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Holliday junction branch migration DNA helicase RuvB [Escherichia coli]

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, ...
 1-334 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: 670.64  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   1 MIEADRLISAGTTlPEDVADRAIRPKLLEEYVGQPQVRSQMEIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMG 80
Cdd:COG2255    1 MAEEDRLSSSASE-EEDALERSLRPKRLDEYIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLAHIIANEMG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  81 VNLRTTSGPVLEKAGDLAAMLTNLEPHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGPAARSIKIDLPPFTLIGA 160
Cdd:COG2255   80 VNIRITSGPAIEKPGDLAAILTNLEEGDVLFIDEIHRLSRVVEEILYPAMEDFRLDIVIGKGPAARSIRLDLPPFTLVGA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 161 TTRAGSLTSPLRDRFGIVQRLEFYQVPDLQYIVSRSARFMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEVKHDG 240
Cdd:COG2255  160 TTRAGLLTSPLRDRFGIVLRLEFYTVEELAEIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDG 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 241 TISADIAAQALDMLNVDAEGFDYMDRKLLLAVIDKFFGGPVGLDNLAAAIGEERETIEDVLEPYLIQQGFLQRTPRGRMA 320
Cdd:COG2255  240 VITLEIADAALELLEVDELGLDEMDRRILETIIEKFGGGPVGLETLAAALGEERDTIEDVYEPYLIQQGFLQRTPRGRVA 319

                        330
                 ....*....|....
gi 446490666 321 TTRAWNHFGITPPE 334
Cdd:COG2255  320 TPKAYEHLGLKPPE 333
 
Name Accession Description Interval E-value
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 1-334 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: 670.64  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   1 MIEADRLISAGTTlPEDVADRAIRPKLLEEYVGQPQVRSQMEIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMG 80
Cdd:COG2255    1 MAEEDRLSSSASE-EEDALERSLRPKRLDEYIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLAHIIANEMG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  81 VNLRTTSGPVLEKAGDLAAMLTNLEPHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGPAARSIKIDLPPFTLIGA 160
Cdd:COG2255   80 VNIRITSGPAIEKPGDLAAILTNLEEGDVLFIDEIHRLSRVVEEILYPAMEDFRLDIVIGKGPAARSIRLDLPPFTLVGA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 161 TTRAGSLTSPLRDRFGIVQRLEFYQVPDLQYIVSRSARFMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEVKHDG 240
Cdd:COG2255  160 TTRAGLLTSPLRDRFGIVLRLEFYTVEELAEIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDG 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 241 TISADIAAQALDMLNVDAEGFDYMDRKLLLAVIDKFFGGPVGLDNLAAAIGEERETIEDVLEPYLIQQGFLQRTPRGRMA 320
Cdd:COG2255  240 VITLEIADAALELLEVDELGLDEMDRRILETIIEKFGGGPVGLETLAAALGEERDTIEDVYEPYLIQQGFLQRTPRGRVA 319

                        330
                 ....*....|....
gi 446490666 321 TTRAWNHFGITPPE 334
Cdd:COG2255  320 TPKAYEHLGLKPPE 333
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
6-332 0e+00

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 658.36  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   6 RLISAGTTLPED-VADRAIRPKLLEEYVGQPQVRSQMEIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMGVNLR 84
Cdd:PRK00080   1 RLVSPETLEEEEdEIERSLRPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  85 TTSGPVLEKAGDLAAMLTNLEPHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGPAARSIKIDLPPFTLIGATTRA 164
Cdd:PRK00080  81 ITSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 165 GSLTSPLRDRFGIVQRLEFYQVPDLQYIVSRSARFMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEVKHDGTISA 244
Cdd:PRK00080 161 GLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITK 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 245 DIAAQALDMLNVDAEGFDYMDRKLLLAVIDKFFGGPVGLDNLAAAIGEERETIEDVLEPYLIQQGFLQRTPRGRMATTRA 324
Cdd:PRK00080 241 EIADKALDMLGVDELGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRGRVATPKA 320


                 ....*...
gi 446490666 325 WNHFGITP 332
Cdd:PRK00080 321 YEHLGLNP 328
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 26-330 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: 521.86  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   26 KLLEEYVGQPQVRSQMEIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVLEKAGDLAAMLTNLE 105
Cdd:TIGR00635   1 KLLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLAAILTNLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  106 PHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGPAARSIKIDLPPFTLIGATTRAGSLTSPLRDRFGIVQRLEFYQ 185
Cdd:TIGR00635  81 EGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRDRFGIILRLEFYT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  186 VPDLQYIVSRSARFMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEVKHDGTISADIAAQALDMLNVDAEGFDYMD 265
Cdd:TIGR00635 161 VEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMIDELGLDEID 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446490666  266 RKLLLAVIDKFFGGPVGLDNLAAAIGEERETIEDVLEPYLIQQGFLQRTPRGRMATTRAWNHFGI 330
Cdd:TIGR00635 241 RKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRGRIATELAYEHLGL 305
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 23-181 3.36e-119

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: 340.25  E-value: 3.36e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   23 IRPKLLEEYVGQPQVRSQMEIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVLEKAGDLAAMLT 102
Cdd:pfam05496   1 LRPRTLDEYIGQEKVKENLKIFIEAAKQRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPAIERPGDLAAILT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446490666  103 NLEPHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGPAARSIKIDLPPFTLIGATTRAGSLTSPLRDRFGIVQRL 181
Cdd:pfam05496  81 NLEPGDVLFIDEIHRLNRAVEEILYPAMEDFRLDIVIGKGPSARSIRLDLPPFTLVGATTRAGLLTSPLRDRFGIVLRL 159
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 41-178 9.35e-13

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: 64.86  E-value: 9.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  41 MEIFIKAAK--LRGDALDHLLIFGPPGLGKTTLANIVANE---MGVNLRTTSGPVLEKAGDLA-----------AMLTNL 104
Cdd:cd00009    3 QEEAIEALReaLELPPPKNLLLYGPPGTGKTTLARAIANElfrPGAPFLYLNASDLLEGLVVAelfghflvrllFELAEK 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446490666 105 EPHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGpaarsikidlppFTLIGATTRA--GSLTSPLRDRFGIV 178
Cdd:cd00009   83 AKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDREN------------VRVIGATNRPllGDLDRALYDRLDIR 146
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 57-182 9.33e-08

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: 50.83  E-value: 9.33e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666    57 HLLIFGPPGLGKTTLANIVANEMGVN-----------------------LRTTSGPVLEKAGDLAAMLTNLE--PHDVLF 111
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPgggviyidgedileevldqllliIVGGKKASGSGELRLRLALALARklKPDVLI 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446490666   112 IDEIHRLSPVVEEVLYPAMEDYQLDIMigegpaarsiKIDLPPFTLIGATTRAG-SLTSPLRDRFGIVQRLE 182
Cdd:smart00382  84 LDEITSLLDAEQEALLLLLEELRLLLL----------LKSEKNLTVILTTNDEKdLGPALLRRRFDRRIVLL 145
 
Name Accession Description Interval E-value
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 1-334 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: 670.64  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   1 MIEADRLISAGTTlPEDVADRAIRPKLLEEYVGQPQVRSQMEIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMG 80
Cdd:COG2255    1 MAEEDRLSSSASE-EEDALERSLRPKRLDEYIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLAHIIANEMG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  81 VNLRTTSGPVLEKAGDLAAMLTNLEPHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGPAARSIKIDLPPFTLIGA 160
Cdd:COG2255   80 VNIRITSGPAIEKPGDLAAILTNLEEGDVLFIDEIHRLSRVVEEILYPAMEDFRLDIVIGKGPAARSIRLDLPPFTLVGA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 161 TTRAGSLTSPLRDRFGIVQRLEFYQVPDLQYIVSRSARFMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEVKHDG 240
Cdd:COG2255  160 TTRAGLLTSPLRDRFGIVLRLEFYTVEELAEIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDG 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 241 TISADIAAQALDMLNVDAEGFDYMDRKLLLAVIDKFFGGPVGLDNLAAAIGEERETIEDVLEPYLIQQGFLQRTPRGRMA 320
Cdd:COG2255  240 VITLEIADAALELLEVDELGLDEMDRRILETIIEKFGGGPVGLETLAAALGEERDTIEDVYEPYLIQQGFLQRTPRGRVA 319

                        330
                 ....*....|....
gi 446490666 321 TTRAWNHFGITPPE 334
Cdd:COG2255  320 TPKAYEHLGLKPPE 333
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
6-332 0e+00

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 658.36  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   6 RLISAGTTLPED-VADRAIRPKLLEEYVGQPQVRSQMEIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMGVNLR 84
Cdd:PRK00080   1 RLVSPETLEEEEdEIERSLRPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  85 TTSGPVLEKAGDLAAMLTNLEPHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGPAARSIKIDLPPFTLIGATTRA 164
Cdd:PRK00080  81 ITSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 165 GSLTSPLRDRFGIVQRLEFYQVPDLQYIVSRSARFMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEVKHDGTISA 244
Cdd:PRK00080 161 GLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITK 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 245 DIAAQALDMLNVDAEGFDYMDRKLLLAVIDKFFGGPVGLDNLAAAIGEERETIEDVLEPYLIQQGFLQRTPRGRMATTRA 324
Cdd:PRK00080 241 EIADKALDMLGVDELGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRGRVATPKA 320


                 ....*...
gi 446490666 325 WNHFGITP 332
Cdd:PRK00080 321 YEHLGLNP 328
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 26-330 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: 521.86  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   26 KLLEEYVGQPQVRSQMEIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVLEKAGDLAAMLTNLE 105
Cdd:TIGR00635   1 KLLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLAAILTNLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  106 PHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGPAARSIKIDLPPFTLIGATTRAGSLTSPLRDRFGIVQRLEFYQ 185
Cdd:TIGR00635  81 EGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRDRFGIILRLEFYT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  186 VPDLQYIVSRSARFMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEVKHDGTISADIAAQALDMLNVDAEGFDYMD 265
Cdd:TIGR00635 161 VEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMIDELGLDEID 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446490666  266 RKLLLAVIDKFFGGPVGLDNLAAAIGEERETIEDVLEPYLIQQGFLQRTPRGRMATTRAWNHFGI 330
Cdd:TIGR00635 241 RKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRGRIATELAYEHLGL 305
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 23-181 3.36e-119

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: 340.25  E-value: 3.36e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   23 IRPKLLEEYVGQPQVRSQMEIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVLEKAGDLAAMLT 102
Cdd:pfam05496   1 LRPRTLDEYIGQEKVKENLKIFIEAAKQRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPAIERPGDLAAILT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446490666  103 NLEPHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGPAARSIKIDLPPFTLIGATTRAGSLTSPLRDRFGIVQRL 181
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 ...
 184-257 3.91e-37

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: 127.94  E-value: 3.91e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446490666  184 YQVPDLQYIVSRSARFMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEVKHDGTISADIAAQALDMLNVD 257
Cdd:pfam17864   1 YSVEELELIVKRSARILGVEIDEEGAAEIARRSRGTPRIANRLLRRVRDFAQVKGDGRITLEIADAALDLLEVD 74
RuvB_C pfam05491
RuvB C-terminal winged helix domain; The RuvB protein makes up part of the RuvABC revolvasome ...
 259-329 3.90e-29

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: 106.87  E-value: 3.90e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446490666  259 EGFDYMDRKLLLAVIDKFFGGPVGLDNLAAAIGEERETIEDVLEPYLIQQGFLQRTPRGRMATTRAWNHFG 329
Cdd:pfam05491   2 YGLDELDINYLKTLYENFKGGPVGLDTLAAILGEDKDTIEDVIEPYLLRLGLIERTSRGRIITPKGYKYLK 72
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 58-182 1.40e-24

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: 96.51  E-value: 1.40e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGP------VLEKAGDLAAMLTNLEPH--DVLFIDEIHRLSP--------- 120
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSelvskyVGESEKRLRELFEAAKKLapCVIFIDEIDALAGsrgsggdse 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446490666  121 --VVEEVLYPAMEDYQLDImigegpaarsikidlPPFTLIGATTRAGSLTSPLRDRFGIVQRLE 182
Cdd:pfam00004  81 srRVVNQLLTELDGFTSSN---------------SKVIVIAATNRPDKLDPALLGRFDRIIEFP 129
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 19-174 9.14e-22

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 95.15  E-value: 9.14e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  19 ADRaIRPKLLEEYVGQPQVRSQMEIFIKAakLRGDALDHLLIFGPPGLGKTTLANIVANEMGVNLR----TTSGpV--LE 92
Cdd:PRK13342   3 AER-MRPKTLDEVVGQEHLLGPGKPLRRM--IEAGRLSSMILWGPPGTGKTTLARIIAGATDAPFEalsaVTSG-VkdLR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  93 KAGDLAAMLTNLEPHDVLFIDEIHRLSPVVEEVLYPAMEDYQldimigegpaarsikidlppFTLIGATTRAGS--LTSP 170
Cdd:PRK13342  79 EVIEEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVEDGT--------------------ITLIGATTENPSfeVNPA 138


                 ....
gi 446490666 171 LRDR 174
Cdd:PRK13342 139 LLSR 142
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 19-252 5.53e-17

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 81.26  E-value: 5.53e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  19 ADRaIRPKLLEEYVGQPQVRSQMEIFIKAakLRGDALDHLLIFGPPGLGKTTLANIVANEMGVNLR----TTSGpV--LE 92
Cdd:COG2256   16 AER-MRPRTLDEVVGQEHLLGPGKPLRRA--IEAGRLSSMILWGPPGTGKTTLARLIANATDAEFValsaVTSG-VkdIR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  93 KAGDLAAMLTNLEPHDVLFIDEIHRLSPVVEEVLYPAMEDyqldimigegpaaRSIkidlppfTLIGATTRAGS--LTSP 170
Cdd:COG2256   92 EVIEEARERRAYGRRTILFVDEIHRFNKAQQDALLPHVED-------------GTI-------TLIGATTENPSfeVNSA 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 171 LRDRfgiVQRLEFYQV--PDLQYIVSR----SARFMG---LEMSDDGALEVARRARGTPRIANRLLRRVRDFAEVKHDGT 241
Cdd:COG2256  152 LLSR---CRVFVLKPLseEDLEQLLERaladDERGLGgykLELDDEALEALARLADGDARRALNALELAVLSAPPDGVIE 228

                        250
                 ....*....|.
gi 446490666 242 ISADIAAQALD 252
Cdd:COG2256  229 ITLELVEEALQ 239
PRK13341 PRK13341
AAA family ATPase;
19-293 2.16e-13

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 70.85  E-value: 2.16e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  19 ADRaIRPKLLEEYVGQPQVRSQMEIFIKAakLRGDALDHLLIFGPPGLGKTTLANIVANEM------------GV-NLRT 85
Cdd:PRK13341  19 ADR-LRPRTLEEFVGQDHILGEGRLLRRA--IKADRVGSLILYGPPGVGKTTLARIIANHTrahfsslnavlaGVkDLRA 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  86 tsgpVLEKAGDlaamltNLEPHD---VLFIDEIHRLSPVVEEVLYPAMEDYQLdimigegpaarsikidlppfTLIGATT 162
Cdd:PRK13341  96 ----EVDRAKE------RLERHGkrtILFIDEVHRFNKAQQDALLPWVENGTI--------------------TLIGATT 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 163 RAGSltsplrdrFGIVQRLefyqvpdlqyiVSRSARFMGLEMSDDGALEVARRArgtprianrLLRRVRDFAEVKHDgtI 242
Cdd:PRK13341 146 ENPY--------FEVNKAL-----------VSRSRLFRLKSLSDEDLHQLLKRA---------LQDKERGYGDRKVD--L 195

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446490666 243 SADIAAQALDMLNVDAegfdymdRKLLLA---VIDKFFGGPVGLDNLAAAIGEE 293
Cdd:PRK13341 196 EPEAEKHLVDVANGDA-------RSLLNAlelAVESTPPDEDGLIDITLAIAEE 242
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 41-178 9.35e-13

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: 64.86  E-value: 9.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  41 MEIFIKAAK--LRGDALDHLLIFGPPGLGKTTLANIVANE---MGVNLRTTSGPVLEKAGDLA-----------AMLTNL 104
Cdd:cd00009    3 QEEAIEALReaLELPPPKNLLLYGPPGTGKTTLARAIANElfrPGAPFLYLNASDLLEGLVVAelfghflvrllFELAEK 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446490666 105 EPHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGpaarsikidlppFTLIGATTRA--GSLTSPLRDRFGIV 178
Cdd:cd00009   83 AKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDREN------------VRVIGATNRPllGDLDRALYDRLDIR 146
MoxR COG0714
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway ...
 20-255 2.88e-09

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: 57.10  E-value: 2.88e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  20 DRAIRPKLLEEYVGQPQVRSQMEIfikAAKLRGdaldHLLIFGPPGLGKTTLANIVANEMGVNLRT---TS--------- 87
Cdd:COG0714    3 EARLRAEIGKVYVGQEELIELVLI---ALLAGG----HLLLEGVPGVGKTTLAKALARALGLPFIRiqfTPdllpsdilg 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  88 ---------------GPVLekagdlaamltnlepHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGPAArsikidl 152
Cdd:COG0714   76 tyiydqqtgefefrpGPLF---------------ANVLLADEINRAPPKTQSALLEAMEERQVTIPGGTYKLP------- 133

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 153 PPFTLIgAT--------TRAgsLTSPLRDRFGIVQRLEFYQVPDLQYIVSRSARFM------GLEMSDDGAL-EVARRAR 217
Cdd:COG0714  134 EPFLVI-ATqnpieqegTYP--LPEAQLDRFLLKLYIGYPDAEEEREILRRHTGRHlaevepVLSPEELLALqELVRQVH 210

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 446490666 218 GTPRIAN---RLLRRVRDFAEVKH----DGTISADIAAQALDMLN 255
Cdd:COG0714  211 VSEAVLDyivDLVRATREHPDLRKgpspRASIALLRAARALALLD 255
PRK14962 PRK14962
DNA polymerase III subunits gamma and tau; Provisional
 21-302 1.31e-08

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237869 [Multi-domain]  Cd Length: 472  Bit Score: 55.93  E-value: 1.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  21 RAIRPKLLEEYVGQPQVRsqmEIFIKAAKLrgDALDHLLIF-GPPGLGKTTLANIVANEMGVNLRTTSGPVLEKAGDLAa 99
Cdd:PRK14962   6 RKYRPKTFSEVVGQDHVK---KLIINALKK--NSISHAYIFaGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRS- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 100 mLTNLEPHDVL--------FIDEIHRLSpvvEEVLY-PAMEDYQLDI------MIGEGPAARSIKIDLPP--FTLIGATT 162
Cdd:PRK14962  80 -IDEGTFMDVIeldaasnrGIDEIRKIR---DAVGYrPMEGKYKVYIidevhmLTKEAFNALLKTLEEPPshVVFVLATT 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 163 RAGSLTSPLRDRfgiVQRLEFYQVPDlQYIVSR---SARFMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEvkhd 239
Cdd:PRK14962 156 NLEKVPPTIISR---CQVIEFRNISD-ELIIKRlqeVAEAEGIEIDREALSFIAKRASGGLRDALTMLEQVWKFSE---- 227

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446490666 240 GTISADIAAQAL---------DMLNVDAEGfdymDRKLLLAVIDKFFGGPVGLDNLAaaigeeRETIEDVLE 302
Cdd:PRK14962 228 GKITLETVHEALglipievvrDYINAIFNG----DVKRVFTVLDDVYYSGKDYEVLI------QQAIEDLVE 289
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 58-176 2.39e-08

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: 52.68  E-value: 2.39e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL---------EKAGDLAAMLTNLEPhDVLFIDEIHRLSPVVEEVLYP 128
Cdd:cd19503   37 VLLHGPPGTGKTLLARAVANEAGANFLSISGPSIvskylgeseKNLREIFEEARSHAP-SIIFIDEIDALAPKREEDQRE 115

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446490666 129 A---MEDYQLDIMIGEGPAARSIkidlppftLIGATTRAGSLTSPLRdRFG 176
Cdd:cd19503  116 VerrVVAQLLTLMDGMSSRGKVV--------VIAATNRPDAIDPALR-RPG 157
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 57-175 3.01e-08

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: 51.91  E-value: 3.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   57 HLLIFGPPGLGKTTLANIVANemgvnlRTTSGPVLEKAG-------------DLAAMLTNLEPH---------DVLFIDE 114
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAA------ALSNRPVFYVQLtrdtteedlfgrrNIDPGGASWVDGplvraaregEIAVLDE 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446490666  115 IHRLSPVVEEVLYPAMEDYQLDIMIGEGPaarsIKIDLPPFTLIGATTRAG----SLTSPLRDRF 175
Cdd:pfam07728  75 INRANPDVLNSLLSLLDERRLLLPDGGEL----VKAAPDGFRLIATMNPLDrglnELSPALRSRF 135
PRK04195 PRK04195
replication factor C large subunit; Provisional
 24-80 4.55e-08

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 54.16  E-value: 4.55e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446490666  24 RPKLLEEYVGQPQVRSQMEIFIKAAkLRGDALDHLLIFGPPGLGKTTLANIVANEMG 80
Cdd:PRK04195   9 RPKTLSDVVGNEKAKEQLREWIESW-LKGKPKKALLLYGPPGVGKTSLAHALANDYG 64
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
28-255 5.73e-08

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 52.96  E-value: 5.73e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  28 LEEYVGQPQVRSQMEIFIK----AAKLRGDAL---DHLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL--EKAGDLA 98
Cdd:COG1223    1 LDDVVGQEEAKKKLKLIIKelrrRENLRKFGLwppRKILFYGPPGTGKTMLAEALAGELKLPLLTVRLDSLigSYLGETA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  99 AMLTNL------EPHdVLFIDEIHRLSpvveevlypAMEDYQLDimIGEGpaARSI-----KIDLPP--FTLIGATTRAG 165
Cdd:COG1223   81 RNLRKLfdfarrAPC-VIFFDEFDAIA---------KDRGDQND--VGEV--KRVVnallqELDGLPsgSVVIAATNHPE 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 166 SLTSPLRDRFGivQRLEFyQVPD---LQYIVSRSARFMGLEMSDDgALEVARRARG-TPRIANRLLRRVRDFAEVKHDGT 241
Cdd:COG1223  147 LLDSALWRRFD--EVIEF-PLPDkeeRKEILELNLKKFPLPFELD-LKKLAKKLEGlSGADIEKVLKTALKKAILEDREK 222

                        250
                 ....*....|....
gi 446490666 242 ISADIAAQALDMLN 255
Cdd:COG1223  223 VTKEDLEEALKQRK 236
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 57-182 9.33e-08

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: 50.83  E-value: 9.33e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666    57 HLLIFGPPGLGKTTLANIVANEMGVN-----------------------LRTTSGPVLEKAGDLAAMLTNLE--PHDVLF 111
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPgggviyidgedileevldqllliIVGGKKASGSGELRLRLALALARklKPDVLI 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446490666   112 IDEIHRLSPVVEEVLYPAMEDYQLDIMigegpaarsiKIDLPPFTLIGATTRAG-SLTSPLRDRFGIVQRLE 182
Cdd:smart00382  84 LDEITSLLDAEQEALLLLLEELRLLLL----------LKSEKNLTVILTTNDEKdLGPALLRRRFDRRIVLL 145
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 3-251 2.46e-07

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: 51.84  E-value: 2.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   3 EADRLISAGTTLPEDVADRAIRPKLLEEYVGQPQVRSQMEIFIKAAKLRGDALD--------HLLIFGPPGLGKTTLANI 74
Cdd:COG0464  131 LAAPLVTYEDIGGLEEELLELREAILDDLGGLEEVKEELRELVALPLKRPELREeyglppprGLLLYGPPGTGKTLLARA 210

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  75 VANEMGVNLRTTSGPVL--------EKAgdLAAMLTNLEPHD--VLFIDEIHRLSP------------VVEEVLYpAMED 132
Cdd:COG0464  211 LAGELGLPLIEVDLSDLvskyvgetEKN--LREVFDKARGLApcVLFIDEADALAGkrgevgdgvgrrVVNTLLT-EMEE 287

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 133 YQldimigegpaarsikidlPPFTLIGATTRAGSLTSPLRDRFGIVQRLEFYQVPDLQYIVSRSARfmGLEMSDDGALE- 211
Cdd:COG0464  288 LR------------------SDVVVIAATNRPDLLDPALLRRFDEIIFFPLPDAEERLEIFRIHLR--KRPLDEDVDLEe 347

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 446490666 212 -VARRARGTPRIANRLLRRVRDFAEVKHDGTISADIAAQAL 251
Cdd:COG0464  348 lAEATEGLSGADIRNVVRRAALQALRLGREPVTTEDLLEAL 388
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 58-250 5.57e-07

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: 51.06  E-value: 5.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL------EKAGDLAAMLTNLEPH--DVLFIDEIHRLSPVVEEV---L 126
Cdd:TIGR01243 215 VLLYGPPGTGKTLLAKAVANEAGAYFISINGPEImskyygESEERLREIFKEAEENapSIIFIDEIDAIAPKREEVtgeV 294

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  127 YPAMEDYQLDIMIGEGPAARSIkidlppftLIGATTRAGSLTSPLRdRFGIVQRLEFYQVPDlqyivsRSARFMGLEMsd 206
Cdd:TIGR01243 295 EKRVVAQLLTLMDGLKGRGRVI--------VIGATNRPDALDPALR-RPGRFDREIVIRVPD------KRARKEILKV-- 357

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 446490666  207 dgalevarRARGTPRIANRLLRRVrdfAEVKHdGTISADIAAQA 250
Cdd:TIGR01243 358 --------HTRNMPLAEDVDLDKL---AEVTH-GFVGADLAALA 389
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 58-131 1.15e-06

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: 47.66  E-value: 1.15e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNL-RTTSGPVLEKA-GDLAAMLTNL------EPHDVLFIDEIHRLSPVVEEVLYPA 129
Cdd:cd19481   29 ILLYGPPGTGKTLLAKALAGELGLPLiVVKLSSLLSKYvGESEKNLRKIferarrLAPCILFIDEIDAIGRKRDSSGESG 108


                 ..
gi 446490666 130 ME 131
Cdd:cd19481  109 EL 110
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 58-172 2.09e-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: 47.01  E-value: 2.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL---------EKAGDLAAMLTNLEPHdVLFIDEIHRLSPvVEEVLYP 128
Cdd:cd19518   37 VLLHGPPGCGKTMLANAIAGELKVPFLKISATEIvsgvsgeseEKIRELFDQAISNAPC-IVFIDEIDAITP-KRESAQR 114

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446490666 129 AMEDY---QL----DIMIGEGPAARSIKIdlppftlIGATTRAGSLTSPLR 172
Cdd:cd19518  115 EMERRivsQLltcmDELNNEKTAGGPVLV-------IGATNRPDSLDPALR 158
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 58-180 2.13e-06

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: 47.05  E-value: 2.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL------EKAGDLAAMLTNLEPH--DVLFIDEIHRLSPVVEEV---L 126
Cdd:cd19519   37 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEImsklagESESNLRKAFEEAEKNapAIIFIDEIDAIAPKREKThgeV 116

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446490666 127 YPAMEDYQLDIMigEGPAARSIKIdlppftLIGATTRAGSLTSPLRdRFGIVQR 180
Cdd:cd19519  117 ERRIVSQLLTLM--DGLKQRAHVI------VMAATNRPNSIDPALR-RFGRFDR 161
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 58-120 4.52e-06

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: 45.95  E-value: 4.52e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL--------EKA-GDLAAMLTNLEPhDVLFIDEIHRLSP 120
Cdd:cd19529   30 ILLYGPPGTGKTLLAKAVATESNANFISVKGPELlskwvgesEKAiREIFRKARQVAP-CVIFFDEIDSIAP 100
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 24-78 7.30e-06

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 47.29  E-value: 7.30e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446490666  24 RPKLLEEYVGQPQVRSQMEIFIKAAKLrgdalDHLLIFGPPGLGKTTLANIVANE 78
Cdd:PRK12402  10 RPALLEDILGQDEVVERLSRAVDSPNL-----PHLLVQGPPGSGKTAAVRALARE 59
rfc PRK00440
replication factor C small subunit; Reviewed
 24-79 8.21e-06

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 46.79  E-value: 8.21e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446490666  24 RPKLLEEYVGQPQVRSQMEIFIKAaklrgDALDHLLIFGPPGLGKTTLANIVANEM 79
Cdd:PRK00440  12 RPRTLDEIVGQEEIVERLKSYVKE-----KNMPHLLFAGPPGTGKTTAALALAREL 62
DnaA COG0593
Chromosomal replication initiation ATPase DnaA [Replication, recombination and repair];
58-252 1.12e-05

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


Pssm-ID: 440358 [Multi-domain]  Cd Length: 303  Bit Score: 46.34  E-value: 1.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNLR-------TTSGPVLE-----KAGDLAAMLTNLEPHDVLFIDEIHRLS--PVVE 123
Cdd:COG0593   37 LFLYGGVGLGKTHLLHAIGNEALENNPgarvvylTAEEFTNDfinaiRNNTIEEFKEKYRSVDVLLIDDIQFLAgkEATQ 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 124 EVLYpamedYQLDIMIGEGpaaRSIKI--DLPPFTLIGATTRagsltspLRDRF--GIVQRLefyQVPDL----QYIVSR 195
Cdd:COG0593  117 EEFF-----HTFNALREAG---KQIVLtsDRPPKELPGLEER-------LRSRLewGLVVDI---QPPDLetriAILRKK 178

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446490666 196 SARfMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEVKHDgTISADIAAQALD 252
Cdd:COG0593  179 AAD-RGLELPDEVLEYLARRIERNVRELEGALNRLDAYALLTGR-PITLELAREVLK 233
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 59-120 1.88e-05

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


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 44.20  E-value: 1.88e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446490666  59 LIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL--------EKA-GDLAAMLTNLEPhDVLFIDEIHRLSP 120
Cdd:cd19511   31 LLYGPPGCGKTLLAKALASEAGLNFISVKGPELfskyvgesERAvREIFQKARQAAP-CIIFFDEIDSLAP 100
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 17-118 2.27e-05

Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is the catalytic subunit of the Katanin complex which is severs microtubules in an ATP-dependent manner, and is implicated in multiple aspects of microtubule dynamics. In addition to the p60 catalytic ATPase subunit, Katanin contains an accessory subunit (p80 or p80-like). The microtubule-severing activity of the ATPase is essential for female meiotic spindle assembly, and male gamete production; and the katanin complex severing microtubules is under tight regulation during the transition from the meiotic to mitotic stage to allow proper embryogenesis. 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: 410930 [Multi-domain]  Cd Length: 170  Bit Score: 44.20  E-value: 2.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  17 DVADRAIRPKLLEEYVGQPQVrsqMEIFIKAAK--LRGdaldhLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL--- 91
Cdd:cd19522    1 DIADLEEAKKLLEEAVVLPMW---MPEFFKGIRrpWKG-----VLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLtsk 72

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446490666  92 -----EKAGDLAAMLTNLEPHDVLFIDEIHRL 118
Cdd:cd19522   73 yrgesEKLVRLLFEMARFYAPTTIFIDEIDSI 104
44 PHA02544
clamp loader, small subunit; Provisional
 24-134 2.41e-05

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 45.37  E-value: 2.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  24 RPKLLEEYVGQPQVRSQMEIFIKAAKLrgdalDHLLIFGP-PGLGKTTLANIVANEMGV----------NLRTTSGPVLE 92
Cdd:PHA02544  16 RPSTIDECILPAADKETFKSIVKKGRI-----PNMLLHSPsPGTGKTTVAKALCNEVGAevlfvngsdcRIDFVRNRLTR 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 446490666  93 kagdLAAMLTNLEPHDVLFIDEIHRLS-PVVEEVLYPAMEDYQ 134
Cdd:PHA02544  91 ----FASTVSLTGGGKVIIIDEFDRLGlADAQRHLRSFMEAYS 129
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 58-188 2.90e-05

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: 45.67  E-value: 2.90e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGP----------------VLEKAGDLAAMltnlephdVLFIDEIHRLSPV 121
Cdd:TIGR01243 490 VLLFGPPGTGKTLLAKAVATESGANFIAVRGPeilskwvgesekaireIFRKARQAAPA--------IIFFDEIDAIAPA 561

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446490666  122 VEEVLYPAMEDYQLDIMIGEGPAArsikIDLPPFTLIGATTRAGSLtSPLRDRFGIVQRLEFYQVPD 188
Cdd:TIGR01243 562 RGARFDTSVTDRIVNQLLTEMDGI----QELSNVVVIAATNRPDIL-DPALLRPGRFDRLILVPPPD 623
PRK06921 PRK06921
hypothetical protein; Provisional
 22-138 6.04e-05

hypothetical protein; Provisional


Pssm-ID: 180750 [Multi-domain]  Cd Length: 266  Bit Score: 44.00  E-value: 6.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  22 AIRPKLLEEYV--GQPQVRSQM-----EIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMgvnLRTTSGPVL--- 91
Cdd:PRK06921  77 AFRKLTFKNFKteGKPQAIKDAyecavEYVKDFEKIQESRKNSIALLGQPGSGKTHLLTAAANEL---MRKKGVPVLyfp 153

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446490666  92 --EKAGDLAAMLTNLEPH-------DVLFIDEIHRlsPVVEEvlyPAMEDYQLDIM 138
Cdd:PRK06921 154 fvEGFGDLKDDFDLLEAKlnrmkkvEVLFIDDLFK--PVNGK---PRATEWQIEQM 204
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 58-115 6.76e-05

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 44.23  E-value: 6.76e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGP-VLEK-AGDLAAMLTNL------EPHDVLFIDEI 115
Cdd:COG1222  115 VLLYGPPGTGKTLLAKAVAGELGAPFIRVRGSeLVSKyIGEGARNVREVfelareKAPSIIFIDEI 180
AAA_3 pfam07726
ATPase family associated with various cellular activities (AAA); This Pfam entry includes some ...
 57-137 9.43e-05

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: 41.77  E-value: 9.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   57 HLLIFGPPGLGKTTLANIVANEMGVNL-RTTSGPVLEKAGDLAAMLTNLE---------P--HDVLFIDEIHRLSPVVEE 124
Cdd:pfam07726   1 HVLLEGVPGLAKTLLVRTLARSLGLDFrRIQFTPDLLPSDITGTEVFDQKtrefefrpgPvfANVLLADEINRAPPKTQS 80

                          90
                  ....*....|...
gi 446490666  125 VLYPAMEDYQLDI 137
Cdd:pfam07726  81 ALLEAMQERQVTI 93
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 58-91 9.55e-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: 42.11  E-value: 9.55e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL 91
Cdd:cd19528   30 VLFYGPPGCGKTLLAKAIANECQANFISVKGPEL 63
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 17-118 1.07e-04

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


Pssm-ID: 410932 [Multi-domain]  Cd Length: 164  Bit Score: 42.14  E-value: 1.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  17 DVADRAIRPKLLEEYVGQPQVRSQMEIFIKAAKlRGdaldhLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVLEK--A 94
Cdd:cd19524    1 DIAGQDLAKQALQEMVILPSLRPELFTGLRAPA-RG-----LLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSkyV 74

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446490666  95 GD-------LAAMLTNLEPhDVLFIDEIHRL 118
Cdd:cd19524   75 GEgeklvraLFAVARELQP-SIIFIDEVDSL 104
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 58-91 1.56e-04

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


Pssm-ID: 410938 [Multi-domain]  Cd Length: 161  Bit Score: 41.70  E-value: 1.56e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL 91
Cdd:cd19530   33 VLLYGPPGCGKTLLAKAVANESGANFISVKGPEL 66
Rad17 pfam03215
Rad17 P-loop domain;
15-96 2.20e-04

Rad17 P-loop domain;


Pssm-ID: 367398 [Multi-domain]  Cd Length: 186  Bit Score: 41.48  E-value: 2.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666   15 PEDVADRAIRPKLLEEyvgqpqvrsqMEIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVLEKA 94
Cdd:pfam03215  15 PNCLEQLAVHKRKIKD----------VQEWLDAMFLENAKHRILLISGPSGCGKSTVIKELSKELGPKYREWSNPTSFRS 84


                  ..
gi 446490666   95 GD 96
Cdd:pfam03215  85 PP 86
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 58-118 2.47e-04

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


Pssm-ID: 410917 [Multi-domain]  Cd Length: 163  Bit Score: 41.18  E-value: 2.47e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL--------EKAGDLAAMLTNLEPHDVLFIDEIHRL 118
Cdd:cd19509   35 ILLYGPPGTGKTLLARAVASESGSTFFSISASSLvskwvgesEKIVRALFALARELQPSIIFIDEIDSL 103
PRK14953 PRK14953
DNA polymerase III subunits gamma and tau; Provisional
 21-76 2.73e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237867 [Multi-domain]  Cd Length: 486  Bit Score: 42.50  E-value: 2.73e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446490666  21 RAIRPKLLEEYVGQPQVrsqMEIFIKAAKLrgDALDHLLIF-GPPGLGKTTLANIVA 76
Cdd:PRK14953   8 RKYRPKFFKEVIGQEIV---VRILKNAVKL--QRVSHAYIFaGPRGTGKTTIARILA 59
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 15-93 3.12e-04

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


Pssm-ID: 129690 [Multi-domain]  Cd Length: 637  Bit Score: 42.64  E-value: 3.12e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446490666   15 PEDVADRAIRPKLLEEyvgqpqvrsqMEIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVLEK 93
Cdd:TIGR00602  80 PETQHELAVHKKKIEE----------VETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELGIQVQEWSNPTLPD 148
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
 16-181 3.50e-04

ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; it may be involved in DNA double-strand break repair via homologous recombination. Caenorhabditis elegans FIGL-1 is a nuclear protein and controls the mitotic progression in the germ line and mouse FIGL-1 may be involved in the control of male meiosis. human FIGL-1 has been shown to be a centrosome protein involved in ciliogenesis perhaps as a microtubule-severing protein. 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: 410933 [Multi-domain]  Cd Length: 186  Bit Score: 41.13  E-value: 3.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  16 EDVADRAIRPKLLEEYVGQPQVRSqmEIFikaAKLRGDAlDHLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL---- 91
Cdd:cd19525   22 ADIAGLEFAKKTIKEIVVWPMLRP--DIF---TGLRGPP-KGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLtskw 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  92 ----EKAGDLAAMLTNLEPHDVLFIDEIHRLSPVVEEvlypamedyqldimiGEGPAARSIKIDL------------PPF 155
Cdd:cd19525   96 vgegEKMVRALFSVARCKQPAVIFIDEIDSLLSQRGE---------------GEHESSRRIKTEFlvqldgattsseDRI 160

                        170       180
                 ....*....|....*....|....*.
gi 446490666 156 TLIGATTRAGSLTSPLRDRFgiVQRL 181
Cdd:cd19525  161 LVVGATNRPQEIDEAARRRL--VKRL 184
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 58-120 5.45e-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: 40.10  E-value: 5.45e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVL---------EKAGDLAAMLTNLEPHdVLFIDEIHRLSP 120
Cdd:cd19526   30 ILLYGPPGCGKTLLASAIASECGLNFISVKGPELlnkyigaseQNVRDLFSRAQSAKPC-ILFFDEFDSIAP 100
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 58-175 6.11e-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: 39.85  E-value: 6.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGP--VLEKAGDLAAMLTNL------EPHDVLFIDEIHRLSPVVEEvlypa 129
Cdd:cd19521   43 ILLYGPPGTGKSYLAKAVATEANSTFFSVSSSdlVSKWMGESEKLVKQLfamareNKPSIIFIDEVDSLCGTRGE----- 117

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446490666 130 medyqldimiGEGPAARSIKIDL-----------PPFTLIGATTRAGSLTSPLRDRF 175
Cdd:cd19521  118 ----------GESEASRRIKTELlvqmngvgndsQGVLVLGATNIPWQLDSAIRRRF 164
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 58-115 1.05e-03

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: 39.33  E-value: 1.05e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMG---VNLRTTS------GPVLEKAGDLAAMLTNLEPhDVLFIDEI 115
Cdd:cd19520   38 VLLYGPPGCGKTMLAKATAKEAGarfINLQVSSltdkwyGESQKLVAAVFSLASKLQP-SIIFIDEI 103
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 18-257 1.93e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 39.86  E-value: 1.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  18 VADRAIRPKLLEEYVGQPQVRSQMEIFIKAAKLRgdalDHLLIFGPPGLGKTTLANIVA---NEMGVN------------ 82
Cdd:PRK14970   6 VSARKYRPQTFDDVVGQSHITNTLLNAIENNHLA----QALLFCGPRGVGKTTCARILArkiNQPGYDdpnedfsfnife 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  83 LRTTSGPVLEKAGDLAAMLtNLEP----HDVLFIDEIHRLSPVVEEVLYPAMEDyqldimigegPAARSIkidlppftLI 158
Cdd:PRK14970  82 LDAASNNSVDDIRNLIDQV-RIPPqtgkYKIYIIDEVHMLSSAAFNAFLKTLEE----------PPAHAI--------FI 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 159 GATTRAGSLTSPLRDRfgiVQRLEF--YQVPDLQYIVSRSARFMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEv 236
Cdd:PRK14970 143 LATTEKHKIIPTILSR---CQIFDFkrITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFDRVVTFCG- 218

                        250       260
                 ....*....|....*....|.
gi 446490666 237 khdGTISADIAAQALDMLNVD 257
Cdd:PRK14970 219 ---KNITRQAVTENLNILDYD 236
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 58-120 2.39e-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: 38.26  E-value: 2.39e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446490666  58 LLIFGPPGLGKTTLANIVANEMGVNLRTTSGP----------------VLEKAGDLAAMltnlephdVLFIDEIHRLSP 120
Cdd:cd19527   29 ILLYGPPGTGKTLLAKAIATECSLNFLSVKGPelinmyigeseanvreVFQKARDAKPC--------VIFFDELDSLAP 99
PRK04132 PRK04132
replication factor C small subunit; Provisional
 24-114 3.14e-03

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 39.44  E-value: 3.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  24 RPKLLEEYVGQPQVRSQMEIFIKAAklrgdALDHLLIFGPPGLGK--TTLANIVANEmgvNLRTTsGPVLEKAGDLAAML 101
Cdd:PRK04132  14 RPQRLDDIVGQEHIVKRLKHYVKTG-----SMPHLLFAGPPGVGKclTGDTKVIANG---ELFEI-GELVEKISNGKFGP 84

                         90
                 ....*....|...
gi 446490666 102 TNLEPHDVLFIDE 114
Cdd:PRK04132  85 TPVNGLKVLGIDE 97
PRK14954 PRK14954
DNA polymerase III subunits gamma and tau; Provisional
 109-274 3.19e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184918 [Multi-domain]  Cd Length: 620  Bit Score: 39.16  E-value: 3.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 109 VLFIDEIHRLSPVVEEVLYPAMEDyqldimigegPAARSIkidlppftLIGATTRAGSLTSPLRDRfgiVQRLEFYQVP- 187
Cdd:PRK14954 130 VYIIDEVHMLSTAAFNAFLKTLEE----------PPPHAI--------FIFATTELHKIPATIASR---CQRFNFKRIPl 188

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 188 -DLQYIVSRSARFMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEVKHDGTIsadIAAQALdmlnvdAEGFDYMDR 266
Cdd:PRK14954 189 dEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDAQSILDQVIAFSVGSEAEKV---IAYQGV------AELLNYIDD 259


                 ....*...
gi 446490666 267 KLLLAVID 274
Cdd:PRK14954 260 EQFFDVTD 267
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
25-276 4.08e-03

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 38.63  E-value: 4.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  25 PKLLEEYVGQPQVrsqMEIFIKAakLRGDALDHLLIF-GPPGLGKTTLANIVAneMGVNlrTTSGPVLEKAGDLAAMLTN 103
Cdd:COG2812    6 PQTFDDVVGQEHV---VRTLKNA--LASGRLAHAYLFtGPRGVGKTTLARILA--KALN--CENGPTGEPCGECESCRAI 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 104 LEPH--DVLFI---------DEIHRLspvVEEVLYPAMED-YQldIMIgegpaarsikIDL------------------- 152
Cdd:COG2812   77 AAGShpDVIEIdaeasnigvDDIREL---IEKVSYAPVEGrYK--VYI----------IDEahmltteafnallktleep 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 153 PPFTL-IGATTRAGSL--TspLRDRfgiVQRLEFYQVPD------LQYIVSRSarfmGLEMSDDGALEVARRARGTPRIA 223
Cdd:COG2812  142 PPHVVfILATTEPQKLlpT--ILSR---CQRFDFRRLPPeeiaehLAKIAERE----GIEIEPEALALIARAADGSMRDA 212

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446490666 224 NRLLRRVRDFAEVkhdgtisaDIAAQALDMLNVDAEGfdymDRKLLLAVIDKF 276
Cdd:COG2812  213 LSLLDQAIAFGLL--------DRRELLLDLLEALLAG----DVAALLALAEEL 253
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 32-80 4.46e-03

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: 38.44  E-value: 4.46e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446490666   32 VGQPQVRSQMEIF---IKAAKLRGDALdhlLIFGPPGLGKTTLANIVANEMG 80
Cdd:pfam06068  27 VGQEKAREAAGVIvemIKEGKIAGRAV---LIAGPPGTGKTALAIAISKELG 75
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 59-88 5.09e-03

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: 37.21  E-value: 5.09e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 446490666  59 LIFGPPGLGKTTLANIVANEMGVNLRTTSG 88
Cdd:cd19501   41 LLVGPPGTGKTLLAKAVAGEAGVPFFSISG 70
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
34-236 8.05e-03

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 37.65  E-value: 8.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666  34 QPQVRSQMEIFIKAAKLRGdaldHLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVLEKAGDLAAMLTN-----LEPH- 107
Cdd:COG0470    1 QEEAWEQLLAAAESGRLPH----ALLLHGPPGIGKTTLALALARDLLCENPEGGKACGQCHSRLMAAGNHpdlleLNPEe 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446490666 108 --DVLFIDEIHRLSP------------VVeeVLYPA--M-EDYQ---LDIMigEGPAARSikidlpPFTLIgaTTRAGSL 167
Cdd:COG0470   77 ksDQIGIDQIRELGEflsltpleggrkVV--IIDEAdaMnEAAAnalLKTL--EEPPKNT------PFILI--ANDPSRL 144

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446490666 168 TSPLRDRfgiVQRLEFYqVPDLQYIVSRsARFMGLEmsDDGALEVARRARGTPRIANRLLRRVRDFAEV 236
Cdd:COG0470  145 LPTIRSR---CQVIRFR-PPSEEEALAW-LREEGVD--EDALEAILRLAGGDPRAAINLLQALAGRKEL 206
 
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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