NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1007385652|ref|NP_001308119|]
View 

ruvB-like 2 isoform 2 [Homo sapiens]

Protein Classification

RuvB-like helicase( domain architecture ID 15918217)

RuvB-like helicase is a DNA helicase that plays an essential role in various complexes involved in fundamental processes such as transcription regulation, DNA damage response and apoptosis (via the chromatin remodelling complexes SWR1, INO80 and TIP60), maturation of small nuclear ribonucleoproteins, cellular development, cancer metastasis, and regulation of mitosis

EC:  3.6.4.12
Gene Ontology:  GO:0005524|GO:0003678|GO:0006259
PubMed:  10787406

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 7-331 0e+00

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: 575.41  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652   7 QASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALT 86
Cdd:pfam06068  21 YVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPFTSISGSEVYSLEMKKTEALT 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652  87 QAFRRSIGVRIKEETEIIEGEVVEIQI---DRPATG-TGSKVGKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITID 162
Cdd:pfam06068 101 QAFRKAIGVRIKEEKEVYEGEVVELEIeeaENPLSGgKTIKGGKITLKTTKMEKTLKLGPKIYEQLQKEKVSAGDVIYID 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 163 KATGKISKLGRSFTRARDYDAmgSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQI 242
Cdd:pfam06068 181 KNTGRVKKLGRSFARATDFDL--EATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARPQGILSLFSPKKGEITSELREEI 258

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 243 NAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLI 322
Cdd:pfam06068 259 NKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATNRGICTIRGTDIISPHGIPLDLLDRLLI 338


                  ....*....
gi 1007385652 323 VSTTPYSEK 331
Cdd:pfam06068 339 ITTEPYTRE 347
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 336-401 2.10e-28

TIP49 AAA-lid 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: 436097 [Multi-domain]  Cd Length: 66  Bit Score: 106.19  E-value: 2.10e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1007385652 336 ILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLD 401
Cdd:pfam17856   1 ILKIRAQEEGVKIDEEALDLLAKIGTETSLRYAIQLLTPASILAKKRGGKEVEVQDVEEAYELFLD 66
 
Name Accession Description Interval E-value
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 7-331 0e+00

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: 575.41  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652   7 QASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALT 86
Cdd:pfam06068  21 YVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPFTSISGSEVYSLEMKKTEALT 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652  87 QAFRRSIGVRIKEETEIIEGEVVEIQI---DRPATG-TGSKVGKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITID 162
Cdd:pfam06068 101 QAFRKAIGVRIKEEKEVYEGEVVELEIeeaENPLSGgKTIKGGKITLKTTKMEKTLKLGPKIYEQLQKEKVSAGDVIYID 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 163 KATGKISKLGRSFTRARDYDAmgSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQI 242
Cdd:pfam06068 181 KNTGRVKKLGRSFARATDFDL--EATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARPQGILSLFSPKKGEITSELREEI 258

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 243 NAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLI 322
Cdd:pfam06068 259 NKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATNRGICTIRGTDIISPHGIPLDLLDRLLI 338


                  ....*....
gi 1007385652 323 VSTTPYSEK 331
Cdd:pfam06068 339 ITTEPYTRE 347
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
11-417 1.53e-172

DNA helicase TIP49, TBP-interacting protein [Transcription];


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 490.64  E-value: 1.53e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652  11 GMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFR 90
Cdd:COG1224    39 GLVGQVEAREAAGIVVKMIKEGKMAGKGILIVGPPGTGKTALAVAIARELGEDTPFVAISGSEIYSAELKKTEFLMQALR 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652  91 RSIGVRIKEETEIIEGEVVEIQIDR---PATGTgSKV---GKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKA 164
Cdd:COG1224   119 KAIGVRVREKRKVYEGVVKEIKIRYarhPYNPY-VKVpreATITLATKDEEKTLTVGEEIAQQLVELGIRKGDVIWIDAE 197

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 165 TGKISKLGRS-FTRARDYDAmgSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQG-FLALFS-GDTGEIKSEVREQ 241
Cdd:COG1224   198 TGRVSKLGRAkGEGAKTYDI--ETKRIVEVPSGPVKKEKEIVRTLTLHDLDLYLAAQRAaFSALFGfFEEREIPSEVRKQ 275

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 242 INAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLL 321
Cdd:COG1224   276 VDELVKKWIEEGKAELVPGVLFIDDAHMLDIEAFSFLTRAMESELAPIIILATNRGITKIRGTDIESPHGIPLDLLDRLL 355

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 322 IVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLD 401
Cdd:COG1224   356 IIPTRPYTEDEIREIIKIRAEEEDIELSDDALEELTKIGVERSLRYAVQLLEPAYIIAKRRGRSKVTVEDVEEASKLFAD 435

                         410
                  ....*....|....*.
gi 1007385652 402 ESRSTQYMKEYQDAFL 417
Cdd:COG1224   436 VKESVEYVKEYEELFL 451
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 336-401 2.10e-28

TIP49 AAA-lid 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: 436097 [Multi-domain]  Cd Length: 66  Bit Score: 106.19  E-value: 2.10e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1007385652 336 ILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLD 401
Cdd:pfam17856   1 ILKIRAQEEGVKIDEEALDLLAKIGTETSLRYAIQLLTPASILAKKRGGKEVEVQDVEEAYELFLD 66
PRK14957 PRK14957
DNA polymerase III subunits gamma and tau; Provisional
 261-402 8.83e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184921 [Multi-domain]  Cd Length: 546  Bit Score: 47.77  E-value: 8.83e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 261 VLFIDEVHMLDIESFSFLNRALESDMAPV-LIMATnrgitrirgTSYqspHGIPIDLLDRLLIVSTTPYSEKDTKQILRI 339
Cdd:PRK14957  122 VYLIDEVHMLSKQSFNALLKTLEEPPEYVkFILAT---------TDY---HKIPVTILSRCIQLHLKHISQADIKDQLKI 189

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1007385652 340 RCEEEDVEMSEDAYTVLTRIGlETSLRYAIQLITAASLVCrkrkGTEVQVDDIKRVYSLFLDE 402
Cdd:PRK14957  190 ILAKENINSDEQSLEYIAYHA-KGSLRDALSLLDQAISFC----GGELKQAQIKQMLGIIDSE 247
DnaB_C cd00984
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ...
 39-83 6.29e-05

C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.


Pssm-ID: 410864 [Multi-domain]  Cd Length: 256  Bit Score: 44.43  E-value: 6.29e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1007385652  39 VLIAGQPGTGKTAIAMGMAQALGPDTPFTAIagseIFSLEMSKTE 83
Cdd:cd00984    22 IIIAARPSMGKTAFALNIAENIALDEGLPVL----FFSLEMSAEQ 62
DnaB TIGR00665
replicative DNA helicase; This model describes the helicase DnaB, a homohexameric protein ...
 39-83 3.81e-04

replicative DNA helicase; This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of > 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273206 [Multi-domain]  Cd Length: 432  Bit Score: 42.41  E-value: 3.81e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1007385652  39 VLIAGQPGTGKTAIAMGMAQ--ALGPDTPfTAIagseiFSLEMSKTE 83
Cdd:TIGR00665 197 IILAARPSMGKTAFALNIAEnaAIKEGKP-VAF-----FSLEMSAEQ 237
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 36-105 5.44e-03

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: 37.35  E-value: 5.44e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1007385652   36 GRAVLIAGQPGTGKTAIAMGMAQALGPDT-PFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIE 105
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGgGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALA 72
 
Name Accession Description Interval E-value
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 7-331 0e+00

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: 575.41  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652   7 QASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALT 86
Cdd:pfam06068  21 YVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPFTSISGSEVYSLEMKKTEALT 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652  87 QAFRRSIGVRIKEETEIIEGEVVEIQI---DRPATG-TGSKVGKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITID 162
Cdd:pfam06068 101 QAFRKAIGVRIKEEKEVYEGEVVELEIeeaENPLSGgKTIKGGKITLKTTKMEKTLKLGPKIYEQLQKEKVSAGDVIYID 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 163 KATGKISKLGRSFTRARDYDAmgSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQI 242
Cdd:pfam06068 181 KNTGRVKKLGRSFARATDFDL--EATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARPQGILSLFSPKKGEITSELREEI 258

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 243 NAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLI 322
Cdd:pfam06068 259 NKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATNRGICTIRGTDIISPHGIPLDLLDRLLI 338


                  ....*....
gi 1007385652 323 VSTTPYSEK 331
Cdd:pfam06068 339 ITTEPYTRE 347
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
11-417 1.53e-172

DNA helicase TIP49, TBP-interacting protein [Transcription];


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 490.64  E-value: 1.53e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652  11 GMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFR 90
Cdd:COG1224    39 GLVGQVEAREAAGIVVKMIKEGKMAGKGILIVGPPGTGKTALAVAIARELGEDTPFVAISGSEIYSAELKKTEFLMQALR 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652  91 RSIGVRIKEETEIIEGEVVEIQIDR---PATGTgSKV---GKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKA 164
Cdd:COG1224   119 KAIGVRVREKRKVYEGVVKEIKIRYarhPYNPY-VKVpreATITLATKDEEKTLTVGEEIAQQLVELGIRKGDVIWIDAE 197

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 165 TGKISKLGRS-FTRARDYDAmgSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQG-FLALFS-GDTGEIKSEVREQ 241
Cdd:COG1224   198 TGRVSKLGRAkGEGAKTYDI--ETKRIVEVPSGPVKKEKEIVRTLTLHDLDLYLAAQRAaFSALFGfFEEREIPSEVRKQ 275

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 242 INAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLL 321
Cdd:COG1224   276 VDELVKKWIEEGKAELVPGVLFIDDAHMLDIEAFSFLTRAMESELAPIIILATNRGITKIRGTDIESPHGIPLDLLDRLL 355

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 322 IVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLD 401
Cdd:COG1224   356 IIPTRPYTEDEIREIIKIRAEEEDIELSDDALEELTKIGVERSLRYAVQLLEPAYIIAKRRGRSKVTVEDVEEASKLFAD 435

                         410
                  ....*....|....*.
gi 1007385652 402 ESRSTQYMKEYQDAFL 417
Cdd:COG1224   436 VKESVEYVKEYEELFL 451
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 336-401 2.10e-28

TIP49 AAA-lid 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: 436097 [Multi-domain]  Cd Length: 66  Bit Score: 106.19  E-value: 2.10e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1007385652 336 ILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLD 401
Cdd:pfam17856   1 ILKIRAQEEGVKIDEEALDLLAKIGTETSLRYAIQLLTPASILAKKRGGKEVEVQDVEEAYELFLD 66
PRK14957 PRK14957
DNA polymerase III subunits gamma and tau; Provisional
 261-402 8.83e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184921 [Multi-domain]  Cd Length: 546  Bit Score: 47.77  E-value: 8.83e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 261 VLFIDEVHMLDIESFSFLNRALESDMAPV-LIMATnrgitrirgTSYqspHGIPIDLLDRLLIVSTTPYSEKDTKQILRI 339
Cdd:PRK14957  122 VYLIDEVHMLSKQSFNALLKTLEEPPEYVkFILAT---------TDY---HKIPVTILSRCIQLHLKHISQADIKDQLKI 189

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1007385652 340 RCEEEDVEMSEDAYTVLTRIGlETSLRYAIQLITAASLVCrkrkGTEVQVDDIKRVYSLFLDE 402
Cdd:PRK14957  190 ILAKENINSDEQSLEYIAYHA-KGSLRDALSLLDQAISFC----GGELKQAQIKQMLGIIDSE 247
DnaB_C pfam03796
DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at ...
 39-83 1.02e-05

DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.


Pssm-ID: 427509 [Multi-domain]  Cd Length: 254  Bit Score: 46.64  E-value: 1.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1007385652  39 VLIAGQPGTGKTAIAMGMAQ--ALGPDTPfTAiagseIFSLEMSKTE 83
Cdd:pfam03796  22 IIIAARPSMGKTAFALNIARnaAVKHKKP-VA-----IFSLEMSAEQ 62
DnaB_C cd00984
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ...
 39-83 6.29e-05

C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.


Pssm-ID: 410864 [Multi-domain]  Cd Length: 256  Bit Score: 44.43  E-value: 6.29e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1007385652  39 VLIAGQPGTGKTAIAMGMAQALGPDTPFTAIagseIFSLEMSKTE 83
Cdd:cd00984    22 IIIAARPSMGKTAFALNIAENIALDEGLPVL----FFSLEMSAEQ 62
PRK14953 PRK14953
DNA polymerase III subunits gamma and tau; Provisional
 261-376 7.37e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237867 [Multi-domain]  Cd Length: 486  Bit Score: 44.81  E-value: 7.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 261 VLFIDEVHMLDIESFSFLNRALEsDMAP--VLIMATnrgitrirgTSYqspHGIPIDLLDRLLIVSTTPYSEKDTKQILR 338
Cdd:PRK14953  122 VYIIDEAHMLTKEAFNALLKTLE-EPPPrtIFILCT---------TEY---DKIPPTILSRCQRFIFSKPTKEQIKEYLK 188

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1007385652 339 IRCEEEDVEMSEDAYTVLTRIgLETSLRYAIQLITAAS 376
Cdd:PRK14953  189 RICNEEKIEYEEKALDLLAQA-SEGGMRDAASLLDQAS 225
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
264-371 7.61e-05

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 44.41  E-value: 7.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 264 IDEVHMLDIESF-SFLnRALESdmaP----VLIMATNrgitrirgtsyqSPHGIPIDLLDRLLIVSTTPYSEKDTKQILR 338
Cdd:COG2812   120 IDEAHMLTTEAFnALL-KTLEE---PpphvVFILATT------------EPQKLLPTILSRCQRFDFRRLPPEEIAEHLA 183

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1007385652 339 IRCEEEDVEMSEDAYTVLTRIGlETSLRYAIQL 371
Cdd:COG2812   184 KIAEREGIEIEPEALALIARAA-DGSMRDALSL 215
DnaB COG0305
Replicative DNA helicase [Replication, recombination and repair];
39-83 2.97e-04

Replicative DNA helicase [Replication, recombination and repair];


Pssm-ID: 440074 [Multi-domain]  Cd Length: 429  Bit Score: 42.76  E-value: 2.97e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1007385652  39 VLIAGQPGTGKTAIAMGMAQ--ALGPDTPfTAiagseIFSLEMSKTE 83
Cdd:COG0305   194 IILAARPSMGKTAFALNIARnaAIKEGKP-VA-----IFSLEMSAEQ 234
PRK07773 PRK07773
replicative DNA helicase; Validated
 36-83 3.24e-04

replicative DNA helicase; Validated


Pssm-ID: 236093 [Multi-domain]  Cd Length: 886  Bit Score: 43.20  E-value: 3.24e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1007385652  36 GRAVLIAGQPGTGKTAIAMGMAQALGpdtpFTAIAGSEIFSLEMSKTE 83
Cdd:PRK07773  217 GQLIIVAARPSMGKTTFGLDFARNCA----IRHRLAVAIFSLEMSKEQ 260
DnaB TIGR00665
replicative DNA helicase; This model describes the helicase DnaB, a homohexameric protein ...
 39-83 3.81e-04

replicative DNA helicase; This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of > 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273206 [Multi-domain]  Cd Length: 432  Bit Score: 42.41  E-value: 3.81e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1007385652  39 VLIAGQPGTGKTAIAMGMAQ--ALGPDTPfTAIagseiFSLEMSKTE 83
Cdd:TIGR00665 197 IILAARPSMGKTAFALNIAEnaAIKEGKP-VAF-----FSLEMSAEQ 237
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 39-89 4.63e-04

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: 39.88  E-value: 4.63e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1007385652  39 VLIAGQPGTGKTAIAMGMAQALGpdTPFTAIAGSEIFSLEMSKTEALTQAF 89
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELG--APFIEISGSELVSKYVGESEKRLREL 49
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 37-91 9.78e-04

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


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 39.58  E-value: 9.78e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1007385652  37 RAVLIAGQPGTGKTAIAMGMAQALGpdTPFTAIAGSEIFSLEMSKTE-ALTQAFRR 91
Cdd:cd19503    35 RGVLLHGPPGTGKTLLARAVANEAG--ANFLSISGPSIVSKYLGESEkNLREIFEE 88
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 30-91 1.16e-03

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: 41.05  E-value: 1.16e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1007385652  30 REGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPdtPFTAIAGSEIFSLEMSKTE-ALTQAFRR 91
Cdd:COG0464   185 EYGLPPPRGLLLYGPPGTGKTLLARALAGELGL--PLIEVDLSDLVSKYVGETEkNLREVFDK 245
PRK14962 PRK14962
DNA polymerase III subunits gamma and tau; Provisional
 261-422 1.50e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237869 [Multi-domain]  Cd Length: 472  Bit Score: 40.90  E-value: 1.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 261 VLFIDEVHMLDIESFSFLNRALESDMAPVL-IMATNrgitrirgtsyqSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRI 339
Cdd:PRK14962  120 VYIIDEVHMLTKEAFNALLKTLEEPPSHVVfVLATT------------NLEKVPPTIISRCQVIEFRNISDELIIKRLQE 187

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 340 RCEEEDVEMSEDAYTVLTRI---GLETSLRYAIQLItaaslvcrKRKGTEVQVDDIKRVYSLFLDESrstqyMKEYQDAF 416
Cdd:PRK14962  188 VAEAEGIEIDREALSFIAKRasgGLRDALTMLEQVW--------KFSEGKITLETVHEALGLIPIEV-----VRDYINAI 254


                  ....*.
gi 1007385652 417 LFNELK 422
Cdd:PRK14962  255 FNGDVK 260
ftsH CHL00176
cell division protein; Validated
 39-73 1.96e-03

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 40.42  E-value: 1.96e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1007385652  39 VLIAGQPGTGKTAIAMGMAQALGpdTPFTAIAGSE 73
Cdd:CHL00176  219 VLLVGPPGTGKTLLAKAIAGEAE--VPFFSISGSE 251
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 30-92 2.24e-03

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: 38.63  E-value: 2.24e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1007385652  30 REGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDtpFTAIAGSEIFSLEMSKTE-ALTQAFRRS 92
Cdd:cd19529    21 RLGIRPPKGILLYGPPGTGKTLLAKAVATESNAN--FISVKGPELLSKWVGESEkAIREIFRKA 82
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 32-91 2.29e-03

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: 38.42  E-value: 2.29e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1007385652  32 GKIAGRAVLIAGQPGTGKTAIAMGMAQALGPdtPFTAIAGSEIFSLEMSKTEA-LTQAFRR 91
Cdd:cd19481    22 GLGLPKGILLYGPPGTGKTLLAKALAGELGL--PLIVVKLSSLLSKYVGESEKnLRKIFER 80
dnaX_nterm TIGR02397
DNA polymerase III, subunit gamma and tau; This model represents the well-conserved first ~ ...
 264-379 2.61e-03

DNA polymerase III, subunit gamma and tau; This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274111 [Multi-domain]  Cd Length: 355  Bit Score: 39.86  E-value: 2.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 264 IDEVHMLDIESFSFLNRALESdmAP---VLIMATNrgitrirgtsyqSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIR 340
Cdd:TIGR02397 123 IDEVHMLSKSAFNALLKTLEE--PPehvVFILATT------------EPHKIPATILSRCQRFDFKRIPLEDIVERLKKI 188

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1007385652 341 CEEEDVEMSEDAYTVLTRIGlETSLRYAIQLITAASLVC 379
Cdd:TIGR02397 189 LDKEGIKIEDEALELIARAA-DGSLRDALSLLDQLISFG 226
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 36-76 2.72e-03

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: 38.28  E-value: 2.72e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1007385652  36 GRAVLIAGQPGTGKTAIAMGMAQALG-PDTPFTAIAGSEIFS 76
Cdd:cd00009    19 PKNLLLYGPPGTGKTTLARAIANELFrPGAPFLYLNASDLLE 60
PRK14965 PRK14965
DNA polymerase III subunits gamma and tau; Provisional
 261-392 3.17e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237871 [Multi-domain]  Cd Length: 576  Bit Score: 39.72  E-value: 3.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 261 VLFIDEVHMLDIESFSFLNRALESDMAPV-LIMATNrgitrirgtsyqSPHGIPIDLLDRLlivsttpySEKDTKQI--- 336
Cdd:PRK14965  122 IFIIDEVHMLSTNAFNALLKTLEEPPPHVkFIFATT------------EPHKVPITILSRC--------QRFDFRRIplq 181

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1007385652 337 -----LRIRCEEEDVEMSEDAYTVLTRIGlETSLRYAIQLITAASLVCrkrkGTEVQVDDI 392
Cdd:PRK14965  182 kivdrLRYIADQEGISISDAALALVARKG-DGSMRDSLSTLDQVLAFC----GDAVGDDDV 237
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
1-60 3.55e-03

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 39.40  E-value: 3.55e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1007385652   1 MCASHPQASQGMVGQLAARRAagvvLE-MIREGKIAGrAVLIAGQPGTGKTAIAMGMAQAL 60
Cdd:COG2812     1 MSYQVPQTFDDVVGQEHVVRT----LKnALASGRLAH-AYLFTGPRGVGKTTLARILAKAL 56
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 30-91 3.82e-03

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: 38.03  E-value: 3.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1007385652  30 REGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDtpFTAIAGSEIFSLEMSKTE-ALTQAFRR 91
Cdd:cd19511    21 RLGIRPPKGVLLYGPPGCGKTLLAKALASEAGLN--FISVKGPELFSKYVGESErAVREIFQK 81
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 235-328 5.18e-03

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: 37.51  E-value: 5.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652 235 KSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALEsdmAPVLIMATNRGITRIRGTSYQSPHGIPI 314
Cdd:cd00009    61 GLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLE---TLNDLRIDRENVRVIGATNRPLLGDLDR 137

                          90
                  ....*....|....
gi 1007385652 315 DLLDRLLIVSTTPY 328
Cdd:cd00009   138 ALYDRLDIRIVIPL 151
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 36-105 5.44e-03

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: 37.35  E-value: 5.44e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1007385652   36 GRAVLIAGQPGTGKTAIAMGMAQALGPDT-PFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIE 105
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGgGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALA 72
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
26-65 5.82e-03

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 38.42  E-value: 5.82e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1007385652  26 LEMIREGKIAgRAVLIAGQPGTGKTAIAMGMAQALGPDTP 65
Cdd:COG0470     9 LAAAESGRLP-HALLLHGPPGIGKTTLALALARDLLCENP 47
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 37-92 6.03e-03

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: 39.12  E-value: 6.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1007385652  37 RAVLIAGQPGTGKTAIAMGMAQALGPDtpFTAIAGSEIFSLEMSKTE-ALTQAFRRS 92
Cdd:TIGR01243 488 KGVLLFGPPGTGKTLLAKAVATESGAN--FIAVRGPEILSKWVGESEkAIREIFRKA 542
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 11-85 8.74e-03

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 38.06  E-value: 8.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007385652  11 GMVGQLAARRAAgVVLEM------IREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGpdTPFTAIAGSEIFSLEMSKTEA 84
Cdd:COG1222    82 GLDEQIEEIREA-VELPLknpelfRKYGIEPPKGVLLYGPPGTGKTLLAKAVAGELG--APFIRVRGSELVSKYIGEGAR 158


                  .
gi 1007385652  85 L 85
Cdd:COG1222   159 N 159
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 37-79 9.43e-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: 36.83  E-value: 9.43e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1007385652  37 RAVLIAGQPGTGKTAIAMGMAQALGpdTPFTAIAGSEIfsLEM 79
Cdd:cd19501    38 KGVLLVGPPGTGKTLLAKAVAGEAG--VPFFSISGSDF--VEM 76
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH