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Conserved domains on  [gi|489521790|ref|WP_003426579|]
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Holliday junction branch migration DNA helicase RuvB [Clostridioides difficile]

Protein Classification

Holliday junction branch migration DNA helicase RuvB( domain architecture ID 11455025)

Holliday junction branch migration DNA helicase RuvB is an ATPase that forms a complex with RuvA; the helicase RuvAB mediates the Holliday junction migration by localized denaturation and reannealing

CATH:  1.10.10.10|1.10.8.60
EC:  3.6.4.12
Gene Symbol:  ruvB
Gene Ontology:  GO:0003677|GO:0005524|GO:0009378
PubMed:  11478862|7625278

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 6-339 0e+00

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


:

Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 672.56  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   6 DENRIITSTMKMEDIDIENSLRPKTLEDYLGQEKSKEQLSIFIEAAKSRNEQLDHVLLYGPPGLGKTTLASIIANEMGVN 85
Cdd:COG2255    2 AEEDRLSSSASEEEDALERSLRPKRLDEYIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLAHIIANEMGVN 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  86 LRITSGPAIERAGDLAAILTNLNENDVLFIDEIHRINRSVEEVLYPAMEDFCLDIIIGKGPSARSIRLDLPKFTLIGATT 165
Cdd:COG2255   82 IRITSGPAIEKPGDLAAILTNLEEGDVLFIDEIHRLSRVVEEILYPAMEDFRLDIVIGKGPAARSIRLDLPPFTLVGATT 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 166 RAGMLTNPLRDRFGVICKLDYYTVDELSKIVLRSSSILDAEIQSNGALELAKRSRGTPRIANRLLKRVRDFAQVRADGKI 245
Cdd:COG2255  162 RAGLLTSPLRDRFGIVLRLEFYTVEELAEIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVI 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 246 TDKVAKDALELLGVDSLGLDFVDEKLLMTIIEKFRGGPVGLDTLAASIGEDRNTIEDVYEPYLLQLGFINRGPRGRVAMP 325
Cdd:COG2255  242 TLEIADAALELLEVDELGLDEMDRRILETIIEKFGGGPVGLETLAAALGEERDTIEDVYEPYLIQQGFLQRTPRGRVATP 321

                        330
                 ....*....|....
gi 489521790 326 LAYEHLKIPYPNEK 339
Cdd:COG2255  322 KAYEHLGLKPPEDA 335
 
Name Accession Description Interval E-value
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 6-339 0e+00

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


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 672.56  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   6 DENRIITSTMKMEDIDIENSLRPKTLEDYLGQEKSKEQLSIFIEAAKSRNEQLDHVLLYGPPGLGKTTLASIIANEMGVN 85
Cdd:COG2255    2 AEEDRLSSSASEEEDALERSLRPKRLDEYIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLAHIIANEMGVN 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  86 LRITSGPAIERAGDLAAILTNLNENDVLFIDEIHRINRSVEEVLYPAMEDFCLDIIIGKGPSARSIRLDLPKFTLIGATT 165
Cdd:COG2255   82 IRITSGPAIEKPGDLAAILTNLEEGDVLFIDEIHRLSRVVEEILYPAMEDFRLDIVIGKGPAARSIRLDLPPFTLVGATT 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 166 RAGMLTNPLRDRFGVICKLDYYTVDELSKIVLRSSSILDAEIQSNGALELAKRSRGTPRIANRLLKRVRDFAQVRADGKI 245
Cdd:COG2255  162 RAGLLTSPLRDRFGIVLRLEFYTVEELAEIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVI 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 246 TDKVAKDALELLGVDSLGLDFVDEKLLMTIIEKFRGGPVGLDTLAASIGEDRNTIEDVYEPYLLQLGFINRGPRGRVAMP 325
Cdd:COG2255  242 TLEIADAALELLEVDELGLDEMDRRILETIIEKFGGGPVGLETLAAALGEERDTIEDVYEPYLIQQGFLQRTPRGRVATP 321

                        330
                 ....*....|....
gi 489521790 326 LAYEHLKIPYPNEK 339
Cdd:COG2255  322 KAYEHLGLKPPEDA 335
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
9-335 0e+00

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 639.48  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   9 RIIT-STMKMEDIDIENSLRPKTLEDYLGQEKSKEQLSIFIEAAKSRNEQLDHVLLYGPPGLGKTTLASIIANEMGVNLR 87
Cdd:PRK00080   1 RLVSpETLEEEEDEIERSLRPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  88 ITSGPAIERAGDLAAILTNLNENDVLFIDEIHRINRSVEEVLYPAMEDFCLDIIIGKGPSARSIRLDLPKFTLIGATTRA 167
Cdd:PRK00080  81 ITSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 168 GMLTNPLRDRFGVICKLDYYTVDELSKIVLRSSSILDAEIQSNGALELAKRSRGTPRIANRLLKRVRDFAQVRADGKITD 247
Cdd:PRK00080 161 GLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITK 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 248 KVAKDALELLGVDSLGLDFVDEKLLMTIIEKFRGGPVGLDTLAASIGEDRNTIEDVYEPYLLQLGFINRGPRGRVAMPLA 327
Cdd:PRK00080 241 EIADKALDMLGVDELGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRGRVATPKA 320


                 ....*...
gi 489521790 328 YEHLKIPY 335
Cdd:PRK00080 321 YEHLGLNP 328
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 29-333 0e+00

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: 519.55  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   29 KTLEDYLGQEKSKEQLSIFIEAAKSRNEQLDHVLLYGPPGLGKTTLASIIANEMGVNLRITSGPAIERAGDLAAILTNLN 108
Cdd:TIGR00635   1 KLLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLAAILTNLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  109 ENDVLFIDEIHRINRSVEEVLYPAMEDFCLDIIIGKGPSARSIRLDLPKFTLIGATTRAGMLTNPLRDRFGVICKLDYYT 188
Cdd:TIGR00635  81 EGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRDRFGIILRLEFYT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  189 VDELSKIVLRSSSILDAEIQSNGALELAKRSRGTPRIANRLLKRVRDFAQVRADGKITDKVAKDALELLGVDSLGLDFVD 268
Cdd:TIGR00635 161 VEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMIDELGLDEID 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489521790  269 EKLLMTIIEKFRGGPVGLDTLAASIGEDRNTIEDVYEPYLLQLGFINRGPRGRVAMPLAYEHLKI 333
Cdd:TIGR00635 241 RKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRGRIATELAYEHLGL 305
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 26-184 1.25e-123

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: 351.42  E-value: 1.25e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   26 LRPKTLEDYLGQEKSKEQLSIFIEAAKSRNEQLDHVLLYGPPGLGKTTLASIIANEMGVNLRITSGPAIERAGDLAAILT 105
Cdd:pfam05496   1 LRPRTLDEYIGQEKVKENLKIFIEAAKQRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPAIERPGDLAAILT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489521790  106 NLNENDVLFIDEIHRINRSVEEVLYPAMEDFCLDIIIGKGPSARSIRLDLPKFTLIGATTRAGMLTNPLRDRFGVICKL 184
Cdd:pfam05496  81 NLEPGDVLFIDEIHRLNRAVEEILYPAMEDFRLDIVIGKGPSARSIRLDLPPFTLVGATTRAGLLTSPLRDRFGIVLRL 159
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 36-186 1.46e-14

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: 70.25  E-value: 1.46e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  36 GQEKSKEQLSIFIEAAKSRneqldHVLLYGPPGLGKTTLASIIANE---MGVNLRITSGPAI-----------ERAGDLA 101
Cdd:cd00009    2 GQEEAIEALREALELPPPK-----NLLLYGPPGTGKTTLARAIANElfrPGAPFLYLNASDLleglvvaelfgHFLVRLL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 102 AILTNLNENDVLFIDEIHRINRSVEEVLYPAMEDFCLDIIIGKGpsarsirldlpkFTLIGATTRA--GMLTNPLRDRFG 179
Cdd:cd00009   77 FELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDREN------------VRVIGATNRPllGDLDRALYDRLD 144


                 ....*..
gi 489521790 180 VICKLDY 186
Cdd:cd00009  145 IRIVIPL 151
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 60-178 8.78e-07

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: 47.75  E-value: 8.78e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790    60 HVLLYGPPGLGKTTLASIIANEMGVN-------------------LRITSGPAIERAGDLAAILTNLNE------NDVLF 114
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPgggviyidgedileevldqLLLIIVGGKKASGSGELRLRLALAlarklkPDVLI 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489521790   115 IDEIHRINRSVEEVLYPAMEDFCLDIIIGKGpsarsirldlPKFTLIGATTRAGML-TNPLRDRF 178
Cdd:smart00382  84 LDEITSLLDAEQEALLLLLEELRLLLLLKSE----------KNLTVILTTNDEKDLgPALLRRRF 138
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 47-118 9.92e-04

IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements.


Pssm-ID: 439516  Cd Length: 232  Bit Score: 40.15  E-value: 9.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  47 FIEAAksRNeqldhVLLYGPPGLGKTTLASIIANE---MGVNLRITSGPAI-------ERAGDLAAILTNLNENDVLFID 116
Cdd:NF038214  86 FIERA--EN-----VLLLGPPGTGKTHLAIALGYAacrQGYRVRFTTAADLveqlaqaRADGRLGRLLRRLARYDLLIID 158


                 ..
gi 489521790 117 EI 118
Cdd:NF038214 159 EL 160
BREX_3_BrxF NF033453
BREX-3 system P-loop-containing protein BrxF; This family of proteins that are about 150 amino ...
 41-118 7.71e-03

BREX-3 system P-loop-containing protein BrxF; This family of proteins that are about 150 amino acids in length includes BrxF from type 3 BREX (bacteriophage exclusion) systems. Most members have the P-loop motif GxxGxGKT, but the region is surprisingly poorly conserved in a sizable fraction of otherwise strongly similar proteins.


Pssm-ID: 468038  Cd Length: 149  Bit Score: 36.32  E-value: 7.71e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  41 KEQLSIFIEAAKSRNEQLdhVLLYGPPGLGKTTLASIIANEMG-----VNLRITSG----PAIERAGDLAAILTNL---N 108
Cdd:NF033453   1 LEKLKRSVDEAESLYYKL--ILLVGPPGSGKTALLRELAAKRGapvinVNLELSRRllelPEKQRALRAPRLLDEIaekS 78

                         90
                 ....*....|
gi 489521790 109 ENDVLFIDEI 118
Cdd:NF033453  79 SGDVVLLDNI 88
 
Name Accession Description Interval E-value
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 6-339 0e+00

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


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 672.56  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   6 DENRIITSTMKMEDIDIENSLRPKTLEDYLGQEKSKEQLSIFIEAAKSRNEQLDHVLLYGPPGLGKTTLASIIANEMGVN 85
Cdd:COG2255    2 AEEDRLSSSASEEEDALERSLRPKRLDEYIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLAHIIANEMGVN 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  86 LRITSGPAIERAGDLAAILTNLNENDVLFIDEIHRINRSVEEVLYPAMEDFCLDIIIGKGPSARSIRLDLPKFTLIGATT 165
Cdd:COG2255   82 IRITSGPAIEKPGDLAAILTNLEEGDVLFIDEIHRLSRVVEEILYPAMEDFRLDIVIGKGPAARSIRLDLPPFTLVGATT 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 166 RAGMLTNPLRDRFGVICKLDYYTVDELSKIVLRSSSILDAEIQSNGALELAKRSRGTPRIANRLLKRVRDFAQVRADGKI 245
Cdd:COG2255  162 RAGLLTSPLRDRFGIVLRLEFYTVEELAEIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVI 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 246 TDKVAKDALELLGVDSLGLDFVDEKLLMTIIEKFRGGPVGLDTLAASIGEDRNTIEDVYEPYLLQLGFINRGPRGRVAMP 325
Cdd:COG2255  242 TLEIADAALELLEVDELGLDEMDRRILETIIEKFGGGPVGLETLAAALGEERDTIEDVYEPYLIQQGFLQRTPRGRVATP 321

                        330
                 ....*....|....
gi 489521790 326 LAYEHLKIPYPNEK 339
Cdd:COG2255  322 KAYEHLGLKPPEDA 335
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
9-335 0e+00

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 639.48  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   9 RIIT-STMKMEDIDIENSLRPKTLEDYLGQEKSKEQLSIFIEAAKSRNEQLDHVLLYGPPGLGKTTLASIIANEMGVNLR 87
Cdd:PRK00080   1 RLVSpETLEEEEDEIERSLRPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  88 ITSGPAIERAGDLAAILTNLNENDVLFIDEIHRINRSVEEVLYPAMEDFCLDIIIGKGPSARSIRLDLPKFTLIGATTRA 167
Cdd:PRK00080  81 ITSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 168 GMLTNPLRDRFGVICKLDYYTVDELSKIVLRSSSILDAEIQSNGALELAKRSRGTPRIANRLLKRVRDFAQVRADGKITD 247
Cdd:PRK00080 161 GLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITK 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 248 KVAKDALELLGVDSLGLDFVDEKLLMTIIEKFRGGPVGLDTLAASIGEDRNTIEDVYEPYLLQLGFINRGPRGRVAMPLA 327
Cdd:PRK00080 241 EIADKALDMLGVDELGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRGRVATPKA 320


                 ....*...
gi 489521790 328 YEHLKIPY 335
Cdd:PRK00080 321 YEHLGLNP 328
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 29-333 0e+00

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: 519.55  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   29 KTLEDYLGQEKSKEQLSIFIEAAKSRNEQLDHVLLYGPPGLGKTTLASIIANEMGVNLRITSGPAIERAGDLAAILTNLN 108
Cdd:TIGR00635   1 KLLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLAAILTNLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  109 ENDVLFIDEIHRINRSVEEVLYPAMEDFCLDIIIGKGPSARSIRLDLPKFTLIGATTRAGMLTNPLRDRFGVICKLDYYT 188
Cdd:TIGR00635  81 EGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRDRFGIILRLEFYT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  189 VDELSKIVLRSSSILDAEIQSNGALELAKRSRGTPRIANRLLKRVRDFAQVRADGKITDKVAKDALELLGVDSLGLDFVD 268
Cdd:TIGR00635 161 VEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMIDELGLDEID 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489521790  269 EKLLMTIIEKFRGGPVGLDTLAASIGEDRNTIEDVYEPYLLQLGFINRGPRGRVAMPLAYEHLKI 333
Cdd:TIGR00635 241 RKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRGRIATELAYEHLGL 305
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 26-184 1.25e-123

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: 351.42  E-value: 1.25e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   26 LRPKTLEDYLGQEKSKEQLSIFIEAAKSRNEQLDHVLLYGPPGLGKTTLASIIANEMGVNLRITSGPAIERAGDLAAILT 105
Cdd:pfam05496   1 LRPRTLDEYIGQEKVKENLKIFIEAAKQRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPAIERPGDLAAILT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489521790  106 NLNENDVLFIDEIHRINRSVEEVLYPAMEDFCLDIIIGKGPSARSIRLDLPKFTLIGATTRAGMLTNPLRDRFGVICKL 184
Cdd:pfam05496  81 NLEPGDVLFIDEIHRLNRAVEEILYPAMEDFRLDIVIGKGPSARSIRLDLPPFTLVGATTRAGLLTSPLRDRFGIVLRL 159
AAA_lid_4 pfam17864
RuvB AAA lid domain; The RuvB protein makes up part of the RuvABC revolvasome which catalyzes ...
 187-260 9.51e-40

RuvB AAA lid 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 entry contains the AAA lid domain that is found to the C-terminus of the AAA domain.


Pssm-ID: 380039 [Multi-domain]  Cd Length: 74  Bit Score: 134.49  E-value: 9.51e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489521790  187 YTVDELSKIVLRSSSILDAEIQSNGALELAKRSRGTPRIANRLLKRVRDFAQVRADGKITDKVAKDALELLGVD 260
Cdd:pfam17864   1 YSVEELELIVKRSARILGVEIDEEGAAEIARRSRGTPRIANRLLRRVRDFAQVKGDGRITLEIADAALDLLEVD 74
RuvB_C pfam05491
RuvB C-terminal winged helix domain; The RuvB protein makes up part of the RuvABC revolvasome ...
 261-332 3.70e-26

RuvB C-terminal winged helix 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 consists of the C-terminal region of the RuvB protein which is thought to be helicase DNA-binding domain.


Pssm-ID: 398896 [Multi-domain]  Cd Length: 72  Bit Score: 99.17  E-value: 3.70e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489521790  261 SLGLDFVDEKLLMTIIEKFRGGPVGLDTLAASIGEDRNTIEDVYEPYLLQLGFINRGPRGRVAMPLAYEHLK 332
Cdd:pfam05491   1 EYGLDELDINYLKTLYENFKGGPVGLDTLAAILGEDKDTIEDVIEPYLLRLGLIERTSRGRIITPKGYKYLK 72
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 61-181 9.60e-26

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: 99.98  E-value: 9.60e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGPAI------ERAGDLAAILTNLNEN--DVLFIDEIHRINRS-------- 124
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELvskyvgESEKRLRELFEAAKKLapCVIFIDEIDALAGSrgsggdse 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  125 ---VEEVLYPAMEDFcldiiigkgpsarsiRLDLPKFTLIGATTRAGMLTNPLRDRFGVI 181
Cdd:pfam00004  81 srrVVNQLLTELDGF---------------TSSNSKVIVIAATNRPDKLDPALLGRFDRI 125
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 26-165 2.09e-25

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 105.55  E-value: 2.09e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  26 LRPKTLEDYLGQEKSKEQLSIFIEAAKSRneQLDHVLLYGPPGLGKTTLASIIANEMGVNLR----ITSGPA-IERAGDL 100
Cdd:PRK13342   6 MRPKTLDEVVGQEHLLGPGKPLRRMIEAG--RLSSMILWGPPGTGKTTLARIIAGATDAPFEalsaVTSGVKdLREVIEE 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489521790 101 AAILTNLNENDVLFIDEIHRINRSVEEVLYPAMEDfcldiiiGkgpsarsirldlpKFTLIGATT 165
Cdd:PRK13342  84 ARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVED-------G-------------TITLIGATT 128
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 26-165 1.02e-21

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 95.12  E-value: 1.02e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  26 LRPKTLEDYLGQEK--SKEQ-LSIFIEAAKSRNeqldhVLLYGPPGLGKTTLASIIANEMGVNLR----ITSGPA-IERA 97
Cdd:COG2256   19 MRPRTLDEVVGQEHllGPGKpLRRAIEAGRLSS-----MILWGPPGTGKTTLARLIANATDAEFValsaVTSGVKdIREV 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489521790  98 GDLAAILTNLNENDVLFIDEIHRINRSVEEVLYPAMEDfcldiiiGkgpsarsirldlpKFTLIGATT 165
Cdd:COG2256   94 IEEARERRAYGRRTILFVDEIHRFNKAQQDALLPHVED-------G-------------TITLIGATT 141
PRK13341 PRK13341
AAA family ATPase;
26-165 2.65e-15

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 77.02  E-value: 2.65e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  26 LRPKTLEDYLGQEkskeqlSIFIEAAKSRN----EQLDHVLLYGPPGLGKTTLASIIANEM------------GV-NLRi 88
Cdd:PRK13341  22 LRPRTLEEFVGQD------HILGEGRLLRRaikaDRVGSLILYGPPGVGKTTLARIIANHTrahfsslnavlaGVkDLR- 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489521790  89 tsgPAIERAGDLaaiLTNLNENDVLFIDEIHRINRSVEEVLYPAMEDFCLdiiigkgpsarsirldlpkfTLIGATT 165
Cdd:PRK13341  95 ---AEVDRAKER---LERHGKRTILFIDEVHRFNKAQQDALLPWVENGTI--------------------TLIGATT 145
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 36-186 1.46e-14

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: 70.25  E-value: 1.46e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  36 GQEKSKEQLSIFIEAAKSRneqldHVLLYGPPGLGKTTLASIIANE---MGVNLRITSGPAI-----------ERAGDLA 101
Cdd:cd00009    2 GQEEAIEALREALELPPPK-----NLLLYGPPGTGKTTLARAIANElfrPGAPFLYLNASDLleglvvaelfgHFLVRLL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 102 AILTNLNENDVLFIDEIHRINRSVEEVLYPAMEDFCLDIIIGKGpsarsirldlpkFTLIGATTRA--GMLTNPLRDRFG 179
Cdd:cd00009   77 FELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDREN------------VRVIGATNRPllGDLDRALYDRLD 144


                 ....*..
gi 489521790 180 VICKLDY 186
Cdd:cd00009  145 IRIVIPL 151
PRK04195 PRK04195
replication factor C large subunit; Provisional
 27-83 3.13e-13

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 70.33  E-value: 3.13e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489521790  27 RPKTLEDYLGQEKSKEQLSIFIEAAKSRNEQlDHVLLYGPPGLGKTTLASIIANEMG 83
Cdd:PRK04195   9 RPKTLSDVVGNEKAKEQLREWIESWLKGKPK-KALLLYGPPGVGKTSLAHALANDYG 64
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
31-255 6.64e-12

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 64.52  E-value: 6.64e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  31 LEDYLGQEKSKEQLSIFIEAAKSRNEQLDH-------VLLYGPPGLGKTTLASIIANEMGVNLRITSGPAI------ERA 97
Cdd:COG1223    1 LDDVVGQEEAKKKLKLIIKELRRRENLRKFglwpprkILFYGPPGTGKTMLAEALAGELKLPLLTVRLDSLigsylgETA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  98 GDLAAILTNLNEND-VLFIDEIHRI-------------NRSVEEVLyPAMEDFCLDIIIgkgpsarsirldlpkftlIGA 163
Cdd:COG1223   81 RNLRKLFDFARRAPcVIFFDEFDAIakdrgdqndvgevKRVVNALL-QELDGLPSGSVV------------------IAA 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 164 TTRAGMLTNPLRDRFGVICKLDYYTVDELSKIVLRSSSILDAEIQSNgALELAKRSRG-TPRIANRLLKRVRDfAQVRAD 242
Cdd:COG1223  142 TNHPELLDSALWRRFDEVIEFPLPDKEERKEILELNLKKFPLPFELD-LKKLAKKLEGlSGADIEKVLKTALK-KAILED 219

                        250
                 ....*....|....
gi 489521790 243 G-KITDKVAKDALE 255
Cdd:COG1223  220 ReKVTKEDLEEALK 233
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 26-255 6.23e-11

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: 6.23e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  26 LRPKTLEDYLGQEKSKEQLSIFIEAAKSRNEQLD--------HVLLYGPPGLGKTTLASIIANEMGVNLRITSGPAI--- 94
Cdd:COG0464  151 LREAILDDLGGLEEVKEELRELVALPLKRPELREeyglppprGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLvsk 230

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  95 ---ERAGDLAAILTNLNEND--VLFIDEIHRI------------NRSVEEVLYpAMEDFCLDIIIgkgpsarsirldlpk 157
Cdd:COG0464  231 yvgETEKNLREVFDKARGLApcVLFIDEADALagkrgevgdgvgRRVVNTLLT-EMEELRSDVVV--------------- 294

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 158 ftlIGATTRAGMLTNPLRDRFGVICKLDYYTVDELSKIVLRSSSilDAEIQSNGALE-LAKRSRG-TPRIANRLLKRVRD 235
Cdd:COG0464  295 ---IAATNRPDLLDPALLRRFDEIIFFPLPDAEERLEIFRIHLR--KRPLDEDVDLEeLAEATEGlSGADIRNVVRRAAL 369

                        250       260
                 ....*....|....*....|
gi 489521790 236 FAQVRADGKITDKVAKDALE 255
Cdd:COG0464  370 QALRLGREPVTTEDLLEALE 389
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 22-199 5.61e-10

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 60.69  E-value: 5.61e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   22 IENSLRPKTLEDYLGQEKSKEQLSIFIEAAKSRNEQLDH--------VLLYGPPGLGKTTLASIIANEMGVNLRITSGPA 93
Cdd:TIGR01243 168 IERKVPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHlgieppkgVLLYGPPGTGKTLLAKAVANEAGAYFISINGPE 247

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   94 I------ERAGDLAAILTNLNEN--DVLFIDEIHRINRSVEEVLYPAMEDFC------LDIIIGKGpsarsirldlpKFT 159
Cdd:TIGR01243 248 ImskyygESEERLREIFKEAEENapSIIFIDEIDAIAPKREEVTGEVEKRVVaqlltlMDGLKGRG-----------RVI 316

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 489521790  160 LIGATTRAGMLTNPLR-----DRFGVICKLDYYTVDELSKIVLRS 199
Cdd:TIGR01243 317 VIGATNRPDALDPALRrpgrfDREIVIRVPDKRARKEILKVHTRN 361
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 60-178 1.45e-09

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: 55.38  E-value: 1.45e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   60 HVLLYGPPGLGKTTLASIIANEM-GVNLRITSGPAIERAGDL---------------AAILTNLNENDVLFIDEIHRINR 123
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAAALsNRPVFYVQLTRDTTEEDLfgrrnidpggaswvdGPLVRAAREGEIAVLDEINRANP 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 489521790  124 SVEEVLYPAMEDFCLDIIIGKGPsarsIRLDLPKFTLIGATTRAGMLTN----PLRDRF 178
Cdd:pfam07728  81 DVLNSLLSLLDERRLLLPDGGEL----VKAAPDGFRLIATMNPLDRGLNelspALRSRF 135
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 61-118 1.71e-09

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: 56.15  E-value: 1.71e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGPAI--ERAGDLAAILTNLNEN------DVLFIDEI 118
Cdd:cd19503   37 VLLHGPPGTGKTLLARAVANEAGANFLSISGPSIvsKYLGESEKNLREIFEEarshapSIIFIDEI 102
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 30-118 1.11e-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: 1.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  30 TLEDYLGQEKSKEQLSIFIEAAKSRNEQLDH--------VLLYGPPGLGKTTLASIIANEMGVNLRITSGPAIERA--GD 99
Cdd:COG1222   76 TFDDIGGLDEQIEEIREAVELPLKNPELFRKygieppkgVLLYGPPGTGKTLLAKAVAGELGAPFIRVRGSELVSKyiGE 155

                         90       100
                 ....*....|....*....|....*
gi 489521790 100 LAAILTNL------NENDVLFIDEI 118
Cdd:COG1222  156 GARNVREVfelareKAPSIIFIDEI 180
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 41-134 1.46e-08

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: 53.06  E-value: 1.46e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  41 KEQLSIFIEAAKSRNEQLDH-------VLLYGPPGLGKTTLASIIANEMGVNLRITSGPAI------ERAGDLAAILTNL 107
Cdd:cd19481    2 KASLREAVEAPRRGSRLRRYglglpkgILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLlskyvgESEKNLRKIFERA 81

                         90       100
                 ....*....|....*....|....*....
gi 489521790 108 NE--NDVLFIDEIHRINRSVEEVLYPAME 134
Cdd:cd19481   82 RRlaPCILFIDEIDAIGRKRDSSGESGEL 110
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 61-128 1.50e-08

first of two ATPase domains of CDC48 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. 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_r1-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: 410927 [Multi-domain]  Cd Length: 166  Bit Score: 53.21  E-value: 1.50e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGPAI------ERAGDLAAILTNLNEN--DVLFIDEIHRINRSVEEV 128
Cdd:cd19519   37 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEImsklagESESNLRKAFEEAEKNapAIIFIDEIDAIAPKREKT 112
rfc PRK00440
replication factor C small subunit; Reviewed
 15-82 5.21e-08

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 53.72  E-value: 5.21e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489521790  15 MKMEDIDIENsLRPKTLEDYLGQEKSKEQLSIFIeaaKSRNeqLDHVLLYGPPGLGKTTLASIIANEM 82
Cdd:PRK00440   1 AMMEEIWVEK-YRPRTLDEIVGQEEIVERLKSYV---KEKN--MPHLLFAGPPGTGKTTAALALAREL 62
MoxR COG0714
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway ...
 17-234 3.39e-07

MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 440478 [Multi-domain]  Cd Length: 292  Bit Score: 50.94  E-value: 3.39e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  17 MEDIDIENSLRpktlEDYLGQEKSKEQLSIFIEAAKsrneqldHVLLYGPPGLGKTTLASIIANEMGVNL-RI--TSG-- 91
Cdd:COG0714    1 MTEARLRAEIG----KVYVGQEELIELVLIALLAGG-------HLLLEGVPGVGKTTLAKALARALGLPFiRIqfTPDll 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  92 PA--------IERAGD----LAAILTNlnendVLFIDEihrINRSVEEV---LYPAMEDFCLDIiigkgpSARSIRLDLP 156
Cdd:COG0714   70 PSdilgtyiyDQQTGEfefrPGPLFAN-----VLLADE---INRAPPKTqsaLLEAMEERQVTI------PGGTYKLPEP 135

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 157 kFTLIgAT--------TRAgmLTNPLRDRFGVICKLDYYTVDELSKIVLRSSSILDAEIQS-------NGALELAKRSRG 221
Cdd:COG0714  136 -FLVI-ATqnpieqegTYP--LPEAQLDRFLLKLYIGYPDAEEEREILRRHTGRHLAEVEPvlspeelLALQELVRQVHV 211

                        250
                 ....*....|...
gi 489521790 222 TPRIANRLLKRVR 234
Cdd:COG0714  212 SEAVLDYIVDLVR 224
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 27-81 4.83e-07

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 50.76  E-value: 4.83e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489521790  27 RPKTLEDYLGQEKSKEQLSifiEAAKSRNeqLDHVLLYGPPGLGKTTLASIIANE 81
Cdd:PRK12402  10 RPALLEDILGQDEVVERLS---RAVDSPN--LPHLLVQGPPGSGKTAAVRALARE 59
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 61-92 6.55e-07

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: 48.43  E-value: 6.55e-07
                         10        20        30
                 ....*....|....*....|....*....|..
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGP 92
Cdd:cd19511   30 VLLYGPPGCGKTLLAKALASEAGLNFISVKGP 61
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 60-178 8.78e-07

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: 47.75  E-value: 8.78e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790    60 HVLLYGPPGLGKTTLASIIANEMGVN-------------------LRITSGPAIERAGDLAAILTNLNE------NDVLF 114
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPgggviyidgedileevldqLLLIIVGGKKASGSGELRLRLALAlarklkPDVLI 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489521790   115 IDEIHRINRSVEEVLYPAMEDFCLDIIIGKGpsarsirldlPKFTLIGATTRAGML-TNPLRDRF 178
Cdd:smart00382  84 LDEITSLLDAEQEALLLLLEELRLLLLLKSE----------KNLTVILTTNDEKDLgPALLRRRF 138
T7SS_EccA TIGR03922
type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the ...
 31-277 1.85e-06

type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccA1, EccA2, etc. [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 188437 [Multi-domain]  Cd Length: 557  Bit Score: 49.46  E-value: 1.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   31 LEDYLGQEKSKEQLSIF---IEAAKSRNE-------QLDHVLLYGPPGLGKTTLASIIANE---MGV----NLRITSGPA 93
Cdd:TIGR03922 275 LAEQIGLERVKRQVAALkssTAMALARAErglpvaqTSNHMLFAGPPGTGKTTIARVVAKIycgLGVlrkpLVREVSRAD 354

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   94 I--ERAGDLAAILTNLNE---NDVLFIDEIHrinrSVEEVLYPAMEDFCLDIIigkgpSARSIRL--DLPKFTLIGATTR 166
Cdd:TIGR03922 355 LigQYIGESEAKTNEIIDsalGGVLFLDEAY----TLVETGYGQKDPFGLEAI-----DTLLARMenDRDRLVVIGAGYR 425

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  167 AGM----LTNP-LRDRFGVICKLDYYTVDELSKIVLRSSSILDAEIQSNGA---LELA-KRSRGTPRIANRLLKRVRDFA 237
Cdd:TIGR03922 426 KDLdkflEVNEgLRSRFTRVIEFPSYSPDELVEIARRMATERDSVLDDAAAdalLEAAtTLAQDTTPDANGDLRRGLDIA 505

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 489521790  238 QvraDGKITDKV---AKDALELLGVDSLGLDFVDEKLLMTIIE 277
Cdd:TIGR03922 506 G---NGRFVRNVverAEEERDFRLDHSDRLDAVTVDDLMEITA 545
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 61-175 2.10e-06

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: 47.40  E-value: 2.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVNL------RITSGPAIERAGDLAAILTNLNEND--VLFIDEIHRINrSVEEVLYPA 132
Cdd:cd19518   37 VLLHGPPGCGKTMLANAIAGELKVPFlkisatEIVSGVSGESEEKIRELFDQAISNApcIVFIDEIDAIT-PKRESAQRE 115

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 489521790 133 MED-------FCLDIIIGKGPSARSIrldlpkfTLIGATTRAGMLTNPLR 175
Cdd:cd19518  116 MERrivsqllTCMDELNNEKTAGGPV-------LVIGATNRPDSLDPALR 158
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 30-84 1.53e-05

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: 44.53  E-value: 1.53e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489521790  30 TLEDYLGQEKSKEQLSIFIEAAKS--RNEQL-----DHVLLYGPPGLGKTTLASIIANEMGV 84
Cdd:cd19501    2 TFKDVAGCEEAKEELKEVVEFLKNpeKFTKLgakipKGVLLVGPPGTGKTLLAKAVAGEAGV 63
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 61-94 1.56e-05

second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ATPase domains; The Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), is an archaeal homolog of the ubiquitous Cdc48/p97. It is a protein unfoldase that functions in concert with the 20S proteasome by unfolding proteasome substrates and passing them on for degradation. VAT forms a homohexamer, each monomer contains two tandem ATPase domains, referred to as D1 and D2, and an N-terminal domain. 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: 410937 [Multi-domain]  Cd Length: 159  Bit Score: 44.41  E-value: 1.56e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGPAI 94
Cdd:cd19529   30 ILLYGPPGTGKTLLAKAVATESNANFISVKGPEL 63
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 61-124 1.85e-05

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: 44.42  E-value: 1.85e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGPAI------ERAGDLAAILTNLNEND--VLFIDEIHRINRS 124
Cdd:cd19528   30 VLFYGPPGCGKTLLAKAIANECQANFISVKGPELltmwfgESEANVRDIFDKARAAApcVLFFDELDSIAKA 101
Mg_chelatase pfam01078
Magnesium chelatase, subunit ChlI; Magnesium-chelatase is a three-component enzyme that ...
 31-164 2.07e-05

Magnesium chelatase, subunit ChlI; Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa.


Pssm-ID: 426032 [Multi-domain]  Cd Length: 207  Bit Score: 44.83  E-value: 2.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   31 LEDYLGQEKSKEQLSIfieAAKSRNeqldHVLLYGPPGLGKTTLASIIAN--------EMGVNLRITS------------ 90
Cdd:pfam01078   2 LADVKGQEQAKRALEI---AAAGGH----NLLMIGPPGSGKTMLAKRLPGilpplteaEALEVTAIHSvaglggdgglir 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   91 ------------------GPAIERAGDLAailtnLNENDVLFIDEIHRINRSVEEVLYPAMEDFclDIIIgkgpSARSIR 152
Cdd:pfam01078  75 rrpfraphhsasaaalvgGGSIPRPGEIS-----LAHNGVLFLDELPEFKRRVLESLRQPLEDG--EITI----SRARAK 143

                         170
                  ....*....|...
gi 489521790  153 LDLP-KFTLIGAT 164
Cdd:pfam01078 144 VTFPaRFQLVAAM 156
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 61-92 2.11e-05

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: 44.02  E-value: 2.11e-05
                         10        20        30
                 ....*....|....*....|....*....|..
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGP 92
Cdd:cd19530   33 VLLYGPPGCGKTLLAKAVANESGANFISVKGP 64
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 61-118 3.52e-05

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: 43.49  E-value: 3.52e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVNL------RITSGPAIERAGDLAAI--LTNLNENDVLFIDEI 118
Cdd:cd19509   35 ILLYGPPGTGKTLLARAVASESGSTFfsisasSLVSKWVGESEKIVRALfaLARELQPSIIFIDEI 100
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 32-181 4.60e-05

lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an evolutionarily conserved ATP-dependent serine protease, present in bacteria and eukaryotic mitochondria and peroxisomes, which mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Lon protease is both an ATP-dependent peptidase and a protein-activated ATPase. This RecA-like Lon domain 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: 410908 [Multi-domain]  Cd Length: 182  Bit Score: 43.32  E-value: 4.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  32 EDYLGQEKSKEQLSIFIEAAKSRNEQLDHVL-LYGPPGLGKTTLASIIANEMGVNL-RITSG------------------ 91
Cdd:cd19500   10 ADHYGLEDVKERILEYLAVRKLKGSMKGPILcLVGPPGVGKTSLGKSIARALGRKFvRISLGgvrdeaeirghrrtyvga 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  92 -P-----AIERAGdlaailtnlNENDVLFIDEIHRINRSVE--------EVLYPAMEDFCLDIIIGkgpsarsIRLDLPK 157
Cdd:cd19500   90 mPgriiqALKKAG---------TNNPVFLLDEIDKIGSSFRgdpasallEVLDPEQNSTFSDHYLD-------VPFDLSK 153

                        170       180
                 ....*....|....*....|....
gi 489521790 158 FTLIGATTRAGMLTNPLRDRFGVI 181
Cdd:cd19500  154 VLFIATANSLDTIPGPLLDRMEII 177
PRK14963 PRK14963
DNA polymerase III subunits gamma and tau; Provisional
 27-128 4.94e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184927 [Multi-domain]  Cd Length: 504  Bit Score: 44.83  E-value: 4.94e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  27 RPKTLEDYLGQEKSKEQLSIFIEAAKsrneqLDHVLLY-GPPGLGKTTLASIIAneMGVNlriTSGPAIERAGDLAAILT 105
Cdd:PRK14963   9 RPITFDEVVGQEHVKEVLLAALRQGR-----LGHAYLFsGPRGVGKTTTARLIA--MAVN---CSGEDPKPCGECESCLA 78

                         90       100
                 ....*....|....*....|....*
gi 489521790 106 --NLNENDVLFIDEIHriNRSVEEV 128
Cdd:PRK14963  79 vrRGAHPDVLEIDAAS--NNSVEDV 101
PRK09862 PRK09862
ATP-dependent protease;
18-272 6.51e-05

ATP-dependent protease;


Pssm-ID: 182120 [Multi-domain]  Cd Length: 506  Bit Score: 44.59  E-value: 6.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  18 EDIDIENSLRPKTLEDYLGQEKSKEQLSIfiEAAKSRNeqldhVLLYGPPGLGKTTLASII-----------ANEMGVNL 86
Cdd:PRK09862 177 KPTDAVSRALQHDLSDVIGQEQGKRGLEI--TAAGGHN-----LLLIGPPGTGKTMLASRIngllpdlsneeALESAAIL 249

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  87 RITSGPAIE--------RAGDLAAILT--------------NLNENDVLFIDEIHRINRSVEEVLYPAMEDFCLDIiigk 144
Cdd:PRK09862 250 SLVNAESVQkqwrqrpfRSPHHSASLTamvgggaipgpgeiSLAHNGVLFLDELPEFERRTLDALREPIESGQIHL---- 325

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 145 gpSARSIRLDLP-KFTLIGA--------------------TTR-AGMLTNPLRDRFGVICKLDYYTVDELSKIVLR--SS 200
Cdd:PRK09862 326 --SRTRAKITYPaRFQLVAAmnpsptghyqgnhnrctpeqTLRyLNRLSGPFLDRFDLSLEIPLPPPGILSKTVVPgeSS 403

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 201 SILDAEIQSNGALELAKRSRGTPRIAN--------------------------------RLLKRVRDFAQVRADGKITDK 248
Cdd:PRK09862 404 ATVKQRVMAARERQFKRQNKLNAWLDSpeirqfcklesedarwleetlihlglsirawqRLLKVARTIADIDQSDIITRQ 483

                        330       340
                 ....*....|....*....|....
gi 489521790 249 VAKDALELLGVDSLGLDFvdEKLL 272
Cdd:PRK09862 484 HLQEAVSYRAIDRLLIHL--QKLL 505
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 61-94 1.03e-04

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 44.13  E-value: 1.03e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 489521790   61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGPAI 94
Cdd:TIGR01243 490 VLLFGPPGTGKTLLAKAVATESGANFIAVRGPEI 523
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 61-94 1.23e-04

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: 42.03  E-value: 1.23e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGPAI 94
Cdd:cd19526   30 ILLYGPPGCGKTLLASAIASECGLNFISVKGPEL 63
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 61-118 1.31e-04

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: 42.03  E-value: 1.31e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMG---VNLR---ITSGPAIERAGDLAAI--LTNLNENDVLFIDEI 118
Cdd:cd19520   38 VLLYGPPGCGKTMLAKATAKEAGarfINLQvssLTDKWYGESQKLVAAVfsLASKLQPSIIFIDEI 103
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
 26-126 1.37e-04

ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent protease ClpXP. In ClpXP, ClpX ATPase serves to specifically recognize, unfold, and translocate protein substrates into the chamber of ClpP protease for degradation. This RecA-like_ClpX domain 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: 410905 [Multi-domain]  Cd Length: 251  Bit Score: 42.59  E-value: 1.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  26 LRPKTLEDYL-----GQEKSKEQLS---------IFIEAAKSRNE---QLDHVLLYGPPGLGKTTLASIIANEMGVNLRI 88
Cdd:cd19497    1 PTPKEIKEHLdkyviGQERAKKVLSvavynhykrIRNNLKQKDDDvelEKSNILLIGPTGSGKTLLAQTLAKILDVPFAI 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489521790  89 TSGPAIERAG----DLAAILTNLNEN---DV-------LFIDEIHRINRSVE 126
Cdd:cd19497   81 ADATTLTEAGyvgeDVENILLKLLQAadyDVeraqrgiVYIDEIDKIARKSE 132
44 PHA02544
clamp loader, small subunit; Provisional
 14-84 1.61e-04

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 43.05  E-value: 1.61e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489521790  14 TMKMEDIDIENSLRPKTLEDYLGQEKSKEQLSIFIEaaksrNEQLDHVLLYGP-PGLGKTTLASIIANEMGV 84
Cdd:PHA02544   3 TVNPNEFMWEQKYRPSTIDECILPAADKETFKSIVK-----KGRIPNMLLHSPsPGTGKTTVAKALCNEVGA 69
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
47-118 1.78e-04

DNA replication protein DnaC [Replication, recombination and repair];


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 42.46  E-value: 1.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  47 FIEAAKsrneqldHVLLYGPPGLGKTTLASIIANE---MGVNLRITSGPAI-------ERAGDLAAILTNLNENDVLFID 116
Cdd:COG1484   95 FIERGE-------NLILLGPPGTGKTHLAIALGHEacrAGYRVRFTTAPDLvnelkeaRADGRLERLLKRLAKVDLLILD 167


                 ..
gi 489521790 117 EI 118
Cdd:COG1484  168 EL 169
DnaA COG0593
Chromosomal replication initiation ATPase DnaA [Replication, recombination and repair];
61-121 2.15e-04

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


Pssm-ID: 440358 [Multi-domain]  Cd Length: 303  Bit Score: 42.49  E-value: 2.15e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVN------LRITSG-------PAIeRAGDLAAILTNLNENDVLFIDEIHRI 121
Cdd:COG0593   37 LFLYGGVGLGKTHLLHAIGNEALENnpgarvVYLTAEeftndfiNAI-RNNTIEEFKEKYRSVDVLLIDDIQFL 109
ftsH CHL00176
cell division protein; Validated
 61-123 3.65e-04

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 42.34  E-value: 3.65e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGP---------AIERAGDLaaiLTNLNEND--VLFIDEIHRINR 123
Cdd:CHL00176 219 VLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSefvemfvgvGAARVRDL---FKKAKENSpcIVFIDEIDAVGR 289
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 38-101 4.77e-04

ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase domains; ATPase AAA-domain protein 3 (ATAD3) is a ubiquitously expressed mitochondrial protein involved in mitochondrial dynamics, DNA-nucleoid structural organization, cholesterol transport and steroidogenesis. The ATAD3 gene family in human comprises three paralog genes: ATAD3A, ATAD3B and ATAD3C. 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: 410920 [Multi-domain]  Cd Length: 150  Bit Score: 40.20  E-value: 4.77e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489521790  38 EKSKEQLSIFIEAAKSRNEQLDHVLLYGPPGLGKTTLASIIANEMGVNLRITSGpaieraGDLA 101
Cdd:cd19512    2 EARVRDIAIATRNTKKNKGLYRNILFYGPPGTGKTLFAKKLALHSGMDYAIMTG------GDVA 59
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 61-121 5.41e-04

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 41.68  E-value: 5.41e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVN-LRITSGPAIER-AGDLAAILTNL------NENDVLFIDEIHRI 121
Cdd:PTZ00361 220 VILYGPPGTGKTLLAKAVANETSATfLRVVGSELIQKyLGDGPKLVRELfrvaeeNAPSIVFIDEIDAI 288
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
30-123 5.47e-04

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 41.56  E-value: 5.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  30 TLEDYLGQEKSKEQLSIFIEAAK--SRNEQL-----DHVLLYGPPGLGKTTLASIIANEMGVNLRITSGPAIER--AGDL 100
Cdd:PRK10733 150 TFADVAGCDEAKEEVAELVEYLRepSRFQKLggkipKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEmfVGVG 229

                         90       100
                 ....*....|....*....|....*....
gi 489521790 101 AAILTNLNEND------VLFIDEIHRINR 123
Cdd:PRK10733 230 ASRVRDMFEQAkkaapcIIFIDEIDAVGR 258
IstB_IS21 pfam01695
IstB-like ATP binding protein; This protein contains an ATP/GTP binding P-loop motif. It is ...
 29-118 5.75e-04

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: 40.89  E-value: 5.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   29 KTLEDY-------LGQEKSKEQLSI-FIEAAKSrneqldhVLLYGPPGLGKTTLASIIANE---MGVNLRITSG------ 91
Cdd:pfam01695  62 KTLEDFdftfapgLDQRIVAELASLsFIDRAQN-------VVLLGPPGVGKTHLAIALGVEacrAGYSVRFTSAadlvnq 134

                          90       100
                  ....*....|....*....|....*...
gi 489521790   92 -PAIERAGDLAAILTNLNENDVLFIDEI 118
Cdd:pfam01695 135 lKRAHGDGKLTRKLQQLLKPDVLILDEW 162
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 26-83 5.82e-04

TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.


Pssm-ID: 399217 [Multi-domain]  Cd Length: 347  Bit Score: 41.14  E-value: 5.82e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 489521790   26 LRPKTLEDYL-GQEKSKEQLSIFIEAAKSRNEQLDHVLLYGPPGLGKTTLASIIANEMG 83
Cdd:pfam06068  17 GEARYVSGGLvGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELG 75
AAA_24 pfam13479
AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.
 61-151 6.93e-04

AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.


Pssm-ID: 433243  Cd Length: 199  Bit Score: 40.39  E-value: 6.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   61 VLLYGPPGLGKTTLAS------IIANEMGVN-LRITSGPAIERA-------GDLAAIL-TNLNENDVLFIDeihrinrSV 125
Cdd:pfam13479   5 ILIYGPSGIGKTTFAKtlpkplFLDTEKGSKaLDGDRFPDIVIRdswqdflDAIDELTaAELADYKTIVID-------TV 77

                          90       100
                  ....*....|....*....|....*.
gi 489521790  126 EEvlypaMEDFCLDIIIGKGPSARSI 151
Cdd:pfam13479  78 DW-----LERLCLAYICKQNGKGSSI 98
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 61-118 8.35e-04

ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein sorting-associated protein 4 (Vps4) is believed to be involved in intracellular protein transport out of a prevacuolar endosomal compartment. 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: 410929 [Multi-domain]  Cd Length: 170  Bit Score: 39.46  E-value: 8.35e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVN-LRITSGPAIER-AGDLAAILTNL------NENDVLFIDEI 118
Cdd:cd19521   43 ILLYGPPGTGKSYLAKAVATEANSTfFSVSSSDLVSKwMGESEKLVKQLfamareNKPSIIFIDEV 108
AAA_3 pfam07726
ATPase family associated with various cellular activities (AAA); This Pfam entry includes some ...
 60-134 9.13e-04

ATPase family associated with various cellular activities (AAA); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.


Pssm-ID: 429622 [Multi-domain]  Cd Length: 131  Bit Score: 38.69  E-value: 9.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790   60 HVLLYGPPGLGKTTLASIIANEMGVNL-RITSGPAIERAGDLAAILTNLNEND-----------VLFIDEIHRINRSVEE 127
Cdd:pfam07726   1 HVLLEGVPGLAKTLLVRTLARSLGLDFrRIQFTPDLLPSDITGTEVFDQKTREfefrpgpvfanVLLADEINRAPPKTQS 80


                  ....*..
gi 489521790  128 VLYPAME 134
Cdd:pfam07726  81 ALLEAMQ 87
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 47-118 9.92e-04

IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements.


Pssm-ID: 439516  Cd Length: 232  Bit Score: 40.15  E-value: 9.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  47 FIEAAksRNeqldhVLLYGPPGLGKTTLASIIANE---MGVNLRITSGPAI-------ERAGDLAAILTNLNENDVLFID 116
Cdd:NF038214  86 FIERA--EN-----VLLLGPPGTGKTHLAIALGYAacrQGYRVRFTTAADLveqlaqaRADGRLGRLLRRLARYDLLIID 158


                 ..
gi 489521790 117 EI 118
Cdd:NF038214 159 EL 160
PRK06835 PRK06835
DNA replication protein DnaC; Validated
 47-81 1.18e-03

DNA replication protein DnaC; Validated


Pssm-ID: 235871 [Multi-domain]  Cd Length: 329  Bit Score: 40.27  E-value: 1.18e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 489521790  47 FIEAAKSRNEQLdhvLLYGPPGLGKTTLASIIANE 81
Cdd:PRK06835 175 FIENFDKNNENL---LFYGNTGTGKTFLSNCIAKE 206
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 61-121 1.25e-03

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: 39.24  E-value: 1.25e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGPAIERA--GDLAAILTNL------NENDVLFIDEIHRI 121
Cdd:cd19502   40 VLLYGPPGTGKTLLAKAVANHTDATFIRVVGSELVQKyiGEGARLVRELfemareKAPSIIFIDEIDAI 108
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 61-92 1.32e-03

second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as Peroxin61)/PEX1 is a protein unfoldase; PEX6 and PEX1 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. This subfamily represents the second ATPase domain of PEX6. 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: 410935 [Multi-domain]  Cd Length: 160  Bit Score: 39.03  E-value: 1.32e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGP 92
Cdd:cd19527   29 ILLYGPPGTGKTLLAKAIATECSLNFLSVKGP 60
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 61-81 1.61e-03

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 39.82  E-value: 1.61e-03
                         10        20
                 ....*....|....*....|.
gi 489521790  61 VLLYGPPGLGKTTLASIIANE 81
Cdd:PRK03992 168 VLLYGPPGTGKTLLAKAVAHE 188
PRK06647 PRK06647
DNA polymerase III subunits gamma and tau; Validated
 27-131 1.70e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235845 [Multi-domain]  Cd Length: 563  Bit Score: 40.14  E-value: 1.70e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  27 RPKTLEDYLGQEKSKEQLSIFIEAAKSRNEqldhVLLYGPPGLGKTTLASIIANEmgvnLRITSGPAIERAGDLAAI--L 104
Cdd:PRK06647  11 RPRDFNSLEGQDFVVETLKHSIESNKIANA----YIFSGPRGVGKTSSARAFARC----LNCVNGPTPMPCGECSSCksI 82

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489521790 105 TNLNENDVLFIDEIHriNRSV-------EEVLYP 131
Cdd:PRK06647  83 DNDNSLDVIEIDGAS--NTSVqdvrqikEEIMFP 114
PRK08116 PRK08116
hypothetical protein; Validated
 62-130 2.42e-03

hypothetical protein; Validated


Pssm-ID: 236153 [Multi-domain]  Cd Length: 268  Bit Score: 39.23  E-value: 2.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  62 LLYGPPGLGKTTLASIIANEM---GVNLRITSGPAI--------ERAGDLA--AILTNLNENDVLFIDE--IHRINRSVE 126
Cdd:PRK08116 118 LLWGSVGTGKTYLAACIANELiekGVPVIFVNFPQLlnrikstyKSSGKEDenEIIRSLVNADLLILDDlgAERDTEWAR 197


                 ....
gi 489521790 127 EVLY 130
Cdd:PRK08116 198 EKVY 201
PRK14952 PRK14952
DNA polymerase III subunits gamma/tau;
27-79 2.67e-03

DNA polymerase III subunits gamma/tau;


Pssm-ID: 237866 [Multi-domain]  Cd Length: 584  Bit Score: 39.48  E-value: 2.67e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489521790  27 RPKTLEDYLGQEKSKEQLSIFIEAAKsrneqLDHVLLY-GPPGLGKTTLASIIA 79
Cdd:PRK14952   8 RPATFAEVVGQEHVTEPLSSALDAGR-----INHAYLFsGPRGCGKTSSARILA 56
PRK14964 PRK14964
DNA polymerase III subunits gamma and tau; Provisional
 27-128 3.97e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237870 [Multi-domain]  Cd Length: 491  Bit Score: 39.00  E-value: 3.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  27 RPKTLEDYLGQEkskeQLSIFIEAAKSRNEQLDHVLLYGPPGLGKTTLASIIAnemgVNLRITSGPAIERAGDLAAILT- 105
Cdd:PRK14964   8 RPSSFKDLVGQD----VLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIIS----LCLNCSNGPTSDPCGTCHNCISi 79

                         90       100
                 ....*....|....*....|....
gi 489521790 106 -NLNENDVLFIDEIHriNRSVEEV 128
Cdd:PRK14964  80 kNSNHPDVIEIDAAS--NTSVDDI 101
PRK04132 PRK04132
replication factor C small subunit; Provisional
 27-80 4.25e-03

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 39.05  E-value: 4.25e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489521790  27 RPKTLEDYLGQEKSKEQLSIFIEAAksrneQLDHVLLYGPPGLGK--TTLASIIAN 80
Cdd:PRK04132  14 RPQRLDDIVGQEHIVKRLKHYVKTG-----SMPHLLFAGPPGVGKclTGDTKVIAN 64
PRK14953 PRK14953
DNA polymerase III subunits gamma and tau; Provisional
 27-79 4.51e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237867 [Multi-domain]  Cd Length: 486  Bit Score: 38.65  E-value: 4.51e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489521790  27 RPKTLEDYLGQEKSKEQLSIFIeaaksRNEQLDHVLLY-GPPGLGKTTLASIIA 79
Cdd:PRK14953  11 RPKFFKEVIGQEIVVRILKNAV-----KLQRVSHAYIFaGPRGTGKTTIARILA 59
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
37-83 4.86e-03

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 38.03  E-value: 4.86e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 489521790  37 QEKSKEQLSIFIEAAKSRNeqldHVLLYGPPGLGKTTLASIIANEMG 83
Cdd:COG0470    1 QEEAWEQLLAAAESGRLPH----ALLLHGPPGIGKTTLALALARDLL 43
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 62-85 5.25e-03

Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of mitochondrial respiratory chain complex III and plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex. 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: 410918 [Multi-domain]  Cd Length: 153  Bit Score: 36.95  E-value: 5.25e-03
                         10        20
                 ....*....|....*....|....
gi 489521790  62 LLYGPPGLGKTTLASIIANEMGVN 85
Cdd:cd19510   27 LLYGPPGTGKSSFIAALAGELDYD 50
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
61-84 6.73e-03

ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 38.09  E-value: 6.73e-03
                         10        20
                 ....*....|....*....|....
gi 489521790  61 VLLYGPPGLGKTTLASIIANEMGV 84
Cdd:COG0465  178 VLLVGPPGTGKTLLAKAVAGEAGV 201
BREX_3_BrxF NF033453
BREX-3 system P-loop-containing protein BrxF; This family of proteins that are about 150 amino ...
 41-118 7.71e-03

BREX-3 system P-loop-containing protein BrxF; This family of proteins that are about 150 amino acids in length includes BrxF from type 3 BREX (bacteriophage exclusion) systems. Most members have the P-loop motif GxxGxGKT, but the region is surprisingly poorly conserved in a sizable fraction of otherwise strongly similar proteins.


Pssm-ID: 468038  Cd Length: 149  Bit Score: 36.32  E-value: 7.71e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  41 KEQLSIFIEAAKSRNEQLdhVLLYGPPGLGKTTLASIIANEMG-----VNLRITSG----PAIERAGDLAAILTNL---N 108
Cdd:NF033453   1 LEKLKRSVDEAESLYYKL--ILLVGPPGSGKTALLRELAAKRGapvinVNLELSRRllelPEKQRALRAPRLLDEIaekS 78

                         90
                 ....*....|
gi 489521790 109 ENDVLFIDEI 118
Cdd:NF033453  79 SGDVVLLDNI 88
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 62-143 7.98e-03

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. Their helicase core is surrounded by C and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains or domains engaged in protein-protein interactions. SF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 35.92  E-value: 7.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  62 LLYGPPGLGKT-TLASIIANEMGvNLRITSGPAieragdLAAILTN--LNENDVLFIDEIHRINRSVEEVLYPAMEDFCL 138
Cdd:cd17914    3 LIQGPPGTGKTrVLVKIVAALMQ-NKNGEPGRI------LLVTPTNkaAAQLDNILVDEAAQILEPETSRLIDLALDQGR 75


                 ....*
gi 489521790 139 DIIIG 143
Cdd:cd17914   76 VILVG 80
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 61-129 8.75e-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: 35.27  E-value: 8.75e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489521790   61 VLLYGPPGLGKTTLASIIANEMGVNLRITSGPAIERAGDLaAILTNLNENDVLFIDEIHRINRSVEEVL 129
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLARALLKKLGLPKDSVYSRNPDD-DFWDGYTGQPVVIIDDFGQNPDGPDEAE 68
PRK07133 PRK07133
DNA polymerase III subunits gamma and tau; Validated
 27-80 8.78e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235943 [Multi-domain]  Cd Length: 725  Bit Score: 37.87  E-value: 8.78e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489521790  27 RPKTLEDYLGQEKSKEQLSIFIeaaksRNEQLDHVLLY-GPPGLGKTTLASIIAN 80
Cdd:PRK07133  13 RPKTFDDIVGQDHIVQTLKNII-----KSNKISHAYLFsGPRGTGKTSVAKIFAN 62
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
42-321 8.87e-03

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 37.52  E-value: 8.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  42 EQLSIFIEAAKsRNEQLDHVLLYGPPGLGKTTLASIIANEMG--------------VNLRITS---------------GP 92
Cdd:COG1474   36 EELASALRPAL-RGERPSNVLIYGPTGTGKTAVAKYVLEELEeeaeergvdvrvvyVNCRQAStryrvlsrileelgsGE 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790  93 AIERAG----DLAAILTN-LNEND---VLFIDEIHRI-NRSVEEVLYP---AMEDfcldiiigkgpsarsirLDLPKFTL 160
Cdd:COG1474  115 DIPSTGlstdELFDRLYEaLDERDgvlVVVLDEIDYLvDDEGDDLLYQllrANEE-----------------LEGARVGV 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 161 IGATTRAGMLTNP---LRDRFG--VIcKLDYYTVDELSKIVL-RSSSILDAEIQSNGALEL----AKRSRGTPRIANRLL 230
Cdd:COG1474  178 IGISNDLEFLENLdprVKSSLGeeEI-VFPPYDADELRDILEdRAELAFYDGVLSDEVIPLiaalAAQEHGDARKAIDLL 256

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489521790 231 KRVRDFAQVRADGKITDKVAKDALELLGVDSL-----GLDfVDEKL-LMTIIEKFRGGPVGLDT---------LAASIGE 295
Cdd:COG1474  257 RVAGEIAEREGSDRVTEEHVREAREKIERDRLlevlrGLP-THEKLvLLAIAELLKDGEDPVRTgevyeayeeLCEELGV 335

                        330       340       350
                 ....*....|....*....|....*....|....
gi 489521790 296 DRNTIEDVYEpY---LLQLGFI-----NRGPRGR 321
Cdd:COG1474  336 DPLSYRRVRD-YlseLEMLGLIeaevsSKGRRGR 368
 
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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