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Conserved domains on  [gi|28201890|sp|Q9Y230|]
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RecName: Full=RuvB-like 2; AltName: Full=48 kDa TATA box-binding protein-interacting protein; Short=48 kDa TBP-interacting protein; AltName: Full=51 kDa erythrocyte cytosolic protein; Short=ECP-51; AltName: Full=INO80 complex subunit J; AltName: Full=Repressing pontin 52; Short=Reptin 52; AltName: Full=TIP49b; AltName: Full=TIP60-associated protein 54-beta; Short=TAP54-beta

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

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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 ...
 21-365 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: 610.08  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890    21 RIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPF 100
Cdd:pfam06068   1 RISAHSHIRGLGLDEDGEARYVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890   101 TAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEGEVVEIQI---DRPATG-TGSKVGKLTLKTTEMETIYDLGT 176
Cdd:pfam06068  81 TSISGSEVYSLEMKKTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIeeaENPLSGgKTIKGGKITLKTTKMEKTLKLGP 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890   177 KMIESLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAmgSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQG 256
Cdd:pfam06068 161 KIYEQLQKEKVSAGDVIYIDKNTGRVKKLGRSFARATDFDL--EATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARPQG 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890   257 FLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIR 336
Cdd:pfam06068 239 ILSLFSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATNRGICTIR 318

                         330       340
                  ....*....|....*....|....*....
gi 28201890   337 GTSYQSPHGIPIDLLDRLLIVSTTPYSEK 365
Cdd:pfam06068 319 GTDIISPHGIPLDLLDRLLIITTEPYTRE 347
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 370-435 5.20e-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: 105.81  E-value: 5.20e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28201890   370 ILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLD 435
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 ...
 21-365 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: 610.08  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890    21 RIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPF 100
Cdd:pfam06068   1 RISAHSHIRGLGLDEDGEARYVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890   101 TAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEGEVVEIQI---DRPATG-TGSKVGKLTLKTTEMETIYDLGT 176
Cdd:pfam06068  81 TSISGSEVYSLEMKKTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIeeaENPLSGgKTIKGGKITLKTTKMEKTLKLGP 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890   177 KMIESLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAmgSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQG 256
Cdd:pfam06068 161 KIYEQLQKEKVSAGDVIYIDKNTGRVKKLGRSFARATDFDL--EATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARPQG 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890   257 FLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIR 336
Cdd:pfam06068 239 ILSLFSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATNRGICTIR 318

                         330       340
                  ....*....|....*....|....*....
gi 28201890   337 GTSYQSPHGIPIDLLDRLLIVSTTPYSEK 365
Cdd:pfam06068 319 GTDIISPHGIPLDLLDRLLIITTEPYTRE 347
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
12-451 0e+00

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


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 525.31  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890  12 EIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMA 91
Cdd:COG1224   6 EIEKVKEFERISAHSHIRGLGLDENGKAKFVADGLVGQVEAREAAGIVVKMIKEGKMAGKGILIVGPPGTGKTALAVAIA 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890  92 QALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEGEVVEIQIDR---PATGTgSKV---GKLTLKT 165
Cdd:COG1224  86 RELGEDTPFVAISGSEIYSAELKKTEFLMQALRKAIGVRVREKRKVYEGVVKEIKIRYarhPYNPY-VKVpreATITLAT 164

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890 166 TEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRS-FTRARDYDAmgSQTKFVQCPDGELQKRKEVVHTVSL 244
Cdd:COG1224 165 KDEEKTLTVGEEIAQQLVELGIRKGDVIWIDAETGRVSKLGRAkGEGAKTYDI--ETKRIVEVPSGPVKKEKEIVRTLTL 242

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890 245 HEIDVINSRTQG-FLALFS-GDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAP 322
Cdd:COG1224 243 HDLDLYLAAQRAaFSALFGfFEEREIPSEVRKQVDELVKKWIEEGKAELVPGVLFIDDAHMLDIEAFSFLTRAMESELAP 322

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890 323 VLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYA 402
Cdd:COG1224 323 IIILATNRGITKIRGTDIESPHGIPLDLLDRLLIIPTRPYTEDEIREIIKIRAEEEDIELSDDALEELTKIGVERSLRYA 402

                       410       420       430       440
                ....*....|....*....|....*....|....*....|....*....
gi 28201890 403 IQLITAASLVCRKRKGTEVQVDDIKRVYSLFLDESRSTQYMKEYQDAFL 451
Cdd:COG1224 403 VQLLEPAYIIAKRRGRSKVTVEDVEEASKLFADVKESVEYVKEYEELFL 451
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 370-435 5.20e-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: 105.81  E-value: 5.20e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28201890   370 ILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLD 435
Cdd:pfam17856   1 ILKIRAQEEGVKIDEEALDLLAKIGTETSLRYAIQLLTPASILAKKRGGKEVEVQDVEEAYELFLD 66
PRK14957 PRK14957
DNA polymerase III subunits gamma and tau; Provisional
 295-436 9.68e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184921 [Multi-domain]  Cd Length: 546  Bit Score: 47.77  E-value: 9.68e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890  295 VLFIDEVHMLDIESFSFLNRALESDMAPV-LIMATnrgitrirgTSYqspHGIPIDLLDRLLIVSTTPYSEKDTKQILRI 373
Cdd:PRK14957 122 VYLIDEVHMLSKQSFNALLKTLEEPPEYVkFILAT---------TDY---HKIPVTILSRCIQLHLKHISQADIKDQLKI 189

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28201890  374 RCEEEDVEMSEDAYTVLTRIGlETSLRYAIQLITAASLVCrkrkGTEVQVDDIKRVYSLFLDE 436
Cdd:PRK14957 190 ILAKENINSDEQSLEYIAYHA-KGSLRDALSLLDQAISFC----GGELKQAQIKQMLGIIDSE 247
DnaB_C cd00984
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ...
 73-117 8.11e-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: 44.04  E-value: 8.11e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 28201890  73 VLIAGQPGTGKTAIAMGMAQALGPDTPFTAIagseIFSLEMSKTE 117
Cdd:cd00984  22 IIIAARPSMGKTAFALNIAENIALDEGLPVL----FFSLEMSAEQ 62
DnaB TIGR00665
replicative DNA helicase; This model describes the helicase DnaB, a homohexameric protein ...
 73-117 5.00e-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: 5.00e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 28201890    73 VLIAGQPGTGKTAIAMGMAQ--ALGPDTPfTAIagseiFSLEMSKTE 117
Cdd:TIGR00665 197 IILAARPSMGKTAFALNIAEnaAIKEGKP-VAF-----FSLEMSAEQ 237
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 70-139 8.87e-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: 36.97  E-value: 8.87e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28201890     70 GRAVLIAGQPGTGKTAIAMGMAQALGPDT-PFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIE 139
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 ...
 21-365 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: 610.08  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890    21 RIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPF 100
Cdd:pfam06068   1 RISAHSHIRGLGLDEDGEARYVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890   101 TAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEGEVVEIQI---DRPATG-TGSKVGKLTLKTTEMETIYDLGT 176
Cdd:pfam06068  81 TSISGSEVYSLEMKKTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIeeaENPLSGgKTIKGGKITLKTTKMEKTLKLGP 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890   177 KMIESLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAmgSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQG 256
Cdd:pfam06068 161 KIYEQLQKEKVSAGDVIYIDKNTGRVKKLGRSFARATDFDL--EATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARPQG 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890   257 FLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIR 336
Cdd:pfam06068 239 ILSLFSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATNRGICTIR 318

                         330       340
                  ....*....|....*....|....*....
gi 28201890   337 GTSYQSPHGIPIDLLDRLLIVSTTPYSEK 365
Cdd:pfam06068 319 GTDIISPHGIPLDLLDRLLIITTEPYTRE 347
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
12-451 0e+00

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


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 525.31  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890  12 EIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMA 91
Cdd:COG1224   6 EIEKVKEFERISAHSHIRGLGLDENGKAKFVADGLVGQVEAREAAGIVVKMIKEGKMAGKGILIVGPPGTGKTALAVAIA 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890  92 QALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEGEVVEIQIDR---PATGTgSKV---GKLTLKT 165
Cdd:COG1224  86 RELGEDTPFVAISGSEIYSAELKKTEFLMQALRKAIGVRVREKRKVYEGVVKEIKIRYarhPYNPY-VKVpreATITLAT 164

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890 166 TEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRS-FTRARDYDAmgSQTKFVQCPDGELQKRKEVVHTVSL 244
Cdd:COG1224 165 KDEEKTLTVGEEIAQQLVELGIRKGDVIWIDAETGRVSKLGRAkGEGAKTYDI--ETKRIVEVPSGPVKKEKEIVRTLTL 242

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890 245 HEIDVINSRTQG-FLALFS-GDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAP 322
Cdd:COG1224 243 HDLDLYLAAQRAaFSALFGfFEEREIPSEVRKQVDELVKKWIEEGKAELVPGVLFIDDAHMLDIEAFSFLTRAMESELAP 322

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890 323 VLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYA 402
Cdd:COG1224 323 IIILATNRGITKIRGTDIESPHGIPLDLLDRLLIIPTRPYTEDEIREIIKIRAEEEDIELSDDALEELTKIGVERSLRYA 402

                       410       420       430       440
                ....*....|....*....|....*....|....*....|....*....
gi 28201890 403 IQLITAASLVCRKRKGTEVQVDDIKRVYSLFLDESRSTQYMKEYQDAFL 451
Cdd:COG1224 403 VQLLEPAYIIAKRRGRSKVTVEDVEEASKLFADVKESVEYVKEYEELFL 451
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 370-435 5.20e-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: 105.81  E-value: 5.20e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28201890   370 ILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLD 435
Cdd:pfam17856   1 ILKIRAQEEGVKIDEEALDLLAKIGTETSLRYAIQLLTPASILAKKRGGKEVEVQDVEEAYELFLD 66
PRK14957 PRK14957
DNA polymerase III subunits gamma and tau; Provisional
 295-436 9.68e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184921 [Multi-domain]  Cd Length: 546  Bit Score: 47.77  E-value: 9.68e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890  295 VLFIDEVHMLDIESFSFLNRALESDMAPV-LIMATnrgitrirgTSYqspHGIPIDLLDRLLIVSTTPYSEKDTKQILRI 373
Cdd:PRK14957 122 VYLIDEVHMLSKQSFNALLKTLEEPPEYVkFILAT---------TDY---HKIPVTILSRCIQLHLKHISQADIKDQLKI 189

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28201890  374 RCEEEDVEMSEDAYTVLTRIGlETSLRYAIQLITAASLVCrkrkGTEVQVDDIKRVYSLFLDE 436
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 ...
 73-117 1.28e-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: 1.28e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 28201890    73 VLIAGQPGTGKTAIAMGMAQ--ALGPDTPfTAiagseIFSLEMSKTE 117
Cdd:pfam03796  22 IIIAARPSMGKTAFALNIARnaAVKHKKP-VA-----IFSLEMSAEQ 62
DnaB_C cd00984
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ...
 73-117 8.11e-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: 44.04  E-value: 8.11e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 28201890  73 VLIAGQPGTGKTAIAMGMAQALGPDTPFTAIagseIFSLEMSKTE 117
Cdd:cd00984  22 IIIAARPSMGKTAFALNIAENIALDEGLPVL----FFSLEMSAEQ 62
PRK14953 PRK14953
DNA polymerase III subunits gamma and tau; Provisional
 295-410 9.15e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237867 [Multi-domain]  Cd Length: 486  Bit Score: 44.81  E-value: 9.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890  295 VLFIDEVHMLDIESFSFLNRALEsDMAP--VLIMATnrgitrirgTSYqspHGIPIDLLDRLLIVSTTPYSEKDTKQILR 372
Cdd:PRK14953 122 VYIIDEAHMLTKEAFNALLKTLE-EPPPrtIFILCT---------TEY---DKIPPTILSRCQRFIFSKPTKEQIKEYLK 188

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 28201890  373 IRCEEEDVEMSEDAYTVLTRIgLETSLRYAIQLITAAS 410
Cdd:PRK14953 189 RICNEEKIEYEEKALDLLAQA-SEGGMRDAASLLDQAS 225
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
298-405 1.07e-04

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 44.03  E-value: 1.07e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890 298 IDEVHMLDIESF-SFLnRALESdmaP----VLIMATNrgitrirgtsyqSPHGIPIDLLDRLLIVSTTPYSEKDTKQILR 372
Cdd:COG2812 120 IDEAHMLTTEAFnALL-KTLEE---PpphvVFILATT------------EPQKLLPTILSRCQRFDFRRLPPEEIAEHLA 183

                        90       100       110
                ....*....|....*....|....*....|...
gi 28201890 373 IRCEEEDVEMSEDAYTVLTRIGlETSLRYAIQL 405
Cdd:COG2812 184 KIAEREGIEIEPEALALIARAA-DGSMRDALSL 215
DnaB COG0305
Replicative DNA helicase [Replication, recombination and repair];
73-117 3.87e-04

Replicative DNA helicase [Replication, recombination and repair];


Pssm-ID: 440074 [Multi-domain]  Cd Length: 429  Bit Score: 42.76  E-value: 3.87e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 28201890  73 VLIAGQPGTGKTAIAMGMAQ--ALGPDTPfTAiagseIFSLEMSKTE 117
Cdd:COG0305 194 IILAARPSMGKTAFALNIARnaAIKEGKP-VA-----IFSLEMSAEQ 234
PRK07773 PRK07773
replicative DNA helicase; Validated
 70-117 4.60e-04

replicative DNA helicase; Validated


Pssm-ID: 236093 [Multi-domain]  Cd Length: 886  Bit Score: 42.82  E-value: 4.60e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 28201890   70 GRAVLIAGQPGTGKTAIAMGMAQALGpdtpFTAIAGSEIFSLEMSKTE 117
Cdd:PRK07773 217 GQLIIVAARPSMGKTTFGLDFARNCA----IRHRLAVAIFSLEMSKEQ 260
DnaB TIGR00665
replicative DNA helicase; This model describes the helicase DnaB, a homohexameric protein ...
 73-117 5.00e-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: 5.00e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 28201890    73 VLIAGQPGTGKTAIAMGMAQ--ALGPDTPfTAIagseiFSLEMSKTE 117
Cdd:TIGR00665 197 IILAARPSMGKTAFALNIAEnaAIKEGKP-VAF-----FSLEMSAEQ 237
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 73-123 6.26e-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: 6.26e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 28201890    73 VLIAGQPGTGKTAIAMGMAQALGpdTPFTAIAGSEIFSLEMSKTEALTQAF 123
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 ...
 71-125 1.41e-03

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: 39.20  E-value: 1.41e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 28201890  71 RAVLIAGQPGTGKTAIAMGMAQALGpdTPFTAIAGSEIFSLEMSKTE-ALTQAFRR 125
Cdd:cd19503  35 RGVLLHGPPGTGKTLLARAVANEAG--ANFLSISGPSIVSKYLGESEkNLREIFEE 88
PRK14962 PRK14962
DNA polymerase III subunits gamma and tau; Provisional
 295-456 1.81e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237869 [Multi-domain]  Cd Length: 472  Bit Score: 40.52  E-value: 1.81e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890  295 VLFIDEVHMLDIESFSFLNRALESDMAPVL-IMATNrgitrirgtsyqSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRI 373
Cdd:PRK14962 120 VYIIDEVHMLTKEAFNALLKTLEEPPSHVVfVLATT------------NLEKVPPTIISRCQVIEFRNISDELIIKRLQE 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890  374 RCEEEDVEMSEDAYTVLTRI---GLETSLRYAIQLITAAslvcrkrkGTEVQVDDIKRVYSLFLDESrstqyMKEYQDAF 450
Cdd:PRK14962 188 VAEAEGIEIDREALSFIAKRasgGLRDALTMLEQVWKFS--------EGKITLETVHEALGLIPIEV-----VRDYINAI 254


                 ....*.
gi 28201890  451 LFNELK 456
Cdd:PRK14962 255 FNGDVK 260
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 64-125 2.19e-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: 40.28  E-value: 2.19e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28201890  64 REGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPdtPFTAIAGSEIFSLEMSKTE-ALTQAFRR 125
Cdd:COG0464 185 EYGLPPPRGLLLYGPPGTGKTLLARALAGELGL--PLIEVDLSDLVSKYVGETEkNLREVFDK 245
ftsH CHL00176
cell division protein; Validated
 73-107 2.46e-03

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 40.42  E-value: 2.46e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 28201890   73 VLIAGQPGTGKTAIAMGMAQALGpdTPFTAIAGSE 107
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 ...
 64-126 2.97e-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: 38.25  E-value: 2.97e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28201890  64 REGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDtpFTAIAGSEIFSLEMSKTE-ALTQAFRRS 126
Cdd:cd19529  21 RLGIRPPKGILLYGPPGTGKTLLAKAVATESNAN--FISVKGPELLSKWVGESEkAIREIFRKA 82
dnaX_nterm TIGR02397
DNA polymerase III, subunit gamma and tau; This model represents the well-conserved first ~ ...
 298-413 2.99e-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: 2.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890   298 IDEVHMLDIESFSFLNRALESdmAP---VLIMATNrgitrirgtsyqSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIR 374
Cdd:TIGR02397 123 IDEVHMLSKSAFNALLKTLEE--PPehvVFILATT------------EPHKIPATILSRCQRFDFKRIPLEDIVERLKKI 188

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 28201890   375 CEEEDVEMSEDAYTVLTRIGlETSLRYAIQLITAASLVC 413
Cdd:TIGR02397 189 LDKEGIKIEDEALELIARAA-DGSLRDALSLLDQLISFG 226
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 66-125 3.19e-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: 38.03  E-value: 3.19e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28201890  66 GKIAGRAVLIAGQPGTGKTAIAMGMAQALGPdtPFTAIAGSEIFSLEMSKTEA-LTQAFRR 125
Cdd:cd19481  22 GLGLPKGILLYGPPGTGKTLLAKALAGELGL--PLIVVKLSSLLSKYVGESEKnLRKIFER 80
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 70-110 3.89e-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: 37.90  E-value: 3.89e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 28201890  70 GRAVLIAGQPGTGKTAIAMGMAQALG-PDTPFTAIAGSEIFS 110
Cdd:cd00009  19 PKNLLLYGPPGTGKTTLARAIANELFrPGAPFLYLNASDLLE 60
PRK14965 PRK14965
DNA polymerase III subunits gamma and tau; Provisional
 295-426 4.81e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237871 [Multi-domain]  Cd Length: 576  Bit Score: 39.34  E-value: 4.81e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890  295 VLFIDEVHMLDIESFSFLNRALESDMAPV-LIMATNrgitrirgtsyqSPHGIPIDLLDRLlivsttpySEKDTKQI--- 370
Cdd:PRK14965 122 IFIIDEVHMLSTNAFNALLKTLEEPPPHVkFIFATT------------EPHKVPITILSRC--------QRFDFRRIplq 181

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28201890  371 -----LRIRCEEEDVEMSEDAYTVLTRIGlETSLRYAIQLITAASLVCrkrkGTEVQVDDI 426
Cdd:PRK14965 182 kivdrLRYIADQEGISISDAALALVARKG-DGSMRDSLSTLDQVLAFC----GDAVGDDDV 237
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 64-125 4.84e-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: 37.65  E-value: 4.84e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28201890  64 REGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDtpFTAIAGSEIFSLEMSKTE-ALTQAFRR 125
Cdd:cd19511  21 RLGIRPPKGVLLYGPPGCGKTLLAKALASEAGLN--FISVKGPELFSKYVGESErAVREIFQK 81
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
60-99 7.58e-03

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 38.03  E-value: 7.58e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 28201890  60 LEMIREGKIAgRAVLIAGQPGTGKTAIAMGMAQALGPDTP 99
Cdd:COG0470   9 LAAAESGRLP-HALLLHGPPGIGKTTLALALARDLLCENP 47
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 269-362 7.61e-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: 37.13  E-value: 7.61e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28201890 269 KSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALEsdmAPVLIMATNRGITRIRGTSYQSPHGIPI 348
Cdd:cd00009  61 GLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLE---TLNDLRIDRENVRVIGATNRPLLGDLDR 137

                        90
                ....*....|....
gi 28201890 349 DLLDRLLIVSTTPY 362
Cdd:cd00009 138 ALYDRLDIRIVIPL 151
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 71-126 8.44e-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: 38.73  E-value: 8.44e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 28201890    71 RAVLIAGQPGTGKTAIAMGMAQALGPDtpFTAIAGSEIFSLEMSKTE-ALTQAFRRS 126
Cdd:TIGR01243 488 KGVLLFGPPGTGKTLLAKAVATESGAN--FIAVRGPEILSKWVGESEkAIREIFRKA 542
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 70-139 8.87e-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: 36.97  E-value: 8.87e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28201890     70 GRAVLIAGQPGTGKTAIAMGMAQALGPDT-PFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIE 139
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGgGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALA 72
 
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.
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