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Conserved domains on  [gi|24497618|ref|NP_054828|]
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ATPase family AAA domain-containing protein 2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
427-596 1.88e-114

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 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: 410925 [Multi-domain]  Cd Length: 170  Bit Score: 355.66  E-value: 1.88e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  427 SVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFFMRKGADCLSKWV 506
Cdd:cd19517    1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  507 GESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRR 586
Cdd:cd19517   81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160
                        170
                 ....*....|
gi 24497618  587 PGRFDREFLF 596
Cdd:cd19517  161 PGRFDREFYF 170
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
445-934 2.38e-61

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


:

Pssm-ID: 223540 [Multi-domain]  Cd Length: 494  Bit Score: 218.92  E-value: 2.38e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  445 PLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANEcsqgdkRVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMR 524
Cdd:COG0464    3 PLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE------GAEFLSINGPEILSKYVGESELRLRELFEEAEKLA 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  525 PSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLdSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEAR 604
Cdd:COG0464   77 PSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGL-KRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGR 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  605 KEILKIHTRdWNPKPLDTFLEELAENCVGYCGADIKSICAEAALCALRRrypqiyttseKLQLDLSSINISAKDFEVAMQ 684
Cdd:COG0464  156 LEILQIHTR-LMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRR----------AIDLVGEYIGVTEDDFEEALK 224
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  685 KMIPAsqRAVTSPGQALSTVVKPLLQNTVDKILEALQRVFPHAEFRTNKTLdsdiscpllesdlaysdddvpsvyengls 764
Cdd:COG0464  225 KVLPS--RGVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGL----------------------------- 273
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  765 qksshkakdnfnflhlnrnacyqpmSFRPRILIVGEPGFGQgSHLAPAVihALE-KFTVYTLDIPVLFGVSTTSPEETCA 843
Cdd:COG0464  274 -------------------------RPPKGVLLYGPPGTGK-TLLAKAV--ALEsRSRFISVKGSELLSKWVGESEKNIR 325
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  844 QVIREAKRTAPSIVYVPHIHVWWEIVGPT-------LKATFTTLLQNIPSFAPVLLLATSDkphsaLPEEVQELFIR--D 914
Cdd:COG0464  326 ELFEKARKLAPSIIFIDEIDSLASGRGPSedgsgrrVVGQLLTELDGIEKAEGVLVIAATN-----RPDDLDPALLRpgR 400
                        490       500
                 ....*....|....*....|
gi 24497618  915 YGEIFNVQLPDKEERTKFFE 934
Cdd:COG0464  401 FDRLIYVPLPDLEERLEIFK 420
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
987-1097 3.03e-55

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


:

Pssm-ID: 99957  Cd Length: 112  Bit Score: 187.18  E-value: 3.03e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  987 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPD 1066
Cdd:cd05528    2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81
                         90       100       110
                 ....*....|....*....|....*....|.
gi 24497618 1067 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 1097
Cdd:cd05528   82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112
 
Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
427-596 1.88e-114

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 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: 410925 [Multi-domain]  Cd Length: 170  Bit Score: 355.66  E-value: 1.88e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  427 SVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFFMRKGADCLSKWV 506
Cdd:cd19517    1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  507 GESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRR 586
Cdd:cd19517   81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160
                        170
                 ....*....|
gi 24497618  587 PGRFDREFLF 596
Cdd:cd19517  161 PGRFDREFYF 170
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
423-694 4.30e-76

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: 268.70  E-value: 4.30e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    423 VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCL 502
Cdd:TIGR01243  175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG-----AYFISINGPEIM 249
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    503 SKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDP 582
Cdd:TIGR01243  250 SKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDP 329
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    583 ALRRPGRFDREFLFSLPDKEARKEILKIHTRDwNPKPLDTFLEELAENCVGYCGADIKSICAEAALCALRRRYPQIYTTS 662
Cdd:TIGR01243  330 ALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKINF 408
                          250       260       270
                   ....*....|....*....|....*....|....*
gi 24497618    663 EKLQLD---LSSINISAKDFEVAMQKMIPASQRAV 694
Cdd:TIGR01243  409 EAEEIPaevLKELKVTMKDFMEALKMVEPSAIREV 443
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
400-688 6.95e-76

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 223540 [Multi-domain]  Cd Length: 494  Bit Score: 260.91  E-value: 6.95e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  400 IYKDRMKIGASLADVDP----MQLDSSVRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTL 475
Cdd:COG0464  212 IGVTEDDFEEALKKVLPsrgvLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTL 291
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  476 VARALANECsqgdkRVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTL 555
Cdd:COG0464  292 LAKAVALES-----RSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQL 366
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  556 LALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPLDTF-LEELAENCVGY 634
Cdd:COG0464  367 LTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVdLEELAEITEGY 446
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24497618  635 CGADIKSICAEAALCALRRRYPqiyttseklqldlssINISAKDFEVAMQKMIP 688
Cdd:COG0464  447 SGADIAALVREAALEALREARR---------------REVTLDDFLDALKKIKP 485
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
417-658 6.39e-70

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 240.12  E-value: 6.39e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   417 MQLDSS--VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrvAFF 494
Cdd:PRK03992  120 MEVIESpnVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATF 193
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   495 MR-KGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLApvrSSRQDQIHS---SIVST---LLALMDGLDSRGE 567
Cdd:PRK03992  194 IRvVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIA---AKRTDSGTSgdrEVQRTlmqLLAEMDGFDPRGN 270
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   568 IVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPlDTFLEELAENCVGYCGADIKSICAEAA 647
Cdd:PRK03992  271 VKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLAD-DVDLEELAELTEGASGADLKAICTEAG 349
                         250
                  ....*....|.
gi 24497618   648 LCALRRRYPQI 658
Cdd:PRK03992  350 MFAIRDDRTEV 360
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
445-934 2.38e-61

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 223540 [Multi-domain]  Cd Length: 494  Bit Score: 218.92  E-value: 2.38e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  445 PLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANEcsqgdkRVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMR 524
Cdd:COG0464    3 PLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE------GAEFLSINGPEILSKYVGESELRLRELFEEAEKLA 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  525 PSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLdSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEAR 604
Cdd:COG0464   77 PSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGL-KRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGR 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  605 KEILKIHTRdWNPKPLDTFLEELAENCVGYCGADIKSICAEAALCALRRrypqiyttseKLQLDLSSINISAKDFEVAMQ 684
Cdd:COG0464  156 LEILQIHTR-LMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRR----------AIDLVGEYIGVTEDDFEEALK 224
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  685 KMIPAsqRAVTSPGQALSTVVKPLLQNTVDKILEALQRVFPHAEFRTNKTLdsdiscpllesdlaysdddvpsvyengls 764
Cdd:COG0464  225 KVLPS--RGVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGL----------------------------- 273
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  765 qksshkakdnfnflhlnrnacyqpmSFRPRILIVGEPGFGQgSHLAPAVihALE-KFTVYTLDIPVLFGVSTTSPEETCA 843
Cdd:COG0464  274 -------------------------RPPKGVLLYGPPGTGK-TLLAKAV--ALEsRSRFISVKGSELLSKWVGESEKNIR 325
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  844 QVIREAKRTAPSIVYVPHIHVWWEIVGPT-------LKATFTTLLQNIPSFAPVLLLATSDkphsaLPEEVQELFIR--D 914
Cdd:COG0464  326 ELFEKARKLAPSIIFIDEIDSLASGRGPSedgsgrrVVGQLLTELDGIEKAEGVLVIAATN-----RPDDLDPALLRpgR 400
                        490       500
                 ....*....|....*....|
gi 24497618  915 YGEIFNVQLPDKEERTKFFE 934
Cdd:COG0464  401 FDRLIYVPLPDLEERLEIFK 420
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
987-1097 3.03e-55

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 187.18  E-value: 3.03e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  987 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPD 1066
Cdd:cd05528    2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81
                         90       100       110
                 ....*....|....*....|....*....|.
gi 24497618 1067 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 1097
Cdd:cd05528   82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
464-598 3.24e-48

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: 425416 [Multi-domain]  Cd Length: 130  Bit Score: 167.77  E-value: 3.24e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    464 LFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSR 543
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKELG-----APFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSG 76
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618    544 QDQIHSSIVSTLLALMDGLDSR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFSL 598
Cdd:pfam00004   77 GDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
459-600 7.98e-20

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: 87.43  E-value: 7.98e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618     459 PPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFF------------MRKGADCLSKWVGESERQLRLLFDQAYQMRPS 526
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIdgedileevldqLLLIIVGGKKASGSGELRLRLALALARKLKPD 80
                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24497618     527 IIFFDEIDGLAPVRSSRQDQihssiVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPgRFDREFLFSLPD 600
Cdd:smart00382   81 VLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
BROMO smart00297
bromo domain;
982-1092 1.75e-17

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 79.24  E-value: 1.75e-17
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618     982 EEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNAL 1061
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80
                            90       100       110
                    ....*....|....*....|....*....|.
gi 24497618    1062 EYNPDrdpgDRLIRHRACALRDTAYAIIKEE 1092
Cdd:smart00297   81 TYNGP----DSEVYKDAKKLEKFFEKKLREL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
1009-1065 1.26e-14

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 70.42  E-value: 1.26e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 24497618   1009 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNP 1065
Cdd:pfam00439   17 FLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNG 73
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
624-658 4.34e-09

AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.


Pssm-ID: 436099 [Multi-domain]  Cd Length: 45  Bit Score: 53.31  E-value: 4.34e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 24497618    624 LEELAENCVGYCGADIKSICAEAALCALRRRYPQI 658
Cdd:pfam17862    4 LEELAERTEGFSGADLEALCREAALAALRRGLEAV 38
ycf46 CHL00195
Ycf46; Provisional
793-934 2.89e-03

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 41.93  E-value: 2.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   793 PR-ILIVGEPGFGQgSHLAPAVIHALeKFTVYTLDIPVLFGVSTTSPEETCAQVIREAKRTAPSIVYVPHIHVWWEIV-- 869
Cdd:CHL00195  259 PRgLLLVGIQGTGK-SLTAKAIANDW-QLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSes 336
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24497618   870 ----GPTLK--ATFTTLLQNIPSfaPVLLLATSDKPHSaLPEEVqelfIRD--YGEIFNVQLPDKEERTKFFE 934
Cdd:CHL00195  337 kgdsGTTNRvlATFITWLSEKKS--PVFVVATANNIDL-LPLEI----LRKgrFDEIFFLDLPSLEEREKIFK 402
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles pfam01695, but was ...
463-539 8.78e-03

IS21-like element helper ATPase IstB; This protein family model resembles pfam01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements.


Pssm-ID: 439516  Cd Length: 232  Bit Score: 39.38  E-value: 8.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   463 CLFYGPPGTGKTLVARALANE-CSQGdKRVAFFmrKGADCLSKWvGESERQLRLlfDQAYQ--MRPSIIFFDEIdGLAPV 539
Cdd:NF038214   93 VLLLGPPGTGKTHLAIALGYAaCRQG-YRVRFT--TAADLVEQL-AQARADGRL--GRLLRrlARYDLLIIDEL-GYLPF 165
 
Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
427-596 1.88e-114

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 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: 410925 [Multi-domain]  Cd Length: 170  Bit Score: 355.66  E-value: 1.88e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  427 SVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFFMRKGADCLSKWV 506
Cdd:cd19517    1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  507 GESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRR 586
Cdd:cd19517   81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160
                        170
                 ....*....|
gi 24497618  587 PGRFDREFLF 596
Cdd:cd19517  161 PGRFDREFYF 170
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
427-596 2.79e-80

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: 261.07  E-value: 2.79e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  427 SVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWV 506
Cdd:cd19503    1 DIGGLDEQIASLKELIELPLKYPELFRALGLKPPRGVLLHGPPGTGKTLLARAVANEAG-----ANFLSISGPSIVSKYL 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  507 GESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRR 586
Cdd:cd19503   76 GESEKNLREIFEEARSHAPSIIFIDEIDALAPKREEDQREVERRVVAQLLTLMDGMSSRGKVVVIAATNRPDAIDPALRR 155
                        170
                 ....*....|
gi 24497618  587 PGRFDREFLF 596
Cdd:cd19503  156 PGRFDREVEI 165
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
423-694 4.30e-76

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: 268.70  E-value: 4.30e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    423 VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCL 502
Cdd:TIGR01243  175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG-----AYFISINGPEIM 249
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    503 SKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDP 582
Cdd:TIGR01243  250 SKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDP 329
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    583 ALRRPGRFDREFLFSLPDKEARKEILKIHTRDwNPKPLDTFLEELAENCVGYCGADIKSICAEAALCALRRRYPQIYTTS 662
Cdd:TIGR01243  330 ALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKINF 408
                          250       260       270
                   ....*....|....*....|....*....|....*
gi 24497618    663 EKLQLD---LSSINISAKDFEVAMQKMIPASQRAV 694
Cdd:TIGR01243  409 EAEEIPaevLKELKVTMKDFMEALKMVEPSAIREV 443
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
400-688 6.95e-76

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 223540 [Multi-domain]  Cd Length: 494  Bit Score: 260.91  E-value: 6.95e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  400 IYKDRMKIGASLADVDP----MQLDSSVRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTL 475
Cdd:COG0464  212 IGVTEDDFEEALKKVLPsrgvLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTL 291
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  476 VARALANECsqgdkRVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTL 555
Cdd:COG0464  292 LAKAVALES-----RSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQL 366
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  556 LALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPLDTF-LEELAENCVGY 634
Cdd:COG0464  367 LTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVdLEELAEITEGY 446
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24497618  635 CGADIKSICAEAALCALRRRYPqiyttseklqldlssINISAKDFEVAMQKMIP 688
Cdd:COG0464  447 SGADIAALVREAALEALREARR---------------REVTLDDFLDALKKIKP 485
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
395-689 1.33e-75

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: 267.16  E-value: 1.33e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    395 DELKGIYKDRMKigaSLADVDPMQLDS------SVRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGP 468
Cdd:TIGR01243  419 KELKVTMKDFME---ALKMVEPSAIREvlvevpNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGP 495
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    469 PGTGKTLVARALANECSQGdkrvaFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQ-I 547
Cdd:TIGR01243  496 PGTGKTLLAKAVATESGAN-----FIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTsV 570
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    548 HSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWnPKPLDTFLEEL 627
Cdd:TIGR01243  571 TDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSM-PLAEDVDLEEL 649
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618    628 AENCVGYCGADIKSICAEAALCALRRRYPQIytTSEKLQLD----LSSINISAKDFEVAMQKMIPA 689
Cdd:TIGR01243  650 AEMTEGYTGADIEAVCREAAMAALRESIGSP--AKEKLEVGeeefLKDLKVEMRHFLEALKKVKPS 713
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
413-698 4.23e-73

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


Pssm-ID: 224143 [Multi-domain]  Cd Length: 406  Bit Score: 249.87  E-value: 4.23e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  413 DVDP----MQLDSS--VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSq 486
Cdd:COG1222  132 EVDPrvsvMEVEEKpdVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTD- 210
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  487 gdkrvAFFMR-KGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLAL---MDGL 562
Cdd:COG1222  211 -----ATFIRvVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELlnqLDGF 285
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  563 DSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPlDTFLEELAENCVGYCGADIKSI 642
Cdd:COG1222  286 DPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLAD-DVDLELLARLTEGFSGADLKAI 364
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618  643 CAEAALCALRRRypqiyttseklqldlsSINISAKDFEVAMQKMIPASQRAVTSPG 698
Cdd:COG1222  365 CTEAGMFAIRER----------------RDEVTMEDFLKAVEKVVKKKKKLSSTAR 404
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
417-658 6.39e-70

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 240.12  E-value: 6.39e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   417 MQLDSS--VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrvAFF 494
Cdd:PRK03992  120 MEVIESpnVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATF 193
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   495 MR-KGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLApvrSSRQDQIHS---SIVST---LLALMDGLDSRGE 567
Cdd:PRK03992  194 IRvVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIA---AKRTDSGTSgdrEVQRTlmqLLAEMDGFDPRGN 270
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   568 IVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPlDTFLEELAENCVGYCGADIKSICAEAA 647
Cdd:PRK03992  271 VKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLAD-DVDLEELAELTEGASGADLKAICTEAG 349
                         250
                  ....*....|.
gi 24497618   648 LCALRRRYPQI 658
Cdd:PRK03992  350 MFAIRDDRTEV 360
26Sp45 TIGR01242
26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an ...
423-654 1.54e-64

26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an internal


Pssm-ID: 130309 [Multi-domain]  Cd Length: 364  Bit Score: 223.91  E-value: 1.54e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    423 VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrvAFFMR-KGADC 501
Cdd:TIGR01242  119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATFIRvVGSEL 192
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    502 LSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVR---SSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLD 578
Cdd:TIGR01242  193 VRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRtdsGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPD 272
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618    579 SIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPlDTFLEELAENCVGYCGADIKSICAEAALCALRRR 654
Cdd:TIGR01242  273 ILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAE-DVDLEAIAKMTEGASGADLKAICTEAGMFAIREE 347
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
428-593 1.32e-62

first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r1-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410927 [Multi-domain]  Cd Length: 166  Bit Score: 210.37  E-value: 1.32e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  428 VGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVG 507
Cdd:cd19519    2 IGGCRKQLAQIREMVELPLRHPELFKAIGIKPPRGILLYGPPGTGKTLIARAVANETG-----AFFFLINGPEIMSKLAG 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  508 ESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRP 587
Cdd:cd19519   77 ESESNLRKAFEEAEKNAPAIIFIDEIDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRF 156

                 ....*.
gi 24497618  588 GRFDRE 593
Cdd:cd19519  157 GRFDRE 162
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
437-592 6.09e-62

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: 208.29  E-value: 6.09e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  437 ALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCLSKWVGESERQLRLL 516
Cdd:cd19511    4 ELKEAVEWPLKHPDAFKRLGIRPPKGVLLYGPPGCGKTLLAKALASEA-----GLNFISVKGPELFSKYVGESERAVREI 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24497618  517 FDQAYQMRPSIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 592
Cdd:cd19511   79 FQKARQAAPCIIFFDEIDSLAPRRGQSDSsGVTDRVVSQLLTELDGIESLKGVVVIAATNRPDMIDPALLRPGRLDK 155
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
445-934 2.38e-61

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 223540 [Multi-domain]  Cd Length: 494  Bit Score: 218.92  E-value: 2.38e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  445 PLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANEcsqgdkRVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMR 524
Cdd:COG0464    3 PLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE------GAEFLSINGPEILSKYVGESELRLRELFEEAEKLA 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  525 PSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLdSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEAR 604
Cdd:COG0464   77 PSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGL-KRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGR 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  605 KEILKIHTRdWNPKPLDTFLEELAENCVGYCGADIKSICAEAALCALRRrypqiyttseKLQLDLSSINISAKDFEVAMQ 684
Cdd:COG0464  156 LEILQIHTR-LMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRR----------AIDLVGEYIGVTEDDFEEALK 224
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  685 KMIPAsqRAVTSPGQALSTVVKPLLQNTVDKILEALQRVFPHAEFRTNKTLdsdiscpllesdlaysdddvpsvyengls 764
Cdd:COG0464  225 KVLPS--RGVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGL----------------------------- 273
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  765 qksshkakdnfnflhlnrnacyqpmSFRPRILIVGEPGFGQgSHLAPAVihALE-KFTVYTLDIPVLFGVSTTSPEETCA 843
Cdd:COG0464  274 -------------------------RPPKGVLLYGPPGTGK-TLLAKAV--ALEsRSRFISVKGSELLSKWVGESEKNIR 325
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  844 QVIREAKRTAPSIVYVPHIHVWWEIVGPT-------LKATFTTLLQNIPSFAPVLLLATSDkphsaLPEEVQELFIR--D 914
Cdd:COG0464  326 ELFEKARKLAPSIIFIDEIDSLASGRGPSedgsgrrVVGQLLTELDGIEKAEGVLVIAATN-----RPDDLDPALLRpgR 400
                        490       500
                 ....*....|....*....|
gi 24497618  915 YGEIFNVQLPDKEERTKFFE 934
Cdd:COG0464  401 FDRLIYVPLPDLEERLEIFK 420
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
390-658 2.41e-57

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 205.39  E-value: 2.41e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   390 LNFRKDELKGIYKDRMKIGASLADVDPMQLDSsvrFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPP 469
Cdd:PTZ00361  150 LHNKTHSVVGILLDEVDPLVSVMKVDKAPLES---YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPP 226
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   470 GTGKTLVARALANECSqgdkrvAFFMR-KGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIH 548
Cdd:PTZ00361  227 GTGKTLLAKAVANETS------ATFLRvVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGE 300
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   549 SSIVSTLLAL---MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPlDTFLE 625
Cdd:PTZ00361  301 KEIQRTMLELlnqLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAE-DVDLE 379
                         250       260       270
                  ....*....|....*....|....*....|...
gi 24497618   626 ELAENCVGYCGADIKSICAEAALCALRRRYPQI 658
Cdd:PTZ00361  380 EFIMAKDELSGADIKAICTEAGLLALRERRMKV 412
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
438-592 1.65e-56

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: 192.71  E-value: 1.65e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  438 LKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANEcsqgdKRVAFFMRKGADCLSKWVGESERQLRLLF 517
Cdd:cd19529    5 LKEAVEWPLLKPEVFKRLGIRPPKGILLYGPPGTGKTLLAKAVATE-----SNANFISVKGPELLSKWVGESEKAIREIF 79
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618  518 DQAYQMRPSIIFFDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 592
Cdd:cd19529   80 RKARQVAPCVIFFDEIDSIAPRRGTTGDSgVTERVVNQLLTELDGLEEMNGVVVIAATNRPDIIDPALLRAGRFDR 155
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
987-1097 3.03e-55

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 187.18  E-value: 3.03e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  987 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPD 1066
Cdd:cd05528    2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81
                         90       100       110
                 ....*....|....*....|....*....|.
gi 24497618 1067 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 1097
Cdd:cd05528   82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112
FtsH_fam TIGR01241
ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct ...
405-658 6.37e-55

ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH. [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273520 [Multi-domain]  Cd Length: 495  Bit Score: 200.20  E-value: 6.37e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    405 MKIGASLADVDpMQLDSSVRFDSVGGLSNHIAALKEMVVFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANEC 484
Cdd:TIGR01241   35 FSFGKSKAKLL-NEEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA 112
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    485 SqgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGlapVRSSRQDQI---HSSIVSTL---LAL 558
Cdd:TIGR01241  113 G-----VPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDA---VGRQRGAGLgggNDEREQTLnqlLVE 184
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    559 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDwnpKPL--DTFLEELAENCVGYCG 636
Cdd:TIGR01241  185 MDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKN---KKLapDVDLKAVARRTPGFSG 261
                          250       260
                   ....*....|....*....|..
gi 24497618    637 ADIKSICAEAALCALRRRYPQI 658
Cdd:TIGR01241  262 ADLANLLNEAALLAARKNKTEI 283
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
425-592 1.29e-52

proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily contains ATPase subunits of the eukaryotic 26S proteasome, and of the archaeal proteasome which carry out ATP-dependent degradation of substrates of the ubiquitin-proteasome pathway. The eukaryotic 26S proteasome consists of a proteolytic 20S core particle (CP), and a 19S regulatory particle (RP) which provides the ATP-dependence and the specificity for ubiquitinated proteins. In the archaea the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). This subfamily also includes various eukaryotic 26S subunits including, proteasome 26S subunit, ATPase 2 (PSMC2, also known as S7 and MSS1) which is a member of the 19S RP and has a chaperone like activity; and proteasome 20S subunit alpha 6 (PSMA6, also known as IOTA, p27K, and PROS27) which is a member of the 20S CP. This RecA-like_PAN subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410910 [Multi-domain]  Cd Length: 171  Bit Score: 182.15  E-value: 1.29e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  425 FDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrvAFFMR-KGADCLS 503
Cdd:cd19502    2 YEDIGGLDEQIREIREVVELPLKHPELFEELGIEPPKGVLLYGPPGTGKTLLAKAVANHTD------ATFIRvVGSELVQ 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  504 KWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLAL---MDGLDSRGEIVVIGATNRLDSI 580
Cdd:cd19502   76 KYIGEGARLVRELFEMAREKAPSIIFIDEIDAIGAKRFDSGTGGDREVQRTMLELlnqLDGFDPRGNIKVIMATNRPDIL 155
                        170
                 ....*....|..
gi 24497618  581 DPALRRPGRFDR 592
Cdd:cd19502  156 DPALLRPGRFDR 167
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
438-592 3.53e-51

second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP in metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the second of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r2-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410936 [Multi-domain]  Cd Length: 161  Bit Score: 177.70  E-value: 3.53e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  438 LKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGdkrvaFFMRKGADCLSKWVGESERQLRLLF 517
Cdd:cd19528    5 LQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQAN-----FISVKGPELLTMWFGESEANVRDIF 79
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24497618  518 DQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSS---IVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 592
Cdd:cd19528   80 DKARAAAPCVLFFDELDSIAKARGGNIGDAGGAadrVINQILTEMDGMNTKKNVFIIGATNRPDIIDPAILRPGRLDQ 157
pup_AAA TIGR03689
proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some ...
423-663 7.63e-51

proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 200312 [Multi-domain]  Cd Length: 512  Bit Score: 188.38  E-value: 7.63e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    423 VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQ-----GDKRVAFFMRK 497
Cdd:TIGR03689  179 VTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVANSLAArigaeGGGKSYFLNIK 258
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    498 GADCLSKWVGESERQLRLLFDQAYQM----RPSIIFFDEIDGLAPVRSS-RQDQIHSSIVSTLLALMDGLDSRGEIVVIG 572
Cdd:TIGR03689  259 GPELLNKYVGETERQIRLIFQRAREKasegRPVIVFFDEMDSLFRTRGSgVSSDVETTVVPQLLAEIDGVESLDNVIVIG 338
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    573 ATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPldtflEELAENcvgycgadikSICAEAALCALR 652
Cdd:TIGR03689  339 ASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFAKYLTDDLPLP-----EDLAAH----------DGDREATAAALI 403
                          250
                   ....*....|..
gi 24497618    653 RR-YPQIYTTSE 663
Cdd:TIGR03689  404 QRvVDALYARSE 415
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
427-593 1.10e-50

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


Pssm-ID: 410926 [Multi-domain]  Cd Length: 169  Bit Score: 176.44  E-value: 1.10e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  427 SVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCLSKWV 506
Cdd:cd19518    1 DIGGMDSTLKELCELLIHPILPPEYFQHLGVEPPRGVLLHGPPGCGKTMLANAIAGEL-----KVPFLKISATEIVSGVS 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  507 GESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL----DSRGEIVVIGATNRLDSIDP 582
Cdd:cd19518   76 GESEEKIRELFDQAISNAPCIVFIDEIDAITPKRESAQREMERRIVSQLLTCMDELnnekTAGGPVLVIGATNRPDSLDP 155
                        170
                 ....*....|.
gi 24497618  583 ALRRPGRFDRE 593
Cdd:cd19518  156 ALRRAGRFDRE 166
ftsH CHL00176
cell division protein; Validated
398-658 4.97e-50

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 189.11  E-value: 4.97e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   398 KGIYKDRMKIGASLADVDpMQLDSSVRFDSVGGLSNHIAALKEMVVFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVA 477
Cdd:CHL00176  156 GGPGQNLMNFGKSKARFQ-MEADTGITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLA 233
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   478 RALANECSqgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSR----QDQiHSSIVS 553
Cdd:CHL00176  234 KAIAGEAE-----VPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGigggNDE-REQTLN 307
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   554 TLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDwnpKPL--DTFLEELAENC 631
Cdd:CHL00176  308 QLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARN---KKLspDVSLELIARRT 384
                         250       260
                  ....*....|....*....|....*..
gi 24497618   632 VGYCGADIKSICAEAALCALRRRYPQI 658
Cdd:CHL00176  385 PGFSGADLANLLNEAAILTARRKKATI 411
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
435-596 5.94e-49

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: 171.31  E-value: 5.94e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  435 IAALKEMVVFPLLYPEVfEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCLSKWVGESERQLR 514
Cdd:cd19481    2 KASLREAVEAPRRGSRL-RRYGLGLPKGILLYGPPGTGKTLLAKALAGEL-----GLPLIVVKLSSLLSKYVGESEKNLR 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  515 LLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSS-IVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDRE 593
Cdd:cd19481   76 KIFERARRLAPCILFIDEIDAIGRKRDSSGESGELRrVLNQLLTELDGVNSRSKVLVIAATNRPDLLDPALLRPGRFDEV 155

                 ...
gi 24497618  594 FLF 596
Cdd:cd19481  156 IEF 158
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
397-692 1.20e-48

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


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 178.80  E-value: 1.20e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   397 LKGIYKDRMKIGASLA---------DVDPMQLDSSVR-----------FDSVGGLSNHIAALKEMVVFPLLYPEVFEKFK 456
Cdd:PTZ00454   96 LSTLNRELLKPNASVAlhrhshavvDILPPEADSSIQllqmsekpdvtYSDIGGLDIQKQEIREAVELPLTCPELYEQIG 175
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   457 IQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGL 536
Cdd:PTZ00454  176 IDPPRGVLLYGPPGTGKTMLAKAVAHHTT-----ATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSI 250
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   537 APVRSSRQ---DQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTR 613
Cdd:PTZ00454  251 ATKRFDAQtgaDREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITS 330
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   614 DWNPKPlDTFLEELAENCVGYCGADIKSICAEAALCALRR-RYPqiyttseklqldlssinISAKDFEVAMQKMIPASQR 692
Cdd:PTZ00454  331 KMNLSE-EVDLEDFVSRPEKISAADIAAICQEAGMQAVRKnRYV-----------------ILPKDFEKGYKTVVRKTDR 392
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
464-598 3.24e-48

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: 425416 [Multi-domain]  Cd Length: 130  Bit Score: 167.77  E-value: 3.24e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    464 LFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSR 543
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKELG-----APFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSG 76
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618    544 QDQIHSSIVSTLLALMDGLDSR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFSL 598
Cdd:pfam00004   77 GDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
423-687 4.21e-47

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


Pssm-ID: 223541 [Multi-domain]  Cd Length: 596  Bit Score: 179.44  E-value: 4.21e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  423 VRFDSVGGLSNHIAALKEMVVFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCL 502
Cdd:COG0465  147 VTFADVAGVDEAKEELSELVDF-LKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEA-----GVPFFSISGSDFV 220
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  503 SKWVGESERQLRLLFDQAYQMRPSIIFFDEID------GLAPvrSSRQDQIHSSIvSTLLALMDGLDSRGEIVVIGATNR 576
Cdd:COG0465  221 EMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDavgrqrGAGL--GGGNDEREQTL-NQLLVEMDGFGGNEGVIVIAATNR 297
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  577 LDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDwnpKPLDTF--LEELAENCVGYCGADIKSICAEAALCALRRR 654
Cdd:COG0465  298 PDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKN---KPLAEDvdLKKIARGTPGFSGADLANLLNEAALLAARRN 374
                        250       260       270
                 ....*....|....*....|....*....|...
gi 24497618  655 YPQiyttseklqldlssinISAKDFEVAMQKMI 687
Cdd:COG0465  375 KKE----------------ITMRDIEEAIDRVI 391
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
438-592 5.65e-46

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


Pssm-ID: 410938 [Multi-domain]  Cd Length: 161  Bit Score: 162.66  E-value: 5.65e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  438 LKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCLSKWVGESERQLRLLF 517
Cdd:cd19530    8 LTMSILRPIKRPDIYKALGIDLPTGVLLYGPPGCGKTLLAKAVANES-----GANFISVKGPELLNKYVGESERAVRQVF 82
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24497618  518 DQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 592
Cdd:cd19530   83 QRARASAPCVIFFDEVDALVPKRGDGGSWASERVVNQLLTEMDGLEERSNVFVIAATNRPDIIDPAMLRPGRLDK 157
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
428-595 6.74e-46

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


Pssm-ID: 410917 [Multi-domain]  Cd Length: 163  Bit Score: 162.52  E-value: 6.74e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  428 VGGLSNHIAALKEMVVFPLLYPEVFeKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVG 507
Cdd:cd19509    1 IAGLDDAKEALKEAVILPSLRPDLF-PGLRGPPRGILLYGPPGTGKTLLARAVASESG-----STFFSISASSLVSKWVG 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  508 ESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL--DSRGEIVVIGATNRLDSIDPALR 585
Cdd:cd19509   75 ESEKIVRALFALARELQPSIIFIDEIDSLLSERGSGEHEASRRVKTEFLVQMDGVlnKPEDRVLVLGATNRPWELDEAFL 154
                        170
                 ....*....|
gi 24497618  586 RpgRFDREFL 595
Cdd:cd19509  155 R--RFEKRIY 162
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
423-593 2.17e-45

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: 161.25  E-value: 2.17e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  423 VRFDSVGGLSNHIAALKEMVVFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCL 502
Cdd:cd19501    1 VTFKDVAGCEEAKEELKEVVEF-LKNPEKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA-----GVPFFSISGSDFV 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  503 SKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTL---LALMDGLDSRGEIVVIGATNRLDS 579
Cdd:cd19501   75 EMFVGVGASRVRDLFEQAKKNAPCIVFIDEIDAVGRKRGAGLGGGHDEREQTLnqlLVEMDGFESNTGVIVIAATNRPDV 154
                        170
                 ....*....|....
gi 24497618  580 IDPALRRPGRFDRE 593
Cdd:cd19501  155 LDPALLRPGRFDRQ 168
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
448-695 3.78e-43

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


Pssm-ID: 224144 [Multi-domain]  Cd Length: 368  Bit Score: 161.90  E-value: 3.78e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  448 YPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSI 527
Cdd:COG1223  139 YLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEA-----KVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCI 213
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  528 IFFDEIDGLAPVR---SSRQDQihSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRrpGRFDREFLFSLPDKEAR 604
Cdd:COG1223  214 VFIDELDAIALDRryqELRGDV--SEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIR--SRFEEEIEFKLPNDEER 289
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  605 KEILKIHTRDWnPKPLDTFLEELAENCVGYCGADIKSICAEAALcalrrrYPQIYTTSEKlqldlssinISAKDFEVAMQ 684
Cdd:COG1223  290 LEILEYYAKKF-PLPVDADLRYLAAKTKGMSGRDIKEKVLKTAL------HRAIAEDREK---------VEREDIEKALK 353
                        250
                 ....*....|.
gi 24497618  685 KMIPASQRAVT 695
Cdd:COG1223  354 KERKRRAPRPK 364
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
440-592 1.34e-42

second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as Peroxin61)/PEX1 is a protein unfoldase; PEX6 and PEX1 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. This subfamily represents the second ATPase domain of PEX6. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410935 [Multi-domain]  Cd Length: 160  Bit Score: 153.05  E-value: 1.34e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  440 EMVVFPLLYPEVFEKfKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQ 519
Cdd:cd19527    7 DTIQLPLEHPELFSS-GLRKRSGILLYGPPGTGKTLLAKAIATECS-----LNFLSVKGPELINMYIGESEANVREVFQK 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618  520 AYQMRPSIIFFDEIDGLAPVRSSRQDQ--IHSSIVSTLLALMDGLDSRGE-IVVIGATNRLDSIDPALRRPGRFDR 592
Cdd:cd19527   81 ARDAKPCVIFFDELDSLAPSRGNSGDSggVMDRVVSQLLAELDGMSSSGQdVFVIGATNRPDLLDPALLRPGRFDK 156
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
425-652 6.29e-42

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 164.44  E-value: 6.29e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   425 FDSVGGLSNHIAALKEMVVFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALAnecsqGDKRVAFFMRKGADCLSK 504
Cdd:PRK10733  151 FADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIA-----GEAKVPFFTISGSDFVEM 224
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   505 WVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTL---LALMDGLDSRGEIVVIGATNRLDSID 581
Cdd:PRK10733  225 FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLnqmLVEMDGFEGNEGIIVIAATNRPDVLD 304
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24497618   582 PALRRPGRFDREFLFSLPDKEARKEILKIHTRDwnpKPLDTFLEE--LAENCVGYCGADIKSICAEAALCALR 652
Cdd:PRK10733  305 PALLRPGRFDRQVVVGLPDVRGREQILKVHMRR---VPLAPDIDAaiIARGTPGFSGADLANLVNEAALFAAR 374
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
436-592 2.03e-40

second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as Peroxin-1)/PEX6 is a protein unfoldase; PEX1 and PEX6 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. PEX-1 is required for stability of PEX5. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410934 [Multi-domain]  Cd Length: 158  Bit Score: 146.80  E-value: 2.03e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  436 AALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVGESERQLRL 515
Cdd:cd19526    3 KALEETIEWPSKYPKIFASSPLRLRSGILLYGPPGCGKTLLASAIASECG-----LNFISVKGPELLNKYIGASEQNVRD 77
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24497618  516 LFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 592
Cdd:cd19526   78 LFSRAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDK 154
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
427-590 9.85e-39

ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase) is an ATPase that plays a critical role in regulating the surface expression of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, thereby regulating synaptic plasticity, learning and memory. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410928 [Multi-domain]  Cd Length: 166  Bit Score: 142.18  E-value: 9.85e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  427 SVGGLSNHIAALKEMVVFPLLYPEVFEKFKI-QPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKW 505
Cdd:cd19520    1 DIGGLDEVITELKELVILPLQRPELFDNSRLlQPPKGVLLYGPPGCGKTMLAKATAKEAG-----ARFINLQVSSLTDKW 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  506 VGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRG--EIVVIGATNRLDSIDPA 583
Cdd:cd19520   76 YGESQKLVAAVFSLASKLQPSIIFIDEIDSFLRQRSSTDHEATAMMKAEFMSLWDGLSTDGncRVIVMGATNRPQDLDEA 155

                 ....*....
gi 24497618  584 LRR--PGRF 590
Cdd:cd19520  156 ILRrmPKRF 164
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
410-586 1.05e-36

ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; it may be involved in DNA double-strand break repair via homologous recombination. Caenorhabditis elegans FIGL-1 is a nuclear protein and controls the mitotic progression in the germ line and mouse FIGL-1 may be involved in the control of male meiosis. human FIGL-1 has been shown to be a centrosome protein involved in ciliogenesis perhaps as a microtubule-severing protein. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410933 [Multi-domain]  Cd Length: 186  Bit Score: 137.04  E-value: 1.05e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  410 SLADVDPMQLDSSVRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKiQPPRGCLFYGPPGTGKTLVARALANECsqgdk 489
Cdd:cd19525    6 ELIMSEIMDHGPPINWADIAGLEFAKKTIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQS----- 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  490 RVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGE-- 567
Cdd:cd19525   80 GATFFSISASSLTSKWVGEGEKMVRALFSVARCKQPAVIFIDEIDSLLSQRGEGEHESSRRIKTEFLVQLDGATTSSEdr 159
                        170
                 ....*....|....*....
gi 24497618  568 IVVIGATNRLDSIDPALRR 586
Cdd:cd19525  160 ILVVGATNRPQEIDEAARR 178
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
422-592 2.38e-36

ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein sorting-associated protein 4 (Vps4) is believed to be involved in intracellular protein transport out of a prevacuolar endosomal compartment. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410929 [Multi-domain]  Cd Length: 170  Bit Score: 135.37  E-value: 2.38e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  422 SVRFDSVGGLSNHIAALKEMVVFPLLYPEVFeKFKIQPPRGCLFYGPPGTGKTLVARALANECSQgdkrvAFFMRKGADC 501
Cdd:cd19521    3 NVKWEDVAGLEGAKEALKEAVILPVKFPHLF-TGNRKPWSGILLYGPPGTGKSYLAKAVATEANS-----TFFSVSSSDL 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  502 LSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL--DSRGeIVVIGATNRLDS 579
Cdd:cd19521   77 VSKWMGESEKLVKQLFAMARENKPSIIFIDEVDSLCGTRGEGESEASRRIKTELLVQMNGVgnDSQG-VLVLGATNIPWQ 155
                        170
                 ....*....|...
gi 24497618  580 IDPALRRpgRFDR 592
Cdd:cd19521  156 LDSAIRR--RFEK 166
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
443-591 2.37e-35

first of two ATPase domains of NSF and SEC18, and similar ATPase domains; N-ethylmaleimide-sensitive factor (NSF) and Saccharomyces cerevisiae Vesicular-fusion protein Sec18, key factors for eukaryotic trafficking, are ATPases and SNARE disassembly chaperones. NSF/Sec18 activate or prime SNAREs, the terminal catalysts of membrane fusion. Sec18/NSF associates with SNARE complexes through binding Sec17/alpha-SNAP. Sec18 has an N-terminal cap domain and two nucleotide-binding domains (D1 and D2) which form the two rings of the hexameric complex. The hydrolysis of ATP by D1 generates most of the energy necessary to disassemble inactive SNARE bundles, while the D2 ring binds ATP to stabilize the homohexamer. This subfamily includes the first (D1) ATPase domain of NSF/Sec18, 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: 410912 [Multi-domain]  Cd Length: 177  Bit Score: 133.00  E-value: 2.37e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  443 VFPllyPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKRVAffmrKGADCLSKWVGESERQLRLLFDQAYQ 522
Cdd:cd19504   21 VFP---PEIVEQLGCKHVKGILLYGPPGTGKTLMARQIGKMLNAREPKIV----NGPEILNKYVGESEANIRKLFADAEE 93
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24497618  523 MRPS--------IIFFDEIDGLAPVRSSRQDQ--IHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFD 591
Cdd:cd19504   94 EQRRlgansglhIIIFDEIDAICKQRGSMAGStgVHDTVVNQLLSKIDGVEQLNNILVIGMTNRKDLIDEALLRPGRLE 172
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
428-586 4.26e-33

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


Pssm-ID: 410932 [Multi-domain]  Cd Length: 164  Bit Score: 126.12  E-value: 4.26e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  428 VGGLSNHIAALKEMVVFPLLYPEVFEKFKiQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVG 507
Cdd:cd19524    2 IAGQDLAKQALQEMVILPSLRPELFTGLR-APARGLLLFGPPGNGKTMLAKAVAAESN-----ATFFNISAASLTSKYVG 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  508 ESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGE--IVVIGATNRLDSIDPA-L 584
Cdd:cd19524   76 EGEKLVRALFAVARELQPSIIFIDEVDSLLSERSEGEHEASRRLKTEFLIEFDGVQSNGDdrVLVMGATNRPQELDDAvL 155

                 ..
gi 24497618  585 RR 586
Cdd:cd19524  156 RR 157
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
428-586 4.65e-33

Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is the catalytic subunit of the Katanin complex which is severs microtubules in an ATP-dependent manner, and is implicated in multiple aspects of microtubule dynamics. In addition to the p60 catalytic ATPase subunit, Katanin contains an accessory subunit (p80 or p80-like). The microtubule-severing activity of the ATPase is essential for female meiotic spindle assembly, and male gamete production; and the katanin complex severing microtubules is under tight regulation during the transition from the meiotic to mitotic stage to allow proper embryogenesis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410930 [Multi-domain]  Cd Length: 170  Bit Score: 126.25  E-value: 4.65e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  428 VGGLSNHIAALKEMVVFPLLYPEVFEKFKiQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVG 507
Cdd:cd19522    2 IADLEEAKKLLEEAVVLPMWMPEFFKGIR-RPWKGVLMVGPPGTGKTLLAKAVATECG-----TTFFNVSSSTLTSKYRG 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  508 ESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIV-STLLALMDGL-------DSRGEIVVIGATNRLDS 579
Cdd:cd19522   76 ESEKLVRLLFEMARFYAPTTIFIDEIDSICSRRGTSEEHEASRRVkSELLVQMDGVggasendDPSKMVMVLAATNFPWD 155

                 ....*..
gi 24497618  580 IDPALRR 586
Cdd:cd19522  156 IDEALRR 162
RecA-like_fidgetin cd19523
ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. ...
428-595 2.87e-27

ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410931 [Multi-domain]  Cd Length: 163  Bit Score: 109.20  E-value: 2.87e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  428 VGGLSNHIAALKEMVVFPLLYPEVFEKFkIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVG 507
Cdd:cd19523    2 IAGLGALKAAIKEEVLWPLLRPDAFSGL-LRLPRSILLFGPRGTGKTLLGRCLASQLG-----ATFLRLRGSTLVAKWAG 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  508 ESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIhSSIVSTLLALMDGLDSRGE--IVVIGATNRLDSIDPALR 585
Cdd:cd19523   76 EGEKILQASFLAARCRQPSVLFISDLDALLSSQDDEASPV-GRLQVELLAQLDGVLGSGEdgVLVVCTTSKPEEIDESLR 154
                        170
                 ....*....|
gi 24497618  586 RpgRFDREFL 595
Cdd:cd19523  155 R--YFSKRLL 162
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
450-598 6.95e-27

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: 107.62  E-value: 6.95e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  450 EVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgDKRVAFFMRKGADCLSKWVGESERQ---LRLLFDQAYQMRPS 526
Cdd:cd00009    9 ALREALELPPPKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDLLEGLVVAELFGhflVRLLFELAEKAKPG 86
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24497618  527 IIFFDEIDGLAPvrssrqdQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSL 598
Cdd:cd00009   87 VLFIDEIDSLSR-------GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
987-1089 6.56e-20

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 85.89  E-value: 6.56e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  987 RELRIFLRNVthRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPD 1066
Cdd:cd04369    3 KKLRSLLDAL--KKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGP 80
                         90       100
                 ....*....|....*....|...
gi 24497618 1067 RDPgdrlIRHRACALRDTAYAII 1089
Cdd:cd04369   81 GSP----IYKDAKKLEKLFEKLL 99
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
459-600 7.98e-20

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: 87.43  E-value: 7.98e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618     459 PPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFF------------MRKGADCLSKWVGESERQLRLLFDQAYQMRPS 526
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIdgedileevldqLLLIIVGGKKASGSGELRLRLALALARKLKPD 80
                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24497618     527 IIFFDEIDGLAPVRSSRQDQihssiVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPgRFDREFLFSLPD 600
Cdd:smart00382   81 VLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
ycf46 CHL00195
Ycf46; Provisional
421-646 9.63e-19

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 91.23  E-value: 9.63e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   421 SSVRFDSVGGLSNHIAALKEMvvfpllyPEVFEK----FKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFfmr 496
Cdd:CHL00195  223 VNEKISDIGGLDNLKDWLKKR-------STSFSKqasnYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDV--- 292
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   497 kgADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIV-STLLALMDglDSRGEIVVIGATN 575
Cdd:CHL00195  293 --GKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKGDSGTTNRVlATFITWLS--EKKSPVFVVATAN 368
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24497618   576 RLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPLDTF-LEELAENCVGYCGADIKSICAEA 646
Cdd:CHL00195  369 NIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYdIKKLSKLSNKFSGAEIEQSIIEA 440
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
1009-1104 1.66e-18

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 81.83  E-value: 1.66e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618 1009 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDrdpgdrlirhracalrDTAYAI 1088
Cdd:cd05509   22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGP----------------DTEYYK 85
                         90
                 ....*....|....*.
gi 24497618 1089 IKEELDEDFEQLCEEI 1104
Cdd:cd05509   86 CANKLEKFFWKKLKEL 101
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
453-594 1.67e-17

ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of photosynthesis in cyanobacteria, especially in CO2 uptake and utilization. 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: 410915 [Multi-domain]  Cd Length: 161  Bit Score: 81.26  E-value: 1.67e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  453 EKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKRV---AFFmrkgadclSKWVGESERQLRLLFDQAYQMRPSIIF 529
Cdd:cd19507   24 SAYGLPTPKGLLLVGIQGTGKSLTAKAIAGVWQLPLLRLdmgRLF--------GGLVGESESRLRQMIQTAEAIAPCVLW 95
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618  530 FDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDglDSRGEIVVIGATNRLDSIDPALRRPGRFDREF 594
Cdd:cd19507   96 IDEIEKGFSNADSKGDSgTSSRVLGTFLTWLQ--EKKKPVFVVATANNVQSLPPELLRKGRFDEIF 159
BROMO smart00297
bromo domain;
982-1092 1.75e-17

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 79.24  E-value: 1.75e-17
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618     982 EEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNAL 1061
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80
                            90       100       110
                    ....*....|....*....|....*....|.
gi 24497618    1062 EYNPDrdpgDRLIRHRACALRDTAYAIIKEE 1092
Cdd:smart00297   81 TYNGP----DSEVYKDAKKLEKFFEKKLREL 107
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
989-1089 3.80e-17

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 77.82  E-value: 3.80e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  989 LRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNpDRD 1068
Cdd:cd05512    2 LEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN-AKD 80
                         90       100
                 ....*....|....*....|..
gi 24497618 1069 PgdrlIRHRACA-LRDTAYAII 1089
Cdd:cd05512   81 T----IFYRAAVrLRDQGGAIL 98
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
1009-1064 3.58e-15

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 72.68  E-value: 3.58e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618 1009 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 1064
Cdd:cd05511   21 FHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYN 76
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
1009-1065 1.26e-14

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 70.42  E-value: 1.26e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 24497618   1009 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNP 1065
Cdd:pfam00439   17 FLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNG 73
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
1008-1069 4.50e-14

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 69.23  E-value: 4.50e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24497618 1008 VFTKPVDP--DEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDP 1069
Cdd:cd05498   23 PFYKPVDPeaLGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHP 86
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
461-592 2.32e-13

Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of mitochondrial respiratory chain complex III and plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex. RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410918 [Multi-domain]  Cd Length: 153  Bit Score: 68.92  E-value: 2.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  461 RGCLFYGPPGTGKTLVARALANEcsqgdkrvaffMRKGADCLS-KWVGESERQLRLLFDQAYQmrPSIIFFDEID----- 534
Cdd:cd19510   24 RGYLLYGPPGTGKSSFIAALAGE-----------LDYDICDLNlSEVVLTDDRLNHLLNTAPK--QSIILLEDIDaafes 90
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24497618  535 GLAPVRSSRQDQIHSSI-VSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 592
Cdd:cd19510   91 REHNKKNPSAYGGLSRVtFSGLLNALDGVASSEERIVFMTTNHIERLDPALIRPGRVDM 149
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
1009-1090 1.03e-12

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 65.93  E-value: 1.03e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618 1009 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNpdRDPGDRLIRHrACALRDTAYAI 1088
Cdd:cd05510   29 FLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYN--SDPSHPLRRH-ANFMKKKAEHL 105

                 ..
gi 24497618 1089 IK 1090
Cdd:cd05510  106 LK 107
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
999-1065 1.11e-12

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 65.43  E-value: 1.11e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24497618  999 RLAIDKRFRVFTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNP 1065
Cdd:cd05506   11 KLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNP 79
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
1004-1064 4.20e-12

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 63.87  E-value: 4.20e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618 1004 KRFRV---FTKPVDPDE--VPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 1064
Cdd:cd05500   17 KRLKDarpFLVPVDPVKlnIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFN 82
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
1008-1069 6.34e-12

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 63.07  E-value: 6.34e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24497618 1008 VFTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDP 1069
Cdd:cd05499   23 PFLDPVDPValNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTD 86
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
464-584 1.51e-11

ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as Thyroid hormone receptor interactor 13 (TRIP13) and 16E1BP) is a key regulator of specific chromosomal events, like the control of G2/prophase processes such as DNA break formation and recombination, checkpoint signaling, and chromosome synapsis. 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: 410916 [Multi-domain]  Cd Length: 199  Bit Score: 65.16  E-value: 1.51e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  464 LFYGPPGTGKTLVARALANECSqgdKRVAFFMRKG-------ADCLSKWVGESERQLRLLFDQAYQM---RPSIIF--FD 531
Cdd:cd19508   56 LLHGPPGTGKTSLCKALAQKLS---IRLSSRYRYGqlieinsHSLFSKWFSESGKLVTKMFQKIQELiddKDALVFvlID 132
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 24497618  532 EIDGLAPVRSSRQDQIHSS----IVSTLLALMDGLDSRGEIVVIGATNRLDSIDPAL 584
Cdd:cd19508  133 EVESLAAARSASSSGTEPSdairVVNAVLTQIDRIKRYHNNVILLTSNLLEKIDVAF 189
T7SS_EccA TIGR03922
type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the ...
464-628 2.88e-11

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


Pssm-ID: 188437 [Multi-domain]  Cd Length: 557  Bit Score: 67.95  E-value: 2.88e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    464 LFYGPPGTGKTLVARALANE-CSQGD-KRVAFFMRKGADCLSKWVGESERQLRLLFDQAYQmrpSIIFFDEIDGLAPVRS 541
Cdd:TIGR03922  316 LFAGPPGTGKTTIARVVAKIyCGLGVlRKPLVREVSRADLIGQYIGESEAKTNEIIDSALG---GVLFLDEAYTLVETGY 392
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    542 SRQDQIHSSIVSTLLALMDglDSRGEIVVIGATNRLD-----SIDPALRRpgRFDR--EFLFSLPDkearkEILKIHTRD 614
Cdd:TIGR03922  393 GQKDPFGLEAIDTLLARME--NDRDRLVVIGAGYRKDldkflEVNEGLRS--RFTRviEFPSYSPD-----ELVEIARRM 463
                          170
                   ....*....|....
gi 24497618    615 WNPKplDTFLEELA 628
Cdd:TIGR03922  464 ATER--DSVLDDAA 475
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
1009-1068 5.81e-11

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 60.87  E-value: 5.81e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618 1009 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRD 1068
Cdd:cd05504   33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHT 92
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
1009-1064 1.52e-10

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 59.35  E-value: 1.52e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618 1009 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 1064
Cdd:cd05513   22 FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYN 77
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
1009-1069 1.28e-09

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 56.61  E-value: 1.28e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24497618 1009 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDP 1069
Cdd:cd05503   21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSE 81
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
1009-1067 1.49e-09

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 57.08  E-value: 1.49e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24497618 1009 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDR 1067
Cdd:cd05496   26 FRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNK 84
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
1009-1064 1.54e-09

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 56.39  E-value: 1.54e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618 1009 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 1064
Cdd:cd05505   21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYY 76
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
915-1153 2.70e-09

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 60.59  E-value: 2.70e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  915 YGEIFNVQLPDKEERTKFFEDLILKQAAKPPISKKKAVLQALevLPVAPPPEPRSLTAEEVKRLEEQEEDTFReLRIFLR 994
Cdd:COG5076   84 GGITYSPFEKNRPESLRFDEIVFLAIESVTPESGLGSLLMAH--LKTSVKKRKTPKIEDELLYADNKAIAKFK-KQLFLR 160
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  995 NvthrlaIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNpdrDPGDRLI 1074
Cdd:COG5076  161 D------GRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVY 231
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618 1075 RHRacalrdtayAIIKEELDEDFEQLCEEIQESRKKRGCSSSKYAPSY-YHVMPKQNSTLVGDKR-SDPEQNEKLKTPST 1152
Cdd:COG5076  232 VDA---------KELEKYFLKLIEEIPEEMLELSIKPGREEREERESVlITNSQAHVGAWPFLRPvSDEEVPDYYKDIRD 302

                 .
gi 24497618 1153 P 1153
Cdd:COG5076  303 P 303
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
988-1065 3.75e-09

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 55.53  E-value: 3.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  988 ELRIFLRNVTHRLAIDKRFRV-FTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 1064
Cdd:cd05495    3 ELRQALMPTLEKLYKQDPESLpFRQPVDPKllGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYN 82

                 .
gi 24497618 1065 P 1065
Cdd:cd05495   83 R 83
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
624-658 4.34e-09

AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.


Pssm-ID: 436099 [Multi-domain]  Cd Length: 45  Bit Score: 53.31  E-value: 4.34e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 24497618    624 LEELAENCVGYCGADIKSICAEAALCALRRRYPQI 658
Cdd:pfam17862    4 LEELAERTEGFSGADLEALCREAALAALRRGLEAV 38
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
1009-1074 1.20e-08

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 53.96  E-value: 1.20e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24497618 1009 FTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPdrdPGDRLI 1074
Cdd:cd05497   26 FQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNK---PGDDVV 90
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
998-1066 1.58e-08

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 53.46  E-value: 1.58e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  998 HRLAIdkrfrVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN-PD 1066
Cdd:cd05515   21 RRLSL-----IFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNePD 85
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
1017-1064 5.36e-08

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 52.04  E-value: 5.36e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 24497618 1017 EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 1064
Cdd:cd05516   36 ELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFN 83
Bromodomain_1 cd05494
Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated ...
980-1110 7.08e-08

Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99926  Cd Length: 114  Bit Score: 52.06  E-value: 7.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  980 EQEEDTFRELRIFLRNvthrlaidKRFRVFTKPVDPDE--VPDYVTVIKQPMDLSsviSKIDLHKYLTVKDYLRdidlic 1057
Cdd:cd05494    3 EALERVLRELKRHRRN--------EDAWPFLEPVNPPRrgAPDYRDVIKRPMSFG---TKVNNIVETGARDLED------ 65
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 24497618 1058 snalEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESRKK 1110
Cdd:cd05494   66 ----LQIVQEDPADKQIDDEGRRSPSNIYAVEALEQLIVFQCKQVKGLKQKRH 114
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
461-591 8.22e-08

ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase domains; ATPase AAA-domain protein 3 (ATAD3) is a ubiquitously expressed mitochondrial protein involved in mitochondrial dynamics, DNA-nucleoid structural organization, cholesterol transport and steroidogenesis. The ATAD3 gene family in human comprises three paralog genes: ATAD3A, ATAD3B and ATAD3C. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410920 [Multi-domain]  Cd Length: 150  Bit Score: 52.91  E-value: 8.22e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  461 RGCLFYGPPGTGKTLVARALANEC-------SQGDkrVAFFMRKGADCLSK---WVGESERQLrllfdqayqmrpsIIFF 530
Cdd:cd19512   23 RNILFYGPPGTGKTLFAKKLALHSgmdyaimTGGD--VAPMGREGVTAIHKvfdWANTSRRGL-------------LLFV 87
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24497618  531 DEIDGLAPVRSSrqDQIHSSIVSTLLALM--DGLDSRgEIVVIGATNRLDSIDPALRrpGRFD 591
Cdd:cd19512   88 DEADAFLRKRST--EKISEDLRAALNAFLyrTGEQSN-KFMLVLASNQPEQFDWAIN--DRID 145
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
464-605 9.52e-08

AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.


Pssm-ID: 400187 [Multi-domain]  Cd Length: 168  Bit Score: 52.97  E-value: 9.52e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    464 LFYGPPGTGKTLVARALANEcsQGDKRVAF-------FMRKGAdcLSKWVGESERQLR-----LLFDQAYQMRPSIIFFD 531
Cdd:pfam07724    7 LFLGPTGVGKTELAKALAEL--LFGDERALiridmseYMEEHS--VSRLIGAPPGYVGyeeggQLTEAVRRKPYSIVLID 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    532 EIdglapvrssrqDQIHSSIVSTLLALMDG---LDSRGE------IVVIGATNrLDSIDP--ALRRPGRFDREFLFSLPD 600
Cdd:pfam07724   83 EI-----------EKAHPGVQNDLLQILEGgtlTDKQGRtvdfknTLFIMTGN-FGSEKIsdASRLGDSPDYELLKEEVM 150

                   ....*
gi 24497618    601 KEARK 605
Cdd:pfam07724  151 DLLKK 155
RecA-like_Ycf2 cd19505
ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; ...
459-592 9.87e-08

ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; however, its function remains unclear. The gene encoding YCF2 is the largest known plastid gene in angiosperms and has been used to predict phylogenetic relationships. 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: 410913 [Multi-domain]  Cd Length: 161  Bit Score: 53.15  E-value: 9.87e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  459 PPRGCLFYGPPGTGKTLVARALA------------NECSqgDKRVAFFMRKGADCLSKWvGESERQLRLLFDQAYQMRPS 526
Cdd:cd19505   11 PSKGILLIGSIETGRSYLIKSLAansyvplirislNKLL--YNKPDFGNDDWIDGMLIL-KESLHRLNLQFELAKAMSPC 87
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24497618  527 IIFFDEIDGLApVRSSRQDQIHSSivSTLLALMDGLDSRG-------EIVVIGATNRLDSIDPALRRPGRFDR 592
Cdd:cd19505   88 IIWIPNIHELN-VNRSTQNLEEDP--KLLLGLLLNYLSRDfeksstrNILVIASTHIPQKVDPALIAPNRLDT 157
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
1008-1068 1.05e-07

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 51.21  E-value: 1.05e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24497618 1008 VFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN-PDRD 1068
Cdd:cd05507   23 VFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNsSDHD 84
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
970-1066 5.57e-07

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 49.21  E-value: 5.57e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  970 LTAEEVKRLEeqeedtfrelRIFLRNVTHRLAIDkrfrvFTKPVDPdEVPDYVTVIKQPMDLSSVISKIDLH---KYLTV 1046
Cdd:cd05502    1 LSPIDQRKCE----------RLLLELYCHELSLP-----FHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKspqHYSSP 64
                         90       100
                 ....*....|....*....|
gi 24497618 1047 KDYLRDIDLICSNALEYNPD 1066
Cdd:cd05502   65 EEFVADVRLMFKNCYKFNEE 84
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
465-651 6.63e-07

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


Pssm-ID: 225165 [Multi-domain]  Cd Length: 436  Bit Score: 53.39  E-value: 6.63e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  465 FYGPPGTGKTLVARALANECSqgdkrvAFFMRKGAdclskwVGESERQLRLLFDQAYQMRPS----IIFFDEIDGLapvR 540
Cdd:COG2256   53 LWGPPGTGKTTLARLIAGTTN------AAFEALSA------VTSGVKDLREIIEEARKNRLLgrrtILFLDEIHRF---N 117
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  541 SSRQDqihssivsTLLALMDgldsRGEIVVIGAT--NRLDSIDPALRrpgrfDREFLFSLP--DKEARKEILKIHTRDwN 616
Cdd:COG2256  118 KAQQD--------ALLPHVE----NGTIILIGATteNPSFELNPALL-----SRARVFELKplSSEDIKKLLKRALLD-E 179
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 24497618  617 PKPLDTFLEELAENC----VGYCGADiksicAEAALCAL 651
Cdd:COG2256  180 ERGLGGQIIVLDEEAldylVRLSNGD-----ARRALNLL 213
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
1005-1064 1.07e-06

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 48.39  E-value: 1.07e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618 1005 RFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 1064
Cdd:cd05522   24 LTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYN 83
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
1007-1064 2.25e-06

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 47.43  E-value: 2.25e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24497618 1007 RVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 1064
Cdd:cd05517   25 ELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN 82
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
463-585 2.92e-06

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 51.24  E-value: 2.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   463 CLFYGPPGTGKTLVARALANECsqgDKRVAFFmrkGAdclskwVGESERQLRLLFDQAYQMRPS----IIFFDEIDGLAp 538
Cdd:PRK13342   39 MILWGPPGTGKTTLARIIAGAT---DAPFEAL---SA------VTSGVKDLREVIEEARQRRSAgrrtILFIDEIHRFN- 105
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 24497618   539 vrSSRQDqihssivsTLLALMDgldsRGEIVVIGAT--NRLDSIDPALR 585
Cdd:PRK13342  106 --KAQQD--------ALLPHVE----DGTITLIGATteNPSFEVNPALL 140
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
1017-1064 2.22e-05

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 44.74  E-value: 2.22e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 24497618 1017 EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 1064
Cdd:cd05518   35 DYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
1019-1065 2.61e-05

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 44.25  E-value: 2.61e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24497618 1019 PDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNP 1065
Cdd:cd05520   37 PDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNV 83
PRK04195 PRK04195
replication factor C large subunit; Provisional
456-536 8.17e-05

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 46.84  E-value: 8.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   456 KIQPPRGCLFYGPPGTGKTLVARALAN-------ECSQGDKRvaffmrkGADCLSKWVGESERQlRLLFDQAYQmrpsII 528
Cdd:PRK04195   35 KGKPKKALLLYGPPGVGKTSLAHALANdygweviELNASDQR-------TADVIERVAGEAATS-GSLFGARRK----LI 102

                  ....*...
gi 24497618   529 FFDEIDGL 536
Cdd:PRK04195  103 LLDEVDGI 110
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
1009-1064 1.12e-04

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 42.37  E-value: 1.12e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24497618 1009 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 1064
Cdd:cd05508   23 FLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYN 78
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
464-580 1.41e-04

Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and eukaryotic Heat shock protein 104 (Hsp104) are ATP-dependent molecular chaperones and essential proteins of the heat-shock response. ClpB/Hsp104 ATPases, in concert with the DnaK/Hsp70 chaperone system, disaggregate and reactivate aggregated proteins. This RecA-like_ClpB_Hsp104_like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410907 [Multi-domain]  Cd Length: 178  Bit Score: 44.09  E-value: 1.41e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  464 LFYGPPGTGKTLVARALANECSQGDK---RVAF--FMRKGADCLSK-----WVGESERQlrLLFDQAYQMRPSIIFFDEI 533
Cdd:cd19499   45 LFLGPTGVGKTELAKALAELLFGDEDnliRIDMseYMEKHSVSRLIgappgYVGYTEGG--QLTEAVRRKPYSVVLLDEI 122
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24497618  534 dglapvrssrqDQIHSSIVSTLLALMD-G--LDSRGEIVVIGAT--------------NRLDSI 580
Cdd:cd19499  123 -----------EKAHPDVQNLLLQVLDdGrlTDSHGRTVDFKNTiiimtsnhfrpeflNRIDEI 175
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
460-494 1.75e-04

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


Pssm-ID: 224401 [Multi-domain]  Cd Length: 254  Bit Score: 44.70  E-value: 1.75e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 24497618  460 PRGCLFYGPPGTGKTLVARALANECSQGDKRVAFF 494
Cdd:COG1484  105 GENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFI 139
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
1019-1063 2.19e-04

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 41.94  E-value: 2.19e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 24497618 1019 PDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEY 1063
Cdd:cd05524   39 PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAY 83
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
979-1065 3.16e-04

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 41.94  E-value: 3.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  979 EEQEEDTFRELRIFLRNVthRLAIDKRFRVftkPVD-PDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLIC 1057
Cdd:cd05529   23 DEERERLISGLDKLLLSL--QLEIAEYFEY---PVDlRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLIL 97

                 ....*...
gi 24497618 1058 SNALEYNP 1065
Cdd:cd05529   98 SNAETFNE 105
ClpA COG0542
ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein ...
467-590 3.34e-04

ATP-dependent Clp protease ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 223616 [Multi-domain]  Cd Length: 786  Bit Score: 44.96  E-value: 3.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618  467 GPPGTGKTLVARALANECSQGD-----KRVAFF------MRKGAdclsKWVGESERQLRLLFDQAYQMRPSIIFFDEID- 534
Cdd:COG0542  198 GEPGVGKTAIVEGLAQRIVNGDvpeslKDKRIYsldlgsLVAGA----KYRGEFEERLKAVLKEVEKSKNVILFIDEIHt 273
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24497618  535 --GLAPVRSSRQDqihssiVSTLL--ALmdgldSRGEIVVIGAT-----NRLDSIDPALRRpgRF 590
Cdd:COG0542  274 ivGAGATEGGAMD------AANLLkpAL-----ARGELRCIGATtldeyRKYIEKDAALER--RF 325
PRK08116 PRK08116
hypothetical protein; Validated
448-493 2.63e-03

hypothetical protein; Validated


Pssm-ID: 236153 [Multi-domain]  Cd Length: 268  Bit Score: 41.16  E-value: 2.63e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 24497618   448 YPEVFEKFKIQPpRGCLFYGPPGTGKTLVARALANECSQGDKRVAF 493
Cdd:PRK08116  103 YVKKFEEMKKEN-VGLLLWGSVGTGKTYLAACIANELIEKGVPVIF 147
ycf46 CHL00195
Ycf46; Provisional
793-934 2.89e-03

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 41.93  E-value: 2.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   793 PR-ILIVGEPGFGQgSHLAPAVIHALeKFTVYTLDIPVLFGVSTTSPEETCAQVIREAKRTAPSIVYVPHIHVWWEIV-- 869
Cdd:CHL00195  259 PRgLLLVGIQGTGK-SLTAKAIANDW-QLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSes 336
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24497618   870 ----GPTLK--ATFTTLLQNIPSfaPVLLLATSDKPHSaLPEEVqelfIRD--YGEIFNVQLPDKEERTKFFE 934
Cdd:CHL00195  337 kgdsGTTNRvlATFITWLSEKKS--PVFVVATANNIDL-LPLEI----LRKgrFDEIFFLDLPSLEEREKIFK 402
AAA_22 pfam13401
AAA domain;
457-580 3.94e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 38.86  E-value: 3.94e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    457 IQPPRGCLF-YGPPGTGKTLVARALANECSQGDKRVAFFMRKGADCLS---KWV-------GESERQLRLLFDQAYQ--- 522
Cdd:pfam13401    1 IRFGAGILVlTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKdllRALlralglpLSGRLSKEELLAALQQlll 80
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    523 --MRPSIIFFDEIDGLapvrssrqdqiHSSIVSTLLALMDGLDSRGEIVVIGaTNRLDSI 580
Cdd:pfam13401   81 alAVAVVLIIDEAQHL-----------SLEALEELRDLLNLSSKLLQLILVG-TPELREL 128
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
1004-1064 4.44e-03

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 38.09  E-value: 4.44e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24497618 1004 KRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 1064
Cdd:cd05519   22 KLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYN 82
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteristic of the ...
460-571 5.17e-03

AAA ATPase domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 39.41  E-value: 5.17e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618    460 PRGCLFYGPPGTGKTLVARALANecSQGDKRVAFFMRKGADCLSK---WVGESERQLRLLFDQAYQMRPSIIFFDEIDGL 536
Cdd:pfam13191   24 PPSVLLTGEAGTGKTTLLRELLR--ALERDGGYFLRGKCDENLPYsplLEALTREGLLRQLLDELESSLLEAWRAALLEA 101
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 24497618    537 APVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVI 571
Cdd:pfam13191  102 LAPVPELPGDLAERLLDLLLRLLDLLARGERPLVL 136
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
1018-1090 6.56e-03

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 37.75  E-value: 6.56e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24497618 1018 VPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRlirhRACALRDtAYAIIK 1090
Cdd:cd05525   38 NPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGR----DVCRLRK-AYYQAK 105
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
463-483 7.06e-03

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 40.11  E-value: 7.06e-03
                          10        20
                  ....*....|....*....|.
gi 24497618   463 CLFYGPPGTGKTLVARALANE 483
Cdd:PRK00080   54 VLLYGPPGLGKTTLANIIANE 74
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles pfam01695, but was ...
463-539 8.78e-03

IS21-like element helper ATPase IstB; This protein family model resembles pfam01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements.


Pssm-ID: 439516  Cd Length: 232  Bit Score: 39.38  E-value: 8.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24497618   463 CLFYGPPGTGKTLVARALANE-CSQGdKRVAFFmrKGADCLSKWvGESERQLRLlfDQAYQ--MRPSIIFFDEIdGLAPV 539
Cdd:NF038214   93 VLLLGPPGTGKTHLAIALGYAaCRQG-YRVRFT--TAADLVEQL-AQARADGRL--GRLLRrlARYDLLIIDEL-GYLPF 165
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit [Replication, ...
463-483 8.99e-03

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


Pssm-ID: 225164 [Multi-domain]  Cd Length: 332  Bit Score: 39.85  E-value: 8.99e-03
                         10        20
                 ....*....|....*....|.
gi 24497618  463 CLFYGPPGTGKTLVARALANE 483
Cdd:COG2255   55 VLLFGPPGLGKTTLAHIIANE 75
PRK13341 PRK13341
AAA family ATPase;
464-482 9.93e-03

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 40.42  E-value: 9.93e-03
                          10
                  ....*....|....*....
gi 24497618   464 LFYGPPGTGKTLVARALAN 482
Cdd:PRK13341   56 ILYGPPGVGKTTLARIIAN 74
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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