPPGCGKTTLAHIIAsnsKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFFKR--KTILFIDEIHRFNKSQQDT 340
Cdd:cd19520  38 VLLYGPPGCGKTMLAKATA---KEAGARFINLQVSSLTDKWYGESQKLVAAVFSLASKlqPSIIFIDEIDSFLRQRSST 113
PRK12422 PRK12422
chromosomal replication initiator protein DnaA;
266-493 6.23e-05

chromosomal replication initiator protein DnaA;


Pssm-ID: 183521 [Multi-domain]  Cd Length: 445  Bit Score: 45.98  E-value: 6.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  266 LWGPPGCGKTTL----AHIIASNSKKhsIRFVtlsATNAKTNDVRDVIK--QAQNEKSFFKRKTILFIDEIHRFNK---S 336
Cdd:PRK12422 146 LFGPEGSGKTHLmqaaVHALRESGGK--ILYV---RSELFTEHLVSAIRsgEMQRFRQFYRNVDALFIEDIEVFSGkgaT 220

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  337 QQDTFLP----HVECGTITLIGATTENPSFQVNAALLSRCR---VIVLEKLPVEAMVTILMRAINSLGIHvldssrptdp 409
Cdd:PRK12422 221 QEEFFHTfnslHTEGKLIVISSTCAPQDLKAMEERLISRFEwgiAIPLHPLTKEGLRSFLERKAEALSIR---------- 290

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  410 lshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLavlarLSSRKMFCKKSGQsyspsrvLITENDVKeglqrsH 489
Cdd:PRK12422 291 --------------IEETALDFLIEALSSNVKSLLHALTL-----LAKRVAYKKLSHQ-------LLYVDDIK------A 338


                 ....
gi 18426902  490 ILYD 493
Cdd:PRK12422 339 LLHD 342
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 266-330 9.46e-05

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 45.21  E-value: 9.46e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18426902  266 LWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATN------AKTndVRDVIKQAQnEKSffkrKTILFIDEI 330
Cdd:PRK03992 170 LYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQkfigegARL--VRELFELAR-EKA----PSIIFIDEI 233
ftsH CHL00176
cell division protein; Validated
 253-330 1.35e-04

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 45.04  E-value: 1.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  253 RSLLETNEIPS-LILWGPPGCGKTTLAHIIASNSKK--HSI-------RFVTLSATNaktndVRDVIKQAQNeksffKRK 322
Cdd:CHL00176 207 RFTAVGAKIPKgVLLVGPPGTGKTLLAKAIAGEAEVpfFSIsgsefveMFVGVGAAR-----VRDLFKKAKE-----NSP 276


                 ....*...
gi 18426902  323 TILFIDEI 330
Cdd:CHL00176 277 CIVFIDEI 284
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 263-371 2.37e-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: 42.34  E-value: 2.37e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 263 SLILWGPPGCGKTTLAHIIASNSkkhSIRFVTLSATN-------AKTNDVRDVIKQAQneksfFKRKTILFIDEIHRFNK 335
Cdd:cd19509  34 GILLYGPPGTGKTLLARAVASES---GSTFFSISASSlvskwvgESEKIVRALFALAR-----ELQPSIIFIDEIDSLLS 105

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 18426902 336 SQQDT-----------FL------PHVECGTITLIGATteNPSFQVNAALLSR 371
Cdd:cd19509 106 ERGSGeheasrrvkteFLvqmdgvLNKPEDRVLVLGAT--NRPWELDEAFLRR 156
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 265-330 2.80e-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: 41.94  E-value: 2.80e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 265 ILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTND----VRDVIKQAQNeksffKRKTILFIDEI 330
Cdd:cd19502  41 LLYGPPGTGKTLLAKAVANHTDATFIRVVGSELVQKYIGEgarlVRELFEMARE-----KAPSIIFIDEI 105
cell_div_CdvC NF041006
cell division protein CdvC;
264-330 3.66e-04

cell division protein CdvC;


Pssm-ID: 468935 [Multi-domain]  Cd Length: 371  Bit Score: 43.18  E-value: 3.66e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18426902  264 LILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATN--------AKTNdVRDVIKQAQNEKSFFKRKTILFIDEI 330
Cdd:NF041006 137 ILLYGPPGCGKTMLAAAVANEIDSE---FIHVDAASimskwlgeAEKN-VAKIFKKAREKSKEEGKPAIIFIDEI 207
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 4.11e-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: 41.51  E-value: 4.11e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18426902 264 LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSA----------TNAKtndVRDVIKQAQNEKsffkrKTILFIDEI 330
Cdd:cd19503  37 VLLHGPPGTGKTLLARAVANEAG---ANFLSISGpsivskylgeSEKN---LREIFEEARSHA-----PSIIFIDEI 102
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 216-290 4.58e-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: 4.58e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18426902 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 4.91e-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: 41.45  E-value: 4.91e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 260 EIP-SLILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATN---------AKTndVRDVIKQAqneksffKRKT--ILFI 327
Cdd:cd19501  35 KIPkGVLLVGPPGTGKTLLAKAVAGEAG---VPFFSISGSDfvemfvgvgASR--VRDLFEQA-------KKNApcIVFI 102


                ...
gi 18426902 328 DEI 330
Cdd:cd19501 103 DEI 105
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
260-330 6.14e-04

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 43.10  E-value: 6.14e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18426902  260 EIPSLILW-GPPGCGKTTLAHIIASNSKkhsIRFVTLSATN-------AKTNDVRDVIKQAQNEKSffkrkTILFIDEI 330
Cdd:PRK10733 183 KIPKGVLMvGPPGTGKTLLAKAIAGEAK---VPFFTISGSDfvemfvgVGASRVRDMFEQAKKAAP-----CIIFIDEI 253
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
18-83 7.48e-04

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


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 42.38  E-value: 7.48e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18426902  18 VQCPVCQQMMPAAHINSHLDRCLLLH--PAGHAEP---AAGSH-RAGERAKGPSPPGAKRRRLSESSALKQP 83
Cdd:COG5432 161 VHCPACSNLVPHNQINQHLDSCLNSPssPSSSSSPyknKDNSKsNSLLSFKTDDDSITKRRLRSFNSADELP 232
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 8.25e-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: 8.25e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18426902 264 LILWGPPGCGKTTLAHIIASNSKKHSI-----RFVTLSATNAKTNdVRDVIKQAQNEKSffkrkTILFIDEIHRFNKSQ 337
Cdd:cd19528  30 VLFYGPPGCGKTLLAKAIANECQANFIsvkgpELLTMWFGESEAN-VRDIFDKARAAAP-----CVLFFDELDSIAKAR 102
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 205-401 8.36e-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: 42.27  E-value: 8.36e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 205 GGRPHPRALAAEE-----IRQmLQGKPLADTMRPDTLQDYFGQSKAV---GQDTLLRSLLETNEIpsLILWGPPGCGKTT 276
Cdd:COG0507  79 GRRYLTRLLEAEQrlarrLRR-LARPALDEADVEAALAALEPRAGITlsdEQREAVALALTTRRV--SVLTGGAGTGKTT 155

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 277 LAHIIASNSKKHSIRFVTLSATNaktndvrdviKQAQN--EKSFFKRKTilfideIHRfnksqqdtflphvecgtitLIG 354
Cdd:COG0507 156 TLRALLAALEALGLRVALAAPTG----------KAAKRlsESTGIEART------IHR-------------------LLG 200

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 18426902 355 ATTENPSFQVNA-ALLSRCRVIVLEklpvEA-MVTI-----LMRAINSLGIHVL 401
Cdd:COG0507 201 LRPDSGRFRHNRdNPLTPADLLVVD----EAsMVDTrlmaaLLEALPRAGARLI 250
clpC CHL00095
Clp protease ATP binding subunit
 265-389 1.13e-03

Clp protease ATP binding subunit


Pssm-ID: 214361 [Multi-domain]  Cd Length: 821  Bit Score: 42.35  E-value: 1.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  265 ILWGPPGCGKTT----LAHIIASNSKK---HSIRFVTLSATN--AKTND-------VRDVIKQAQNEKsffkrKTILFID 328
Cdd:CHL00095 204 ILIGEPGVGKTAiaegLAQRIVNRDVPdilEDKLVITLDIGLllAGTKYrgefeerLKRIFDEIQENN-----NIILVID 278

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18426902  329 EIHR-FNKSQQDT-------FLPHVECGTITLIGATTEN---PSFQVNAALLSRCRVIVLEKLPVEAMVTIL 389
Cdd:CHL00095 279 EVHTlIGAGAAEGaidaaniLKPALARGELQCIGATTLDeyrKHIEKDPALERRFQPVYVGEPSVEETIEIL 350
Rad17 pfam03215
Rad17 P-loop domain;
223-381 1.45e-03

Rad17 P-loop domain;


Pssm-ID: 367398 [Multi-domain]  Cd Length: 186  Bit Score: 40.33  E-value: 1.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   223 QGKPLADTMRPDTLQDYFGQSKAVG--QDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIasnSKKHSIRFVT-LSATN 299
Cdd:pfam03215   5 GGEQWYEKYKPNCLEQLAVHKRKIKdvQEWLDAMFLENAKHRILLISGPSGCGKSTVIKEL---SKELGPKYREwSNPTS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   300 AKTNDvrdvikqaqNEKSFFKRKTILFideihrfnksqqDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVIVLEK 379
Cdd:pfam03215  82 FRSPP---------NQVTDFRGDCIVN------------SRFLSQMESFSEFELKGARYLVMQKRGKNAQGNKKLILIED 140


                  ..
gi 18426902   380 LP 381
Cdd:pfam03215 141 LP 142
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 264-330 1.65e-03

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


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 41.29  E-value: 1.65e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18426902  264 LILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTND----VRDVIKQAQnEKSffkrKTILFIDEI 330
Cdd:PTZ00454 182 VLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKYLGEgprmVRDVFRLAR-ENA----PSIIFIDEV 247
AAA_7 pfam12775
P-loop containing dynein motor region; This domain is found in human cytoplasmic dynein-2 ...
 251-331 1.76e-03

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: 1.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   251 LLRSLLeTNEIPSLiLWGPPGCGKTTLAH--IIASNSKKHSIRFVTLSA-TNAktNDVRDVIkqaqnEKSFFKR------ 321
Cdd:pfam12775  23 LLDLLL-KNGKPVL-LVGPTGTGKTVIIQnlLRKLDKEKYLPLFINFSAqTTS--NQTQDII-----ESKLEKRrkgvyg 93

                          90
                  ....*....|....*
gi 18426902   322 -----KTILFIDEIH 331
Cdd:pfam12775  94 ppggkKLVVFIDDLN 108
IstB_IS21 pfam01695
IstB-like ATP binding protein; This protein contains an ATP/GTP binding P-loop motif. It is ...
 235-330 1.93e-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: 1.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   235 TLQDY-FGQSKAVGQDTL--LRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKH--SIRFVTlsatnakTNDVRDVI 309
Cdd:pfam01695  63 TLEDFdFTFAPGLDQRIVaeLASLSFIDRAQNVVLLGPPGVGKTHLAIALGVEACRAgySVRFTS-------AADLVNQL 135

                          90       100
                  ....*....|....*....|....*..
gi 18426902   310 KQAQNEKSF------FKRKTILFIDEI 330
Cdd:pfam01695 136 KRAHGDGKLtrklqqLLKPDVLILDEW 162
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 246-330 2.16e-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: 39.45  E-value: 2.16e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902 246 VGQDTLLRSLLETNEIPS---------------LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATNAKTNDVRDVIK 310
Cdd:cd19524   3 AGQDLAKQALQEMVILPSlrpelftglrapargLLLFGPPGNGKTMLAKAVAAESN---ATFFNISAASLTSKYVGEGEK 79

                        90       100
                ....*....|....*....|....*
gi 18426902 311 QAqneKSFFK-----RKTILFIDEI 330
Cdd:cd19524  80 LV---RALFAvarelQPSIIFIDEV 101
PRK04132 PRK04132
replication factor C small subunit; Provisional
 225-274 2.80e-03

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 40.98  E-value: 2.80e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 18426902  225 KPLADTMRPDTLQDYFGQSKAVGQdtlLRSLLETNEIPSLILWGPPGCGK 274
Cdd:PRK04132   7 KPWVEKYRPQRLDDIVGQEHIVKR---LKHYVKTGSMPHLLFAGPPGVGK 53
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 264-283 3.69e-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: 3.69e-03
                          10        20
                  ....*....|....*....|
gi 18426902   264 LILWGPPGCGKTTLAHIIAS 283
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLAR 20
AAA_22 pfam13401
AAA domain;
263-333 4.63e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 37.71  E-value: 4.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   263 SLILWGPPGCGKTTLAHIIASNSKKHSIR--FVTLSATNAKTNDVRDVIKQAQNEKSFFKRKTILF-------------- 326
Cdd:pfam13401   7 ILVLTGESGTGKTTLLRRLLEQLPEVRDSvvFVDLPSGTSPKDLLRALLRALGLPLSGRLSKEELLaalqqlllalavav 86

                          90
                  ....*....|
gi 18426902   327 ---IDEIHRF 333
Cdd:pfam13401  87 vliIDEAQHL 96
PRK08451 PRK08451
DNA polymerase III subunits gamma and tau; Validated
 227-335 5.20e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236267 [Multi-domain]  Cd Length: 535  Bit Score: 40.02  E-value: 5.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902  227 LADTMRPDTLqdyfgqSKAVGQDTLLRSL---LETNEIPSLILW-GPPGCGKTTLAHI---------------------- 280
Cdd:PRK08451   4 LALKYRPKHF------DELIGQESVSKTLslaLDNNRLAHAYLFsGLRGSGKTSSARIfaralvceqgpsstpcdtciqc 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 18426902  281 IASNSKKHsIRFVTL-SATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNK 335
Cdd:PRK08451  78 QSALENRH-IDIIEMdAASNRGIDDIRELIEQTKYKPSMARFK-IFIIDEVHMLTK 131
Bac_DnaA pfam00308
Bacterial dnaA protein;
264-338 6.27e-03

Bacterial dnaA protein;


Pssm-ID: 278724 [Multi-domain]  Cd Length: 219  Bit Score: 38.85  E-value: 6.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426902   264 LILWGPPGCGKTTLAHIIASN--SKKHSIRFVTLSATNAkTNDVRDVIKqaQNEKSFFKRK----TILFIDEIHRFNKSQ 337
Cdd:pfam00308  37 LFIYGGVGLGKTHLLHAIGNYalQNAPNLRVVYLTAEEF-LNDFVDAIR--DNKTNQFKEKyrnvDVLLIDDIQFLAGKE 113


                  .
gi 18426902   338 Q 338
Cdd:pfam00308 114 G 114
 
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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