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Conserved domains on  [gi|2462619170|ref|XP_054216339|]
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ATPase family AAA domain-containing protein 2 isoform X2 [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 ...
 257-426 2.34e-115

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: 2.34e-115
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  257 SVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFFMRKGADCLSKWV 336
Cdd:cd19517      1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  337 GESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRR 416
Cdd:cd19517     81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160

                          170
                   ....*....|
gi 2462619170  417 PGRFDREFLF 426
Cdd:cd19517    161 PGRFDREFYF 170
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 817-927 5.37e-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: 186.41  E-value: 5.37e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  817 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPD 896
Cdd:cd05528      2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2462619170  897 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 927
Cdd:cd05528     82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 454-488 2.00e-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: 465537 [Multi-domain]  Cd Length: 45  Bit Score: 54.08  E-value: 2.00e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2462619170  454 LEELAENCVGYCGADIKSICAEAALCALRRRYPQI 488
Cdd:pfam17862    4 LEELAERTEGFSGADLEALCREAALAALRRGLEAV 38
ycf46 super family cl31783
Ycf46; Provisional
 623-764 3.01e-03

Ycf46; Provisional


The actual alignment was detected with superfamily member CHL00195:

Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 41.54  E-value: 3.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  623 PR-ILIVGEPGFGQgSHLAPAVIHALeKFTVYTLDIPVLFGVSTTSPEETCAQVIREAKRTAPSIVYVPHIHVWWEIV-- 699
Cdd:CHL00195   259 PRgLLLVGIQGTGK-SLTAKAIANDW-QLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSes 336

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462619170  700 ----GPTLK--ATFTTLLQNIPSfaPVLLLATSDKPHSaLPEEVqelfIRD--YGEIFNVQLPDKEERTKFFE 764
Cdd:CHL00195   337 kgdsGTTNRvlATFITWLSEKKS--PVFVVATANNIDL-LPLEI----LRKgrFDEIFFLDLPSLEEREKIFK 402
 
Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 257-426 2.34e-115

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: 2.34e-115
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  257 SVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFFMRKGADCLSKWV 336
Cdd:cd19517      1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  337 GESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRR 416
Cdd:cd19517     81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160

                          170
                   ....*....|
gi 2462619170  417 PGRFDREFLF 426
Cdd:cd19517    161 PGRFDREFYF 170
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 252-523 8.61e-93

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 301.15  E-value: 8.61e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  252 SVRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADC 331
Cdd:COG1222     74 DVTFDDIGGLDEQIEEIREAVELPLKNPELFRKYGIEPPKGVLLYGPPGTGKTLLAKAVAGELG-----APFIRVRGSEL 148

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  332 LSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSI 410
Cdd:COG1222    149 VSKYIGEGARNVREVFELAREKAPSIIFIDEIDAIAARRTDDGTsGEVQRTVNQLLAELDGFESRGDVLIIAATNRPDLL 228

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  411 DPALRRPGRFDREFLFSLPDKEARKEILKIHTRDwnpKPL--DTFLEELAENCVGYCGADIKSICAEAALCALRRRYPQi 488
Cdd:COG1222    229 DPALLRPGRFDRVIEVPLPDEEAREEILKIHLRD---MPLadDVDLDKLAKLTEGFSGADLKAIVTEAGMFAIREGRDT- 304

                          250       260       270
                   ....*....|....*....|....*....|....*
gi 2462619170  489 yttseklqldlssinISAKDFEVAMQKMIPASQRA 523
Cdd:COG1222    305 ---------------VTMEDLEKAIEKVKKKTETA 324
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 253-524 2.51e-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: 268.31  E-value: 2.51e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  253 VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCL 332
Cdd:TIGR01243  175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG-----AYFISINGPEIM 249

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  333 SKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDP 412
Cdd:TIGR01243  250 SKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDP 329

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  413 ALRRPGRFDREFLFSLPDKEARKEILKIHTRDwNPKPLDTFLEELAENCVGYCGADIKSICAEAALCALRRRYPQIYTTS 492
Cdd:TIGR01243  330 ALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKINF 408

                          250       260       270
                   ....*....|....*....|....*....|....*
gi 2462619170  493 EKLQLD---LSSINISAKDFEVAMQKMIPASQRAV 524
Cdd:TIGR01243  409 EAEEIPaevLKELKVTMKDFMEALKMVEPSAIREV 443
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 247-488 3.88e-70

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 240.50  E-value: 3.88e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  247 MQLDSS--VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrvAFF 324
Cdd:PRK03992   120 MEVIESpnVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATF 193

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  325 MR-KGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLApvrSSRQDQIHS---SIVST---LLALMDGLDSRGE 397
Cdd:PRK03992   194 IRvVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIA---AKRTDSGTSgdrEVQRTlmqLLAEMDGFDPRGN 270

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  398 IVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPlDTFLEELAENCVGYCGADIKSICAEAA 477
Cdd:PRK03992   271 VKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLAD-DVDLEELAELTEGASGADLKAICTEAG 349

                          250
                   ....*....|.
gi 2462619170  478 LCALRRRYPQI 488
Cdd:PRK03992   350 MFAIRDDRTEV 360
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 817-927 5.37e-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: 186.41  E-value: 5.37e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  817 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPD 896
Cdd:cd05528      2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2462619170  897 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 927
Cdd:cd05528     82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 294-428 3.72e-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: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 167.77  E-value: 3.72e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  294 LFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSR 373
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKELG-----APFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSG 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462619170  374 QDQIHSSIVSTLLALMDGLDSR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFSL 428
Cdd:pfam00004   77 GDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 289-430 5.91e-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: 87.81  E-value: 5.91e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170   289 PPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFF------------MRKGADCLSKWVGESERQLRLLFDQAYQMRPS 356
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIdgedileevldqLLLIIVGGKKASGSGELRLRLALALARKLKPD 80

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462619170   357 IIFFDEIDGLAPVRSSRQDQihssiVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPgRFDREFLFSLPD 430
Cdd:smart00382   81 VLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
BROMO smart00297
bromo domain;
812-922 2.88e-17

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 78.47  E-value: 2.88e-17
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170   812 EEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNAL 891
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100       110
                    ....*....|....*....|....*....|.
gi 2462619170   892 EYNPDrdpgDRLIRHRACALRDTAYAIIKEE 922
Cdd:smart00297   81 TYNGP----DSEVYKDAKKLEKFFEKKLREL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 839-895 2.01e-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: 69.65  E-value: 2.01e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462619170  839 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNP 895
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 ...
 454-488 2.00e-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: 465537 [Multi-domain]  Cd Length: 45  Bit Score: 54.08  E-value: 2.00e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2462619170  454 LEELAENCVGYCGADIKSICAEAALCALRRRYPQI 488
Cdd:pfam17862    4 LEELAERTEGFSGADLEALCREAALAALRRGLEAV 38
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 745-942 3.49e-09

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 60.20  E-value: 3.49e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  745 YGEIFNVQLPDKEERTKFFEDLILKQAAKPPISKKKAVLQALevLPVAPPPEPRSLTAEEVKRLEEQEEDTFReLRIFLR 824
Cdd:COG5076     84 GGITYSPFEKNRPESLRFDEIVFLAIESVTPESGLGSLLMAH--LKTSVKKRKTPKIEDELLYADNKAIAKFK-KQLFLR 160

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  825 NvthrlaIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNpdrDPGDRLI 904
Cdd:COG5076    161 D------GRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVY 231

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 2462619170  905 RHRacalrdtayAIIKEELDEDFEQLCEEIQESRKKRG 942
Cdd:COG5076    232 VDA---------KELEKYFLKLIEEIPEEMLELSIKPG 260
ycf46 CHL00195
Ycf46; Provisional
 623-764 3.01e-03

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 41.54  E-value: 3.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  623 PR-ILIVGEPGFGQgSHLAPAVIHALeKFTVYTLDIPVLFGVSTTSPEETCAQVIREAKRTAPSIVYVPHIHVWWEIV-- 699
Cdd:CHL00195   259 PRgLLLVGIQGTGK-SLTAKAIANDW-QLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSes 336

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462619170  700 ----GPTLK--ATFTTLLQNIPSfaPVLLLATSDKPHSaLPEEVqelfIRD--YGEIFNVQLPDKEERTKFFE 764
Cdd:CHL00195   337 kgdsGTTNRvlATFITWLSEKKS--PVFVVATANNIDL-LPLEI----LRKgrFDEIFFLDLPSLEEREKIFK 402
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 293-369 5.20e-03

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


Pssm-ID: 439516  Cd Length: 232  Bit Score: 39.76  E-value: 5.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  293 CLFYGPPGTGKTLVARALANE-CSQGdKRVAFFmrKGADCLSKWvGESERQLRLlfDQAYQ--MRPSIIFFDEIdGLAPV 369
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 ...
 257-426 2.34e-115

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: 2.34e-115
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  257 SVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFFMRKGADCLSKWV 336
Cdd:cd19517      1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  337 GESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRR 416
Cdd:cd19517     81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160

                          170
                   ....*....|
gi 2462619170  417 PGRFDREFLF 426
Cdd:cd19517    161 PGRFDREFYF 170
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 252-523 8.61e-93

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 301.15  E-value: 8.61e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  252 SVRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADC 331
Cdd:COG1222     74 DVTFDDIGGLDEQIEEIREAVELPLKNPELFRKYGIEPPKGVLLYGPPGTGKTLLAKAVAGELG-----APFIRVRGSEL 148

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  332 LSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSI 410
Cdd:COG1222    149 VSKYIGEGARNVREVFELAREKAPSIIFIDEIDAIAARRTDDGTsGEVQRTVNQLLAELDGFESRGDVLIIAATNRPDLL 228

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  411 DPALRRPGRFDREFLFSLPDKEARKEILKIHTRDwnpKPL--DTFLEELAENCVGYCGADIKSICAEAALCALRRRYPQi 488
Cdd:COG1222    229 DPALLRPGRFDRVIEVPLPDEEAREEILKIHLRD---MPLadDVDLDKLAKLTEGFSGADLKAIVTEAGMFAIREGRDT- 304

                          250       260       270
                   ....*....|....*....|....*....|....*
gi 2462619170  489 yttseklqldlssinISAKDFEVAMQKMIPASQRA 523
Cdd:COG1222    305 ---------------VTMEDLEKAIEKVKKKTETA 324
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 257-426 9.16e-81

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: 261.46  E-value: 9.16e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  257 SVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWV 336
Cdd:cd19503      1 DIGGLDEQIASLKELIELPLKYPELFRALGLKPPRGVLLHGPPGTGKTLLARAVANEAG-----ANFLSISGPSIVSKYL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  337 GESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRR 416
Cdd:cd19503     76 GESEKNLREIFEEARSHAPSIIFIDEIDALAPKREEDQREVERRVVAQLLTLMDGMSSRGKVVVIAATNRPDAIDPALRR 155

                          170
                   ....*....|
gi 2462619170  417 PGRFDREFLF 426
Cdd:cd19503    156 PGRFDREVEI 165
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 253-524 2.51e-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: 268.31  E-value: 2.51e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  253 VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCL 332
Cdd:TIGR01243  175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG-----AYFISINGPEIM 249

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  333 SKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDP 412
Cdd:TIGR01243  250 SKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDP 329

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  413 ALRRPGRFDREFLFSLPDKEARKEILKIHTRDwNPKPLDTFLEELAENCVGYCGADIKSICAEAALCALRRRYPQIYTTS 492
Cdd:TIGR01243  330 ALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKINF 408

                          250       260       270
                   ....*....|....*....|....*....|....*
gi 2462619170  493 EKLQLD---LSSINISAKDFEVAMQKMIPASQRAV 524
Cdd:TIGR01243  409 EAEEIPaevLKELKVTMKDFMEALKMVEPSAIREV 443
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 225-519 7.98e-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: 266.77  E-value: 7.98e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  225 DELKGIYKDRMKigaSLADVDPMQLDS------SVRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGP 298
Cdd:TIGR01243  419 KELKVTMKDFME---ALKMVEPSAIREvlvevpNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGP 495

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  299 PGTGKTLVARALANECSQGdkrvaFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQ-I 377
Cdd:TIGR01243  496 PGTGKTLLAKAVATESGAN-----FIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTsV 570

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  378 HSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWnPKPLDTFLEEL 457
Cdd:TIGR01243  571 TDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSM-PLAEDVDLEEL 649

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462619170  458 AENCVGYCGADIKSICAEAALCALRRRYPQIytTSEKLQLD----LSSINISAKDFEVAMQKMIPA 519
Cdd:TIGR01243  650 AEMTEGYTGADIEAVCREAAMAALRESIGSP--AKEKLEVGeeefLKDLKVEMRHFLEALKKVKPS 713
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 244-488 1.66e-75

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


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 255.99  E-value: 1.66e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  244 VDPMQLDSSVRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAF 323
Cdd:COG0464    145 EEELLELREAILDDLGGLEEVKEELRELVALPLKRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL-----GLPL 219

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  324 FMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLdsRGEIVVIGA 403
Cdd:COG0464    220 IEVDLSDLVSKYVGETEKNLREVFDKARGLAPCVLFIDEADALAGKRGEVGDGVGRRVVNTLLTEMEEL--RSDVVVIAA 297

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  404 TNRLDSIDPALRRpgRFDREFLFSLPDKEARKEILKIHTRDwNPKPLDTFLEELAENCVGYCGADIKSICAEAALCALRR 483
Cdd:COG0464    298 TNRPDLLDPALLR--RFDEIIFFPLPDAEERLEIFRIHLRK-RPLDEDVDLEELAEATEGLSGADIRNVVRRAALQALRL 374


                   ....*
gi 2462619170  484 RYPQI 488
Cdd:COG0464    375 GREPV 379
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 247-488 3.88e-70

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 240.50  E-value: 3.88e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  247 MQLDSS--VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrvAFF 324
Cdd:PRK03992   120 MEVIESpnVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATF 193

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  325 MR-KGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLApvrSSRQDQIHS---SIVST---LLALMDGLDSRGE 397
Cdd:PRK03992   194 IRvVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIA---AKRTDSGTSgdrEVQRTlmqLLAEMDGFDPRGN 270

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  398 IVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPlDTFLEELAENCVGYCGADIKSICAEAA 477
Cdd:PRK03992   271 VKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLAD-DVDLEELAELTEGASGADLKAICTEAG 349

                          250
                   ....*....|.
gi 2462619170  478 LCALRRRYPQI 488
Cdd:PRK03992   350 MFAIRDDRTEV 360
26Sp45 TIGR01242
26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an ...
 253-484 1.20e-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: 1.20e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  253 VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrvAFFMR-KGADC 331
Cdd:TIGR01242  119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATFIRvVGSEL 192

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  332 LSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVR---SSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLD 408
Cdd:TIGR01242  193 VRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRtdsGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPD 272

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462619170  409 SIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPlDTFLEELAENCVGYCGADIKSICAEAALCALRRR 484
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 ...
 258-423 1.28e-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: 1.28e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  258 VGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVG 337
Cdd:cd19519      2 IGGCRKQLAQIREMVELPLRHPELFKAIGIKPPRGILLYGPPGTGKTLIARAVANETG-----AFFFLINGPEIMSKLAG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  338 ESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRP 417
Cdd:cd19519     77 ESESNLRKAFEEAEKNAPAIIFIDEIDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRF 156


                   ....*.
gi 2462619170  418 GRFDRE 423
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 ...
 267-422 4.91e-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: 4.91e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  267 ALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCLSKWVGESERQLRLL 346
Cdd:cd19511      4 ELKEAVEWPLKHPDAFKRLGIRPPKGVLLYGPPGCGKTLLAKALASEA-----GLNFISVKGPELFSKYVGESERAVREI 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462619170  347 FDQAYQMRPSIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 422
Cdd:cd19511     79 FQKARQAAPCIIFFDEIDSLAPRRGQSDSsGVTDRVVSQLLTELDGIESLKGVVVIAATNRPDMIDPALLRPGRLDK 155
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 220-488 2.68e-57

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 205.00  E-value: 2.68e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  220 LNFRKDELKGIYKDRMKIGASLADVDPMQLDSsvrFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPP 299
Cdd:PTZ00361   150 LHNKTHSVVGILLDEVDPLVSVMKVDKAPLES---YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPP 226

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  300 GTGKTLVARALANECSqgdkrvAFFMR-KGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIH 378
Cdd:PTZ00361   227 GTGKTLLAKAVANETS------ATFLRvVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGE 300

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  379 SSIVSTLLAL---MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPlDTFLE 455
Cdd:PTZ00361   301 KEIQRTMLELlnqLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAE-DVDLE 379

                          250       260       270
                   ....*....|....*....|....*....|...
gi 2462619170  456 ELAENCVGYCGADIKSICAEAALCALRRRYPQI 488
Cdd:PTZ00361   380 EFIMAKDELSGADIKAICTEAGLLALRERRMKV 412
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 268-422 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 2462619170  268 LKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANEcsqgdKRVAFFMRKGADCLSKWVGESERQLRLLF 347
Cdd:cd19529      5 LKEAVEWPLLKPEVFKRLGIRPPKGILLYGPPGTGKTLLAKAVATE-----SNANFISVKGPELLSKWVGESEKAIREIF 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462619170  348 DQAYQMRPSIIFFDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 422
Cdd:cd19529     80 RKARQVAPCVIFFDEIDSIAPRRGTTGDSgVTERVVNQLLTELDGLEEMNGVVVIAATNRPDIIDPALLRAGRFDR 155
FtsH_fam TIGR01241
ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct ...
 235-488 4.97e-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: 4.97e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  235 MKIGASLADVDpMQLDSSVRFDSVGGLSNHIAALKEMVVFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANEC 314
Cdd:TIGR01241   35 FSFGKSKAKLL-NEEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA 112

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  315 SqgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGlapVRSSRQDQI---HSSIVSTL---LAL 388
Cdd:TIGR01241  113 G-----VPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDA---VGRQRGAGLgggNDEREQTLnqlLVE 184

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  389 MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDwnpKPL--DTFLEELAENCVGYCG 466
Cdd:TIGR01241  185 MDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKN---KKLapDVDLKAVARRTPGFSG 261

                          250       260
                   ....*....|....*....|..
gi 2462619170  467 ADIKSICAEAALCALRRRYPQI 488
Cdd:TIGR01241  262 ADLANLLNEAALLAARKNKTEI 283
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 817-927 5.37e-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: 186.41  E-value: 5.37e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  817 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPD 896
Cdd:cd05528      2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2462619170  897 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 927
Cdd:cd05528     82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 255-422 1.27e-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: 1.27e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  255 FDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrvAFFMR-KGADCLS 333
Cdd:cd19502      2 YEDIGGLDEQIREIREVVELPLKHPELFEELGIEPPKGVLLYGPPGTGKTLLAKAVANHTD------ATFIRvVGSELVQ 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  334 KWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLAL---MDGLDSRGEIVVIGATNRLDSI 410
Cdd:cd19502     76 KYIGEGARLVRELFEMAREKAPSIIFIDEIDAIGAKRFDSGTGGDREVQRTMLELlnqLDGFDPRGNIKVIMATNRPDIL 155

                          170
                   ....*....|..
gi 2462619170  411 DPALRRPGRFDR 422
Cdd:cd19502    156 DPALLRPGRFDR 167
pup_AAA TIGR03689
proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some ...
 253-493 2.34e-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: 189.92  E-value: 2.34e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  253 VRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQ-----GDKRVAFFMRK 327
Cdd:TIGR03689  179 VTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVANSLAArigaeGGGKSYFLNIK 258

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  328 GADCLSKWVGESERQLRLLFDQAYQM----RPSIIFFDEIDGLAPVRSS-RQDQIHSSIVSTLLALMDGLDSRGEIVVIG 402
Cdd:TIGR03689  259 GPELLNKYVGETERQIRLIFQRAREKasegRPVIVFFDEMDSLFRTRGSgVSSDVETTVVPQLLAEIDGVESLDNVIVIG 338

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  403 ATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPldtflEELAENcvgycgadikSICAEAALCALR 482
Cdd:TIGR03689  339 ASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFAKYLTDDLPLP-----EDLAAH----------DGDREATAAALI 403

                          250
                   ....*....|..
gi 2462619170  483 RR-YPQIYTTSE 493
Cdd:TIGR03689  404 QRvVDALYARSE 415
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 268-422 3.20e-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: 3.20e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  268 LKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGdkrvaFFMRKGADCLSKWVGESERQLRLLF 347
Cdd:cd19528      5 LQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQAN-----FISVKGPELLTMWFGESEANVRDIF 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462619170  348 DQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSS---IVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 422
Cdd:cd19528     80 DKARAAAPCVLFFDELDSIAKARGGNIGDAGGAadrVINQILTEMDGMNTKKNVFIIGATNRPDIIDPAILRPGRLDQ 157
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 257-423 1.00e-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: 1.00e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  257 SVGGLSNHIAALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCLSKWV 336
Cdd:cd19518      1 DIGGMDSTLKELCELLIHPILPPEYFQHLGVEPPRGVLLHGPPGCGKTMLANAIAGEL-----KVPFLKISATEIVSGVS 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  337 GESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL----DSRGEIVVIGATNRLDSIDP 412
Cdd:cd19518     76 GESEEKIRELFDQAISNAPCIVFIDEIDAITPKRESAQREMERRIVSQLLTCMDELnnekTAGGPVLVIGATNRPDSLDP 155

                          170
                   ....*....|.
gi 2462619170  413 ALRRPGRFDRE 423
Cdd:cd19518    156 ALRRAGRFDRE 166
ftsH CHL00176
cell division protein; Validated
 228-488 4.14e-50

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 189.11  E-value: 4.14e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  228 KGIYKDRMKIGASLADVDpMQLDSSVRFDSVGGLSNHIAALKEMVVFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVA 307
Cdd:CHL00176   156 GGPGQNLMNFGKSKARFQ-MEADTGITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLA 233

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  308 RALANECSqgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSR----QDQiHSSIVS 383
Cdd:CHL00176   234 KAIAGEAE-----VPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGigggNDE-REQTLN 307

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  384 TLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDwnpKPL--DTFLEELAENC 461
Cdd:CHL00176   308 QLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARN---KKLspDVSLELIARRT 384

                          250       260
                   ....*....|....*....|....*..
gi 2462619170  462 VGYCGADIKSICAEAALCALRRRYPQI 488
Cdd:CHL00176   385 PGFSGADLANLLNEAAILTARRKKATI 411
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
253-484 8.80e-50

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


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 186.78  E-value: 8.80e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  253 VRFDSVGGLSNHIAALKEMVVFpLLYPEVFEKF--KIqpPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFF------ 324
Cdd:COG0465    139 VTFDDVAGVDEAKEELQEIVDF-LKDPEKFTRLgaKI--PKGVLLVGPPGTGKTLLAKAVAGEAG-----VPFFsisgsd 210

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  325 ---MRKGadclskwVGESeRqLRLLFDQAYQMRPSIIFFDEIDGLAPVRSS--------RqDQihssivsTL---LALMD 390
Cdd:COG0465    211 fveMFVG-------VGAS-R-VRDLFEQAKKNAPCIIFIDEIDAVGRQRGAglggghdeR-EQ-------TLnqlLVEMD 273

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  391 GLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDwnpKPL--DTFLEELAENCVGYCGAD 468
Cdd:COG0465    274 GFEGNEGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDVKGREAILKVHARK---KPLapDVDLEVIARRTPGFSGAD 350

                          250
                   ....*....|....*.
gi 2462619170  469 IKSICAEAALCALRRR 484
Cdd:COG0465    351 LANLVNEAALLAARRN 366
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
255-476 2.38e-49

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 175.46  E-value: 2.38e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  255 FDSVGGLSNHIAALKEMVVFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCLSK 334
Cdd:COG1223      1 LDDVVGQEEAKKKLKLIIKE-LRRRENLRKFGLWPPRKILFYGPPGTGKTMLAEALAGEL-----KLPLLTVRLDSLIGS 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  335 WVGESERQLRLLFDQAYQmRPSIIFFDEIDGLAPVRSSRQD--QIHsSIVSTLLALMDGLDSrgEIVVIGATNRLDSIDP 412
Cdd:COG1223     75 YLGETARNLRKLFDFARR-APCVIFFDEFDAIAKDRGDQNDvgEVK-RVVNALLQELDGLPS--GSVVIAATNHPELLDS 150

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462619170  413 ALRRpgRFDREFLFSLPDKEARKEILKIHTRDWnPKPLDTFLEELAENCVGYCGADIKSICAEA 476
Cdd:COG1223    151 ALWR--RFDEVIEFPLPDKEERKEILELNLKKF-PLPFELDLKKLAKKLEGLSGADIEKVLKTA 211
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 265-426 3.91e-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: 171.70  E-value: 3.91e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  265 IAALKEMVVFPLLYPEVfEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCLSKWVGESERQLR 344
Cdd:cd19481      2 KASLREAVEAPRRGSRL-RRYGLGLPKGILLYGPPGTGKTLLAKALAGEL-----GLPLIVVKLSSLLSKYVGESEKNLR 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  345 LLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSS-IVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDRE 423
Cdd:cd19481     76 KIFERARRLAPCILFIDEIDAIGRKRDSSGESGELRrVLNQLLTELDGVNSRSKVLVIAATNRPDLLDPALLRPGRFDEV 155


                   ...
gi 2462619170  424 FLF 426
Cdd:cd19481    156 IEF 158
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 227-522 6.67e-49

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


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 179.57  E-value: 6.67e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  227 LKGIYKDRMKIGASLA---------DVDPMQLDSSVR-----------FDSVGGLSNHIAALKEMVVFPLLYPEVFEKFK 286
Cdd:PTZ00454    96 LSTLNRELLKPNASVAlhrhshavvDILPPEADSSIQllqmsekpdvtYSDIGGLDIQKQEIREAVELPLTCPELYEQIG 175

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  287 IQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGL 366
Cdd:PTZ00454   176 IDPPRGVLLYGPPGTGKTMLAKAVAHHTT-----ATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSI 250

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  367 APVRSSRQ---DQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTR 443
Cdd:PTZ00454   251 ATKRFDAQtgaDREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITS 330

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  444 DWNPKPlDTFLEELAENCVGYCGADIKSICAEAALCALRR-RYPqiyttseklqldlssinISAKDFEVAMQKMIPASQR 522
Cdd:PTZ00454   331 KMNLSE-EVDLEDFVSRPEKISAADIAAICQEAGMQAVRKnRYV-----------------ILPKDFEKGYKTVVRKTDR 392
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 294-428 3.72e-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: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 167.77  E-value: 3.72e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  294 LFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSR 373
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKELG-----APFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSG 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462619170  374 QDQIHSSIVSTLLALMDGLDSR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFSL 428
Cdd:pfam00004   77 GDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 258-425 4.61e-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: 162.91  E-value: 4.61e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  258 VGGLSNHIAALKEMVVFPLLYPEVFeKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVG 337
Cdd:cd19509      1 IAGLDDAKEALKEAVILPSLRPDLF-PGLRGPPRGILLYGPPGTGKTLLARAVASESG-----STFFSISASSLVSKWVG 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  338 ESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL--DSRGEIVVIGATNRLDSIDPALR 415
Cdd:cd19509     75 ESEKIVRALFALARELQPSIIFIDEIDSLLSERGSGEHEASRRVKTEFLVQMDGVlnKPEDRVLVLGATNRPWELDEAFL 154

                          170
                   ....*....|
gi 2462619170  416 RpgRFDREFL 425
Cdd:cd19509    155 R--RFEKRIY 162
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 268-422 5.80e-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: 5.80e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  268 LKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCLSKWVGESERQLRLLF 347
Cdd:cd19530      8 LTMSILRPIKRPDIYKALGIDLPTGVLLYGPPGCGKTLLAKAVANES-----GANFISVKGPELLNKYVGESERAVRQVF 82

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462619170  348 DQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 422
Cdd:cd19530     83 QRARASAPCVIFFDEVDALVPKRGDGGSWASERVVNQLLTEMDGLEERSNVFVIAATNRPDIIDPAMLRPGRLDK 157
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 253-423 1.96e-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: 1.96e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  253 VRFDSVGGLSNHIAALKEMVVFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkRVAFFMRKGADCL 332
Cdd:cd19501      1 VTFKDVAGCEEAKEELKEVVEF-LKNPEKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA-----GVPFFSISGSDFV 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  333 SKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTL---LALMDGLDSRGEIVVIGATNRLDS 409
Cdd:cd19501     75 EMFVGVGASRVRDLFEQAKKNAPCIVFIDEIDAVGRKRGAGLGGGHDEREQTLnqlLVEMDGFESNTGVIVIAATNRPDV 154

                          170
                   ....*....|....
gi 2462619170  410 IDPALRRPGRFDRE 423
Cdd:cd19501    155 LDPALLRPGRFDRQ 168
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 270-422 1.28e-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: 1.28e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  270 EMVVFPLLYPEVFEKfKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQ 349
Cdd:cd19527      7 DTIQLPLEHPELFSS-GLRKRSGILLYGPPGTGKTLLAKAIATECS-----LNFLSVKGPELINMYIGESEANVREVFQK 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462619170  350 AYQMRPSIIFFDEIDGLAPVRSSRQDQ--IHSSIVSTLLALMDGLDSRGE-IVVIGATNRLDSIDPALRRPGRFDR 422
Cdd:cd19527     81 ARDAKPCVIFFDELDSLAPSRGNSGDSggVMDRVVSQLLAELDGMSSSGQdVFVIGATNRPDLLDPALLRPGRFDK 156
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
255-533 3.14e-42

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 165.21  E-value: 3.14e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  255 FDSVGGLSNHIAALKEMVVFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALAnecsqGDKRVAFFMRKGADCLSK 334
Cdd:PRK10733   151 FADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIA-----GEAKVPFFTISGSDFVEM 224

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  335 WVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTL---LALMDGLDSRGEIVVIGATNRLDSID 411
Cdd:PRK10733   225 FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLnqmLVEMDGFEGNEGIIVIAATNRPDVLD 304

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  412 PALRRPGRFDREFLFSLPDKEARKEILKIHTRDwnpKPLDTFLEE--LAENCVGYCGADIKSICAEAALCALR--RRYpq 487
Cdd:PRK10733   305 PALLRPGRFDRQVVVGLPDVRGREQILKVHMRR---VPLAPDIDAaiIARGTPGFSGADLANLVNEAALFAARgnKRV-- 379

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*...
gi 2462619170  488 iyttseklqldlssinISAKDFEVAMQKMIPASQR--AVTSPGQALST 533
Cdd:PRK10733   380 ----------------VSMVEFEKAKDKIMMGAERrsMVMTEAQKEST 411
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 266-422 2.09e-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: 146.42  E-value: 2.09e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  266 AALKEMVVFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVGESERQLRL 345
Cdd:cd19526      3 KALEETIEWPSKYPKIFASSPLRLRSGILLYGPPGCGKTLLASAIASECG-----LNFISVKGPELLNKYIGASEQNVRD 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462619170  346 LFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 422
Cdd:cd19526     78 LFSRAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDK 154
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 257-420 1.05e-38

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: 1.05e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  257 SVGGLSNHIAALKEMVVFPLLYPEVFEKFKI-QPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKW 335
Cdd:cd19520      1 DIGGLDEVITELKELVILPLQRPELFDNSRLlQPPKGVLLYGPPGCGKTMLAKATAKEAG-----ARFINLQVSSLTDKW 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  336 VGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRG--EIVVIGATNRLDSIDPA 413
Cdd:cd19520     76 YGESQKLVAAVFSLASKLQPSIIFIDEIDSFLRQRSSTDHEATAMMKAEFMSLWDGLSTDGncRVIVMGATNRPQDLDEA 155


                   ....*....
gi 2462619170  414 LRR--PGRF 420
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; ...
 240-416 7.21e-37

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: 137.43  E-value: 7.21e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  240 SLADVDPMQLDSSVRFDSVGGLSNHIAALKEMVVFPLLYPEVFEKFKiQPPRGCLFYGPPGTGKTLVARALANECsqgdk 319
Cdd:cd19525      6 ELIMSEIMDHGPPINWADIAGLEFAKKTIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQS----- 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  320 RVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGE-- 397
Cdd:cd19525     80 GATFFSISASSLTSKWVGEGEKMVRALFSVARCKQPAVIFIDEIDSLLSQRGEGEHESSRRIKTEFLVQLDGATTSSEdr 159

                          170
                   ....*....|....*....
gi 2462619170  398 IVVIGATNRLDSIDPALRR 416
Cdd:cd19525    160 ILVVGATNRPQEIDEAARR 178
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 252-422 1.47e-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: 136.15  E-value: 1.47e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  252 SVRFDSVGGLSNHIAALKEMVVFPLLYPEVFeKFKIQPPRGCLFYGPPGTGKTLVARALANECSQgdkrvAFFMRKGADC 331
Cdd:cd19521      3 NVKWEDVAGLEGAKEALKEAVILPVKFPHLF-TGNRKPWSGILLYGPPGTGKSYLAKAVATEANS-----TFFSVSSSDL 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  332 LSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL--DSRGeIVVIGATNRLDS 409
Cdd:cd19521     77 VSKWMGESEKLVKQLFAMARENKPSIIFIDEVDSLCGTRGEGESEASRRIKTELLVQMNGVgnDSQG-VLVLGATNIPWQ 155

                          170
                   ....*....|...
gi 2462619170  410 IDPALRRpgRFDR 422
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; ...
 273-421 1.62e-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: 133.38  E-value: 1.62e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  273 VFPllyPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKRVAffmrKGADCLSKWVGESERQLRLLFDQAYQ 352
Cdd:cd19504     21 VFP---PEIVEQLGCKHVKGILLYGPPGTGKTLMARQIGKMLNAREPKIV----NGPEILNKYVGESEANIRKLFADAEE 93

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462619170  353 MRPS--------IIFFDEIDGLAPVRSSRQDQ--IHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFD 421
Cdd:cd19504     94 EQRRlgansglhIIIFDEIDAICKQRGSMAGStgVHDTVVNQLLSKIDGVEQLNNILVIGMTNRKDLIDEALLRPGRLE 172
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 258-416 2.22e-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: 126.50  E-value: 2.22e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  258 VGGLSNHIAALKEMVVFPLLYPEVFEKFKiQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVG 337
Cdd:cd19524      2 IAGQDLAKQALQEMVILPSLRPELFTGLR-APARGLLLFGPPGNGKTMLAKAVAAESN-----ATFFNISAASLTSKYVG 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  338 ESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGE--IVVIGATNRLDSIDPA-L 414
Cdd:cd19524     76 EGEKLVRALFAVARELQPSIIFIDEVDSLLSERSEGEHEASRRLKTEFLIEFDGVQSNGDdrVLVMGATNRPQELDDAvL 155


                   ..
gi 2462619170  415 RR 416
Cdd:cd19524    156 RR 157
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 258-416 4.20e-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: 4.20e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  258 VGGLSNHIAALKEMVVFPLLYPEVFEKFKiQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVG 337
Cdd:cd19522      2 IADLEEAKKLLEEAVVLPMWMPEFFKGIR-RPWKGVLMVGPPGTGKTLLAKAVATECG-----TTFFNVSSSTLTSKYRG 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  338 ESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIV-STLLALMDGL-------DSRGEIVVIGATNRLDS 409
Cdd:cd19522     76 ESEKLVRLLFEMARFYAPTTIFIDEIDSICSRRGTSEEHEASRRVkSELLVQMDGVggasendDPSKMVMVLAATNFPWD 155


                   ....*..
gi 2462619170  410 IDPALRR 416
Cdd:cd19522    156 IDEALRR 162
RecA-like_fidgetin cd19523
ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. ...
 258-425 2.60e-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: 2.60e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  258 VGGLSNHIAALKEMVVFPLLYPEVFEKFkIQPPRGCLFYGPPGTGKTLVARALANECSqgdkrVAFFMRKGADCLSKWVG 337
Cdd:cd19523      2 IAGLGALKAAIKEEVLWPLLRPDAFSGL-LRLPRSILLFGPRGTGKTLLGRCLASQLG-----ATFLRLRGSTLVAKWAG 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  338 ESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIhSSIVSTLLALMDGLDSRGE--IVVIGATNRLDSIDPALR 415
Cdd:cd19523     76 EGEKILQASFLAARCRQPSVLFISDLDALLSSQDDEASPV-GRLQVELLAQLDGVLGSGEdgVLVVCTTSKPEEIDESLR 154

                          170
                   ....*....|
gi 2462619170  416 RpgRFDREFL 425
Cdd:cd19523    155 R--YFSKRLL 162
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 280-428 6.54e-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: 6.54e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  280 EVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgDKRVAFFMRKGADCLSKWVGESERQ---LRLLFDQAYQMRPS 356
Cdd:cd00009      9 ALREALELPPPKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDLLEGLVVAELFGhflVRLLFELAEKAKPG 86

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462619170  357 IIFFDEIDGLAPvrssrqdQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSL 428
Cdd:cd00009     87 VLFIDEIDSLSR-------GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 289-430 5.91e-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: 87.81  E-value: 5.91e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170   289 PPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFF------------MRKGADCLSKWVGESERQLRLLFDQAYQMRPS 356
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIdgedileevldqLLLIIVGGKKASGSGELRLRLALALARKLKPD 80

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462619170   357 IIFFDEIDGLAPVRSSRQDQihssiVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPgRFDREFLFSLPD 430
Cdd:smart00382   81 VLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 817-919 1.38e-19

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: 84.73  E-value: 1.38e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  817 RELRIFLRNVthRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPD 896
Cdd:cd04369      3 KKLRSLLDAL--KKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGP 80

                           90       100
                   ....*....|....*....|...
gi 2462619170  897 RDPgdrlIRHRACALRDTAYAII 919
Cdd:cd04369     81 GSP----IYKDAKKLEKLFEKLL 99
ycf46 CHL00195
Ycf46; Provisional
 251-476 1.01e-18

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 90.85  E-value: 1.01e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  251 SSVRFDSVGGLSNHIAALKEMvvfpllyPEVFEK----FKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFfmr 326
Cdd:CHL00195   223 VNEKISDIGGLDNLKDWLKKR-------STSFSKqasnYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDV--- 292

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  327 kgADCLSKWVGESERQLRLLFDQAYQMRPSIIFFDEIDGLAPVRSSRQDQIHSSIV-STLLALMDglDSRGEIVVIGATN 405
Cdd:CHL00195   293 --GKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKGDSGTTNRVlATFITWLS--EKKSPVFVVATAN 368

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462619170  406 RLDSIDPALRRPGRFDREFLFSLPDKEARKEILKIHTRDWNPKPLDTF-LEELAENCVGYCGADIKSICAEA 476
Cdd:CHL00195   369 NIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYdIKKLSKLSNKFSGAEIEQSIIEA 440
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 839-934 2.69e-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: 81.06  E-value: 2.69e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  839 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDrdpgdrlirhracalrDTAYAI 918
Cdd:cd05509     22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGP----------------DTEYYK 85

                           90
                   ....*....|....*.
gi 2462619170  919 IKEELDEDFEQLCEEI 934
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 ...
 283-424 1.51e-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: 1.51e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  283 EKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKRV---AFFmrkgadclSKWVGESERQLRLLFDQAYQMRPSIIF 359
Cdd:cd19507     24 SAYGLPTPKGLLLVGIQGTGKSLTAKAIAGVWQLPLLRLdmgRLF--------GGLVGESESRLRQMIQTAEAIAPCVLW 95

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462619170  360 FDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDglDSRGEIVVIGATNRLDSIDPALRRPGRFDREF 424
Cdd:cd19507     96 IDEIEKGFSNADSKGDSgTSSRVLGTFLTWLQ--EKKKPVFVVATANNVQSLPPELLRKGRFDEIF 159
BROMO smart00297
bromo domain;
812-922 2.88e-17

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 78.47  E-value: 2.88e-17
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170   812 EEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNAL 891
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100       110
                    ....*....|....*....|....*....|.
gi 2462619170   892 EYNPDrdpgDRLIRHRACALRDTAYAIIKEE 922
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 ...
 819-919 5.80e-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: 77.44  E-value: 5.80e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  819 LRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNpDRD 898
Cdd:cd05512      2 LEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN-AKD 80

                           90       100
                   ....*....|....*....|..
gi 2462619170  899 PgdrlIRHRACA-LRDTAYAII 919
Cdd:cd05512     81 T----IFYRAAVrLRDQGGAIL 98
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 839-894 4.27e-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: 72.30  E-value: 4.27e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462619170  839 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 894
Cdd:cd05511     21 FHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYN 76
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 839-895 2.01e-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: 69.65  E-value: 2.01e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462619170  839 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNP 895
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 ...
 838-899 6.86e-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: 68.84  E-value: 6.86e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462619170  838 VFTKPVDP--DEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDP 899
Cdd:cd05498     23 PFYKPVDPeaLGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHP 86
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 291-422 1.98e-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: 1.98e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  291 RGCLFYGPPGTGKTLVARALANEcsqgdkrvaffMRKGADCLS-KWVGESERQLRLLFDQAYQmrPSIIFFDEID----- 364
Cdd:cd19510     24 RGYLLYGPPGTGKSSFIAALAGE-----------LDYDICDLNlSEVVLTDDRLNHLLNTAPK--QSIILLEDIDaafes 90

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462619170  365 GLAPVRSSRQDQIHSSI-VSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 422
Cdd:cd19510     91 REHNKKNPSAYGGLSRVtFSGLLNALDGVASSEERIVFMTTNHIERLDPALIRPGRVDM 149
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 829-895 1.01e-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: 1.01e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462619170  829 RLAIDKRFRVFTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNP 895
Cdd:cd05506     11 KLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNP 79
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 839-920 1.09e-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: 65.54  E-value: 1.09e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  839 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNpdRDPGDRLIRHrACALRDTAYAI 918
Cdd:cd05510     29 FLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYN--SDPSHPLRRH-ANFMKKKAEHL 105


                   ..
gi 2462619170  919 IK 920
Cdd:cd05510    106 LK 107
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 837-894 4.88e-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: 63.49  E-value: 4.88e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  837 RVFTKPVDPDE--VPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 894
Cdd:cd05500     23 RPFLVPVDPVKlnIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFN 82
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 838-899 9.86e-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: 62.69  E-value: 9.86e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462619170  838 VFTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDP 899
Cdd:cd05499     23 PFLDPVDPValNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTD 86
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
 294-414 1.06e-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: 1.06e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  294 LFYGPPGTGKTLVARALANECSqgdKRVAFFMRKG-------ADCLSKWVGESERQLRLLFDQAYQM---RPSIIF--FD 361
Cdd:cd19508     56 LLHGPPGTGKTSLCKALAQKLS---IRLSSRYRYGqlieinsHSLFSKWFSESGKLVTKMFQKIQELiddKDALVFvlID 132

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462619170  362 EIDGLAPVRSSRQDQIHSS----IVSTLLALMDGLDSRGEIVVIGATNRLDSIDPAL 414
Cdd:cd19508    133 EVESLAAARSASSSGTEPSdairVVNAVLTQIDRIKRYHNNVILLTSNLLEKIDVAF 189
T7SS_EccA TIGR03922
type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the ...
 294-458 1.15e-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: 68.72  E-value: 1.15e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  294 LFYGPPGTGKTLVARALANE-CSQGD-KRVAFFMRKGADCLSKWVGESERQLRLLFDQAYQmrpSIIFFDEIDGLAPVRS 371
Cdd:TIGR03922  316 LFAGPPGTGKTTIARVVAKIyCGLGVlRKPLVREVSRADLIGQYIGESEAKTNEIIDSALG---GVLFLDEAYTLVETGY 392

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  372 SRQDQIHSSIVSTLLALMDglDSRGEIVVIGA--TNRLD---SIDPALRRpgRFDR--EFLFSLPDkearkEILKIHTRD 444
Cdd:TIGR03922  393 GQKDPFGLEAIDTLLARME--NDRDRLVVIGAgyRKDLDkflEVNEGLRS--RFTRviEFPSYSPD-----ELVEIARRM 463

                          170
                   ....*....|....
gi 2462619170  445 WNPKplDTFLEELA 458
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 ...
 839-898 5.65e-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: 5.65e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  839 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRD 898
Cdd:cd05504     33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHT 92
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 839-894 2.08e-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: 58.58  E-value: 2.08e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462619170  839 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 894
Cdd:cd05513     22 FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYN 77
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 839-897 1.50e-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: 1.50e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462619170  839 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDR 897
Cdd:cd05496     26 FRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNK 84
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 839-899 1.56e-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: 56.23  E-value: 1.56e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462619170  839 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDP 899
Cdd:cd05503     21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSE 81
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 839-894 1.85e-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: 56.01  E-value: 1.85e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462619170  839 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 894
Cdd:cd05505     21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYY 76
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 454-488 2.00e-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: 465537 [Multi-domain]  Cd Length: 45  Bit Score: 54.08  E-value: 2.00e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2462619170  454 LEELAENCVGYCGADIKSICAEAALCALRRRYPQI 488
Cdd:pfam17862    4 LEELAERTEGFSGADLEALCREAALAALRRGLEAV 38
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 745-942 3.49e-09

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 60.20  E-value: 3.49e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  745 YGEIFNVQLPDKEERTKFFEDLILKQAAKPPISKKKAVLQALevLPVAPPPEPRSLTAEEVKRLEEQEEDTFReLRIFLR 824
Cdd:COG5076     84 GGITYSPFEKNRPESLRFDEIVFLAIESVTPESGLGSLLMAH--LKTSVKKRKTPKIEDELLYADNKAIAKFK-KQLFLR 160

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  825 NvthrlaIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNpdrDPGDRLI 904
Cdd:COG5076    161 D------GRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVY 231

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 2462619170  905 RHRacalrdtayAIIKEELDEDFEQLCEEIQESRKKRG 942
Cdd:COG5076    232 VDA---------KELEKYFLKLIEEIPEEMLELSIKPG 260
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 818-895 6.00e-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: 54.76  E-value: 6.00e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  818 ELRIFLRNVTHRLAIDKRFRV-FTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 894
Cdd:cd05495      3 ELRQALMPTLEKLYKQDPESLpFRQPVDPKllGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYN 82


                   .
gi 2462619170  895 P 895
Cdd:cd05495     83 R 83
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 839-904 1.63e-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: 53.58  E-value: 1.63e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462619170  839 FTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPdrdPGDRLI 904
Cdd:cd05497     26 FQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNK---PGDDVV 90
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 828-896 1.91e-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: 1.91e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  828 HRLAIdkrfrVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN-PD 896
Cdd:cd05515     21 RRLSL-----IFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNePD 85
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 847-894 5.65e-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: 5.65e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2462619170  847 EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 894
Cdd:cd05516     36 ELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFN 83
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 291-421 5.87e-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: 53.30  E-value: 5.87e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  291 RGCLFYGPPGTGKTLVARALANEC-------SQGDkrVAFFMRKGADCLSK---WVGESERQLrllfdqayqmrpsIIFF 360
Cdd:cd19512     23 RNILFYGPPGTGKTLFAKKLALHSgmdyaimTGGD--VAPMGREGVTAIHKvfdWANTSRRGL-------------LLFV 87

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462619170  361 DEIDGLAPVRSSrqDQIHSSIVSTLLALM--DGLDSRgEIVVIGATNRLDSIDPALRrpGRFD 421
Cdd:cd19512     88 DEADAFLRKRST--EKISEDLRAALNAFLyrTGEQSN-KFMLVLASNQPEQFDWAIN--DRID 145
Bromodomain_1 cd05494
Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated ...
 810-940 7.75e-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 [Multi-domain]  Cd Length: 114  Bit Score: 51.68  E-value: 7.75e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  810 EQEEDTFRELRIFLRNvthrlaidKRFRVFTKPVDPDE--VPDYVTVIKQPMDLSsviSKIDLHKYLTVKDYLRdidlic 887
Cdd:cd05494      3 EALERVLRELKRHRRN--------EDAWPFLEPVNPPRrgAPDYRDVIKRPMSFG---TKVNNIVETGARDLED------ 65

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2462619170  888 snalEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESRKK 940
Cdd:cd05494     66 ----LQIVQEDPADKQIDDEGRRSPSNIYAVEALEQLIVFQCKQVKGLKQKRH 114
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 838-898 8.81e-08

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: 8.81e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462619170  838 VFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN-PDRD 898
Cdd:cd05507     23 VFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNsSDHD 84
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 294-435 9.30e-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: 9.30e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  294 LFYGPPGTGKTLVARALANEcsQGDKRVAF-------FMRKGAdcLSKWVGESERQLR-----LLFDQAYQMRPSIIFFD 361
Cdd:pfam07724    7 LFLGPTGVGKTELAKALAEL--LFGDERALiridmseYMEEHS--VSRLIGAPPGYVGyeeggQLTEAVRRKPYSIVLID 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  362 EIdglapvrssrqDQIHSSIVSTLLALMDG---LDSRGE------IVVIGATNrLDSIDP--ALRRPGRFDREFLFSLPD 430
Cdd:pfam07724   83 EI-----------EKAHPGVQNDLLQILEGgtlTDKQGRtvdfknTLFIMTGN-FGSEKIsdASRLGDSPDYELLKEEVM 150


                   ....*
gi 2462619170  431 KEARK 435
Cdd:pfam07724  151 DLLKK 155
RecA-like_Ycf2 cd19505
ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; ...
 289-422 1.18e-07

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: 52.76  E-value: 1.18e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  289 PPRGCLFYGPPGTGKTLVARALA------------NECSqgDKRVAFFMRKGADCLSKWvGESERQLRLLFDQAYQMRPS 356
Cdd:cd19505     11 PSKGILLIGSIETGRSYLIKSLAansyvplirislNKLL--YNKPDFGNDDWIDGMLIL-KESLHRLNLQFELAKAMSPC 87

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462619170  357 IIFFDEIDGLApVRSSRQDQIHSSivSTLLALMDGLDSRG-------EIVVIGATNRLDSIDPALRRPGRFDR 422
Cdd:cd19505     88 IIWIPNIHELN-VNRSTQNLEEDP--KLLLGLLLNYLSRDfeksstrNILVIASTHIPQKVDPALIAPNRLDT 157
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 800-896 7.63e-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: 48.83  E-value: 7.63e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  800 LTAEEVKRLEeqeedtfrelRIFLRNVTHRLAIDkrfrvFTKPVDPdEVPDYVTVIKQPMDLSSVISKIDLH---KYLTV 876
Cdd:cd05502      1 LSPIDQRKCE----------RLLLELYCHELSLP-----FHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKspqHYSSP 64

                           90       100
                   ....*....|....*....|
gi 2462619170  877 KDYLRDIDLICSNALEYNPD 896
Cdd:cd05502     65 EEFVADVRLMFKNCYKFNEE 84
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 835-894 1.09e-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: 1.09e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  835 RFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 894
Cdd:cd05522     24 LTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYN 83
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 293-415 2.18e-06

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 51.62  E-value: 2.18e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  293 CLFYGPPGTGKTLVARALANECsqgDKRVAFFmrkGAdclskwVGESERQLRLLFDQAYQMRPS----IIFFDEIDGLAp 368
Cdd:PRK13342    39 MILWGPPGTGKTTLARIIAGAT---DAPFEAL---SA------VTSGVKDLREVIEEARQRRSAgrrtILFIDEIHRFN- 105

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2462619170  369 vrSSRQDqihssivsTLLALMDgldsRGEIVVIGAT--NRLDSIDPALR 415
Cdd:PRK13342   106 --KAQQD--------ALLPHVE----DGTITLIGATteNPSFEVNPALL 140
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 837-894 2.46e-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: 2.46e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462619170  837 RVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 894
Cdd:cd05517     25 ELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN 82
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 847-894 2.49e-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: 44.36  E-value: 2.49e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2462619170  847 EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 894
Cdd:cd05518     35 DYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 294-404 2.49e-05

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 48.13  E-value: 2.49e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  294 LFYGPPGTGKTLVARALANECSqgdkrvAFFMRkgadcLSKwVGESERQLRLLFDQAYQMR----PSIIFFDEIDglapv 369
Cdd:COG2256     53 ILWGPPGTGKTTLARLIANATD------AEFVA-----LSA-VTSGVKDIREVIEEARERRaygrRTILFVDEIH----- 115

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 2462619170  370 R--SSRQDqihssivsTLLALMDgldsRGEIVVIGAT 404
Cdd:COG2256    116 RfnKAQQD--------ALLPHVE----DGTITLIGAT 140
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 849-895 3.07e-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: 3.07e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2462619170  849 PDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNP 895
Cdd:cd05520     37 PDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNV 83
PRK04195 PRK04195
replication factor C large subunit; Provisional
 286-366 6.67e-05

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 46.84  E-value: 6.67e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  286 KIQPPRGCLFYGPPGTGKTLVARALAN-------ECSQGDKRvaffmrkGADCLSKWVGESERQlRLLFDQAYQmrpsII 358
Cdd:PRK04195    35 KGKPKKALLLYGPPGVGKTSLAHALANdygweviELNASDQR-------TADVIERVAGEAATS-GSLFGARRK----LI 102


                   ....*...
gi 2462619170  359 FFDEIDGL 366
Cdd:PRK04195   103 LLDEVDGI 110
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
287-324 7.45e-05

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


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 45.54  E-value: 7.45e-05
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 2462619170  287 IQPPRGCLFYGPPGTGKTLVARALANECSQGDKRVAFF 324
Cdd:COG1484     96 IERGENLILLGPPGTGKTHLAIALGHEACRAGYRVRFT 133
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 294-410 1.15e-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: 1.15e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  294 LFYGPPGTGKTLVARALANECSQGDK---RVAF--FMRKGADCLSK-----WVGESERQlrLLFDQAYQMRPSIIFFDEI 363
Cdd:cd19499     45 LFLGPTGVGKTELAKALAELLFGDEDnliRIDMseYMEKHSVSRLIgappgYVGYTEGG--QLTEAVRRKPYSVVLLDEI 122

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462619170  364 dglapvrssrqDQIHSSIVSTLLALMD-G--LDSRGEIVVIGAT--------------NRLDSI 410
Cdd:cd19499    123 -----------EKAHPDVQNLLLQVLDdGrlTDSHGRTVDFKNTiiimtsnhfrpeflNRIDEI 175
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 839-894 1.17e-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: 1.17e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462619170  839 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 894
Cdd:cd05508     23 FLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYN 78
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 849-893 2.28e-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: 2.28e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2462619170  849 PDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEY 893
Cdd:cd05524     39 PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAY 83
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
288-439 2.66e-04

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


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 44.84  E-value: 2.66e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  288 QPPRGCLFYGPPGTGKTLVARA----LANECSQGDKRVAF-------------FMRKGADCLSKWVGESERQLRL--LFD 348
Cdd:COG1474     49 ERPSNVLIYGPTGTGKTAVAKYvleeLEEEAEERGVDVRVvyvncrqastryrVLSRILEELGSGEDIPSTGLSTdeLFD 128

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  349 QAYQM-----RPSIIFFDEIDGLapvrssrQDQIHSSIVSTLLALMDGLDSRGeIVVIGATNRL---DSIDPALRRpgRF 420
Cdd:COG1474    129 RLYEAlderdGVLVVVLDEIDYL-------VDDEGDDLLYQLLRANEELEGAR-VGVIGISNDLeflENLDPRVKS--SL 198

                          170       180
                   ....*....|....*....|
gi 2462619170  421 -DREFLFSLPDKEARKEILK 439
Cdd:COG1474    199 gEEEIVFPPYDADELRDILE 218
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 809-895 3.32e-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: 3.32e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  809 EEQEEDTFRELRIFLRNVthRLAIDKRFRVftkPVD-PDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLIC 887
Cdd:cd05529     23 DEERERLISGLDKLLLSL--QLEIAEYFEY---PVDlRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLIL 97


                   ....*...
gi 2462619170  888 SNALEYNP 895
Cdd:cd05529     98 SNAETFNE 105
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
290-428 4.91e-04

RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 42.98  E-value: 4.91e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  290 PRGC--LFYGPPGTGKTLVARALANE-CSQGDKrVAFFMrkgadclskwVGESERQLR-----LLFD-QAYQMRPSIIFF 360
Cdd:COG0467     18 PRGSstLLSGPPGTGKTTLALQFLAEgLRRGEK-GLYVS----------FEESPEQLLrraesLGLDlEEYIESGLLRII 86

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462619170  361 DeidglapVRSSRQDQIHSSIVSTLLALMDGLDSRgeIVVIgatnrlDSIDP---ALRRPGRFdREFLFSL 428
Cdd:COG0467     87 D-------LSPEELGLDLEELLARLREAVEEFGAK--RVVI------DSLSGlllALPDPERL-REFLHRL 141
PRK08116 PRK08116
hypothetical protein; Validated
 278-323 2.44e-03

hypothetical protein; Validated


Pssm-ID: 236153 [Multi-domain]  Cd Length: 268  Bit Score: 41.16  E-value: 2.44e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2462619170  278 YPEVFEKFKIQPpRGCLFYGPPGTGKTLVARALANECSQGDKRVAF 323
Cdd:PRK08116   103 YVKKFEEMKKEN-VGLLLWGSVGTGKTYLAACIANELIEKGVPVIF 147
ycf46 CHL00195
Ycf46; Provisional
 623-764 3.01e-03

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 41.54  E-value: 3.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  623 PR-ILIVGEPGFGQgSHLAPAVIHALeKFTVYTLDIPVLFGVSTTSPEETCAQVIREAKRTAPSIVYVPHIHVWWEIV-- 699
Cdd:CHL00195   259 PRgLLLVGIQGTGK-SLTAKAIANDW-QLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSes 336

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462619170  700 ----GPTLK--ATFTTLLQNIPSfaPVLLLATSDKPHSaLPEEVqelfIRD--YGEIFNVQLPDKEERTKFFE 764
Cdd:CHL00195   337 kgdsGTTNRvlATFITWLSEKKS--PVFVVATANNIDL-LPLEI----LRKgrFDEIFFLDLPSLEEREKIFK 402
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 290-401 3.44e-03

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


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 39.79  E-value: 3.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  290 PRGCLFYGPPGTGKTLVARALANecSQGDKRVAFFMRKGADCLSK---WVGESERQLRLLFDQAYQMRPSIIFFDEIDGL 366
Cdd:pfam13191   24 PPSVLLTGEAGTGKTTLLRELLR--ALERDGGYFLRGKCDENLPYsplLEALTREGLLRQLLDELESSLLEAWRAALLEA 101

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 2462619170  367 APVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVI 401
Cdd:pfam13191  102 LAPVPELPGDLAERLLDLLLRLLDLLARGERPLVL 136
AAA_22 pfam13401
AAA domain;
287-410 3.58e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 38.86  E-value: 3.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  287 IQPPRGCLF-YGPPGTGKTLVARALANECSQGDKRVAFFMRKGADCLS---KWV-------GESERQLRLLFDQAYQ--- 352
Cdd:pfam13401    1 IRFGAGILVlTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKdllRALlralglpLSGRLSKEELLAALQQlll 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  353 --MRPSIIFFDEIDGLapvrssrqdqiHSSIVSTLLALMDGLDSRGEIVVIGaTNRLDSI 410
Cdd:pfam13401   81 alAVAVVLIIDEAQHL-----------SLEALEELRDLLNLSSKLLQLILVG-TPELREL 128
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 834-894 4.96e-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: 37.70  E-value: 4.96e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462619170  834 KRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 894
Cdd:cd05519     22 KLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYN 82
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 293-369 5.20e-03

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


Pssm-ID: 439516  Cd Length: 232  Bit Score: 39.76  E-value: 5.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462619170  293 CLFYGPPGTGKTLVARALANE-CSQGdKRVAFFmrKGADCLSKWvGESERQLRLlfDQAYQ--MRPSIIFFDEIdGLAPV 369
Cdd:NF038214    93 VLLLGPPGTGKTHLAIALGYAaCRQG-YRVRFT--TAADLVEQL-AQARADGRL--GRLLRrlARYDLLIIDEL-GYLPF 165
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 848-920 6.15e-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: 6.15e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462619170  848 VPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRlirhRACALRDtAYAIIK 920
Cdd:cd05525     38 NPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGR----DVCRLRK-AYYQAK 105
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
293-313 6.31e-03

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 40.11  E-value: 6.31e-03
                           10        20
                   ....*....|....*....|.
gi 2462619170  293 CLFYGPPGTGKTLVARALANE 313
Cdd:PRK00080    54 VLLYGPPGLGKTTLANIIANE 74
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
294-318 7.16e-03

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 40.17  E-value: 7.16e-03
                           10        20
                   ....*....|....*....|....*...
gi 2462619170  294 LFYGPPGTGKTLVARALA---NeCSQGD 318
Cdd:COG2812     36 LFTGPRGVGKTTLARILAkalN-CENGP 62
PRK13341 PRK13341
AAA family ATPase;
294-312 7.87e-03

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 40.42  E-value: 7.87e-03
                           10
                   ....*....|....*....
gi 2462619170  294 LFYGPPGTGKTLVARALAN 312
Cdd:PRK13341    56 ILYGPPGVGKTTLARIIAN 74
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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