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Conserved domains on  [gi|199560855|ref|NP_001128351|]
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ATPase family AAA domain-containing protein 2 [Rattus norvegicus]

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 ...
 412-581 2.43e-113

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: 352.58  E-value: 2.43e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  412 SVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSRGDKRVAFFMRKGADCLSKWV 491
Cdd:cd19517     1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  492 GESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRR 571
Cdd:cd19517    81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160

                         170
                  ....*....|
gi 199560855  572 PGRFDREFLF 581
Cdd:cd19517   161 PGRFDREFYF 170
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 972-1082 2.44e-56

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: 190.26  E-value: 2.44e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  972 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPD 1051
Cdd:cd05528     2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 199560855 1052 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 1082
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 ...
 609-643 2.96e-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: 53.70  E-value: 2.96e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 199560855   609 LEELAENCVGYCGADIKSICAEAALCALRRRYPQI 643
Cdd:pfam17862    4 LEELAERTEGFSGADLEALCREAALAALRRGLEAV 38
ycf46 super family cl31783
Ycf46; Provisional
 778-919 2.18e-05

Ycf46; Provisional


The actual alignment was detected with superfamily member CHL00195:

Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 48.86  E-value: 2.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  778 PR-LLIVGEPGFGQSshLAPAVIHALEKFTVYTLDIPVLFGISTTSPEEACSQMIREAKRTAPSIvyvphvhLWW-EI-- 853
Cdd:CHL00195  259 PRgLLLVGIQGTGKS--LTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCI-------LWIdEIdk 329

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 199560855  854 ----------VGPTLR--ATFTTLLQNIPSfaPVLLLATSERPYSaLPEEVqeLFTHDYGEIFNVQLPDKEERTKFFE 919
Cdd:CHL00195  330 afsnseskgdSGTTNRvlATFITWLSEKKS--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 ...
 412-581 2.43e-113

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: 352.58  E-value: 2.43e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  412 SVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSRGDKRVAFFMRKGADCLSKWV 491
Cdd:cd19517     1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  492 GESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRR 571
Cdd:cd19517    81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160

                         170
                  ....*....|
gi 199560855  572 PGRFDREFLF 581
Cdd:cd19517   161 PGRFDREFYF 170
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 407-678 4.73e-93

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 303.47  E-value: 4.73e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  407 SVRFDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADC 486
Cdd:COG1222    74 DVTFDDIGGLDEQIEEIREAVELPLKNPELFRKYGIEPPKGVLLYGPPGTGKTLLAKAVAGELG-----APFIRVRGSEL 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  487 LSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSI 565
Cdd:COG1222   149 VSKYIGEGARNVREVFELAREKAPSIIFIDEIDAIAARRTDDGTsGEVQRTVNQLLAELDGFESRGDVLIIAATNRPDLL 228

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  566 DPALRRPGRFDREFLFSLPDKDARKEILKIHTRDwNPKPVDMFLEELAENCVGYCGADIKSICAEAALCALRRRYPQiyt 645
Cdd:COG1222   229 DPALLRPGRFDRVIEVPLPDEEAREEILKIHLRD-MPLADDVDLDKLAKLTEGFSGADLKAIVTEAGMFAIREGRDT--- 304

                         250       260       270
                  ....*....|....*....|....*....|...
gi 199560855  646 tseklqldlssinISAKDFETAMQKIIPASQRA 678
Cdd:COG1222   305 -------------VTMEDLEKAIEKVKKKTETA 324
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 408-679 3.04e-77

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: 271.78  E-value: 3.04e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   408 VRFDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCL 487
Cdd:TIGR01243  175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG-----AYFISINGPEIM 249

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   488 SKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDP 567
Cdd:TIGR01243  250 SKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDP 329

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   568 ALRRPGRFDREFLFSLPDKDARKEILKIHTRDwNPKPVDMFLEELAENCVGYCGADIKSICAEAALCALRRRYPQIYTTS 647
Cdd:TIGR01243  330 ALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKINF 408

                          250       260       270
                   ....*....|....*....|....*....|....*
gi 199560855   648 EKLQLD---LSSINISAKDFETAMQKIIPASQRAV 679
Cdd:TIGR01243  409 EAEEIPaevLKELKVTMKDFMEALKMVEPSAIREV 443
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 402-671 9.08e-71

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 242.82  E-value: 9.08e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  402 MQLDSS--VRFDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrvAFF 479
Cdd:PRK03992  120 MEVIESpnVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATF 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  480 MR-KGADCLSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLApvrSSRQDQIHS---SIVST---LLALMDGLDSRGE 552
Cdd:PRK03992  194 IRvVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIA---AKRTDSGTSgdrEVQRTlmqLLAEMDGFDPRGN 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  553 IVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKDARKEILKIHTRDWNPKP-VDmfLEELAENCVGYCGADIKSICAEA 631
Cdd:PRK03992  271 VKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADdVD--LEELAELTEGASGADLKAICTEA 348

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 199560855  632 ALCALRRRYPQiyttseklqldlssinISAKDFETAMQKI 671
Cdd:PRK03992  349 GMFAIRDDRTE----------------VTMEDFLKAIEKV 372
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 972-1082 2.44e-56

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: 190.26  E-value: 2.44e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  972 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPD 1051
Cdd:cd05528     2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 199560855 1052 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 1082
Cdd:cd05528    82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 449-583 7.25e-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: 167.00  E-value: 7.25e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   449 LFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSR 528
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKELG-----APFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSG 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 199560855   529 QDQIHSSIVSTLLALMDGLDSR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFSL 583
Cdd:pfam00004   77 GDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 444-585 4.82e-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: 88.20  E-value: 4.82e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855    444 PPRGCLFYGPPGTGKTLVARALANECSRGDKRVAFF------------MRKGADCLSKWVGESERQLRLLFDQAYQMRPA 511
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIdgedileevldqLLLIIVGGKKASGSGELRLRLALALARKLKPD 80

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 199560855    512 IIFFDEIDGLAPVRSSRQDQihssiVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPgRFDREFLFSLPD 585
Cdd:smart00382   81 VLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
BROMO smart00297
bromo domain;
967-1077 2.38e-17

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 78.86  E-value: 2.38e-17
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855    967 EEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNAL 1046
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100       110
                    ....*....|....*....|....*....|.
gi 199560855   1047 EYNPDrdpgDRLIRHRACALRDTAYAIIKEE 1077
Cdd:smart00297   81 TYNGP----DSEVYKDAKKLEKFFEKKLREL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 994-1050 5.46e-15

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: 71.19  E-value: 5.46e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 199560855   994 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNP 1050
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 ...
 609-643 2.96e-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: 53.70  E-value: 2.96e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 199560855   609 LEELAENCVGYCGADIKSICAEAALCALRRRYPQI 643
Cdd:pfam17862    4 LEELAERTEGFSGADLEALCREAALAALRRGLEAV 38
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 987-1097 2.41e-08

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 57.89  E-value: 2.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  987 IDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNpdrDPGDRLIRHRacal 1066
Cdd:COG5076   162 GRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVYVDA---- 234

                          90       100       110
                  ....*....|....*....|....*....|.
gi 199560855 1067 rdtayAIIKEELDEDFEQLCEEIQESRKKRG 1097
Cdd:COG5076   235 -----KELEKYFLKLIEEIPEEMLELSIKPG 260
ycf46 CHL00195
Ycf46; Provisional
 778-919 2.18e-05

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 48.86  E-value: 2.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  778 PR-LLIVGEPGFGQSshLAPAVIHALEKFTVYTLDIPVLFGISTTSPEEACSQMIREAKRTAPSIvyvphvhLWW-EI-- 853
Cdd:CHL00195  259 PRgLLLVGIQGTGKS--LTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCI-------LWIdEIdk 329

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 199560855  854 ----------VGPTLR--ATFTTLLQNIPSfaPVLLLATSERPYSaLPEEVqeLFTHDYGEIFNVQLPDKEERTKFFE 919
Cdd:CHL00195  330 afsnseskgdSGTTNRvlATFITWLSEKKS--PVFVVATANNIDL-LPLEI--LRKGRFDEIFFLDLPSLEEREKIFK 402
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 758-892 2.51e-03

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: 40.04  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  758 ENLNFLHLNRNACYQPMSFR-----PR-LLIVGEPGFGQSshLAPAVIHALEKFTVYTLDIPVLFGISTTSPEEACSQMI 831
Cdd:cd19507     6 DNLKDWLKKRKAAFSKQASAyglptPKgLLLVGIQGTGKS--LTAKAIAGVWQLPLLRLDMGRLFGGLVGESESRLRQMI 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 199560855  832 REAKRTAPSIVYVPhvhlwwEI------------VGPTLR--ATFTTLLQNipSFAPVLLLATSERpYSALPEEV 892
Cdd:cd19507    84 QTAEAIAPCVLWID------EIekgfsnadskgdSGTSSRvlGTFLTWLQE--KKKPVFVVATANN-VQSLPPEL 149
 
Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 412-581 2.43e-113

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: 352.58  E-value: 2.43e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  412 SVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSRGDKRVAFFMRKGADCLSKWV 491
Cdd:cd19517     1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  492 GESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRR 571
Cdd:cd19517    81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160

                         170
                  ....*....|
gi 199560855  572 PGRFDREFLF 581
Cdd:cd19517   161 PGRFDREFYF 170
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 407-678 4.73e-93

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 303.47  E-value: 4.73e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  407 SVRFDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADC 486
Cdd:COG1222    74 DVTFDDIGGLDEQIEEIREAVELPLKNPELFRKYGIEPPKGVLLYGPPGTGKTLLAKAVAGELG-----APFIRVRGSEL 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  487 LSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSI 565
Cdd:COG1222   149 VSKYIGEGARNVREVFELAREKAPSIIFIDEIDAIAARRTDDGTsGEVQRTVNQLLAELDGFESRGDVLIIAATNRPDLL 228

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  566 DPALRRPGRFDREFLFSLPDKDARKEILKIHTRDwNPKPVDMFLEELAENCVGYCGADIKSICAEAALCALRRRYPQiyt 645
Cdd:COG1222   229 DPALLRPGRFDRVIEVPLPDEEAREEILKIHLRD-MPLADDVDLDKLAKLTEGFSGADLKAIVTEAGMFAIREGRDT--- 304

                         250       260       270
                  ....*....|....*....|....*....|...
gi 199560855  646 tseklqldlssinISAKDFETAMQKIIPASQRA 678
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 ...
 412-581 6.60e-80

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


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 259.92  E-value: 6.60e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  412 SVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKWV 491
Cdd:cd19503     1 DIGGLDEQIASLKELIELPLKYPELFRALGLKPPRGVLLHGPPGTGKTLLARAVANEAG-----ANFLSISGPSIVSKYL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  492 GESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRR 571
Cdd:cd19503    76 GESEKNLREIFEEARSHAPSIIFIDEIDALAPKREEDQREVERRVVAQLLTLMDGMSSRGKVVVIAATNRPDAIDPALRR 155

                         170
                  ....*....|
gi 199560855  572 PGRFDREFLF 581
Cdd:cd19503   156 PGRFDREVEI 165
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 408-679 3.04e-77

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: 271.78  E-value: 3.04e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   408 VRFDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCL 487
Cdd:TIGR01243  175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG-----AYFISINGPEIM 249

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   488 SKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDP 567
Cdd:TIGR01243  250 SKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDP 329

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   568 ALRRPGRFDREFLFSLPDKDARKEILKIHTRDwNPKPVDMFLEELAENCVGYCGADIKSICAEAALCALRRRYPQIYTTS 647
Cdd:TIGR01243  330 ALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKINF 408

                          250       260       270
                   ....*....|....*....|....*....|....*
gi 199560855   648 EKLQLD---LSSINISAKDFETAMQKIIPASQRAV 679
Cdd:TIGR01243  409 EAEEIPaevLKELKVTMKDFMEALKMVEPSAIREV 443
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 375-674 9.49e-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: 267.54  E-value: 9.49e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   375 LNFRKDEIRGIYKDRMKIGAN-----LADVDPMQLDS------SVRFDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQ 443
Cdd:TIGR01243  406 INFEAEEIPAEVLKELKVTMKdfmeaLKMVEPSAIREvlvevpNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIR 485

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   444 PPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAP 523
Cdd:TIGR01243  486 PPKGVLLFGPPGTGKTLLAKAVATESG-----ANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAP 560

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   524 VRSSRQDQ-IHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKDARKEILKIHTRDWnP 602
Cdd:TIGR01243  561 ARGARFDTsVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSM-P 639

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 199560855   603 KPVDMFLEELAENCVGYCGADIKSICAEAALCALRRRYPQIytTSEKLQLD----LSSINISAKDFETAMQKIIPA 674
Cdd:TIGR01243  640 LAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGSP--AKEKLEVGeeefLKDLKVEMRHFLEALKKVKPS 713
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 399-671 1.30e-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: 256.76  E-value: 1.30e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  399 VDPMQLDSSVRFDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsrgdkRVAF 478
Cdd:COG0464   145 EEELLELREAILDDLGGLEEVKEELRELVALPLKRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL-----GLPL 219

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  479 FMRKGADCLSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLdsRGEIVVIGA 558
Cdd:COG0464   220 IEVDLSDLVSKYVGETEKNLREVFDKARGLAPCVLFIDEADALAGKRGEVGDGVGRRVVNTLLTEMEEL--RSDVVVIAA 297

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  559 TNRLDSIDPALRRpgRFDREFLFSLPDKDARKEILKIHTRDwNPKPVDMFLEELAENCVGYCGADIKSICAEAALCALRr 638
Cdd:COG0464   298 TNRPDLLDPALLR--RFDEIIFFPLPDAEERLEIFRIHLRK-RPLDEDVDLEELAEATEGLSGADIRNVVRRAALQALR- 373

                         250       260       270
                  ....*....|....*....|....*....|...
gi 199560855  639 rypqiyttseklqldLSSINISAKDFETAMQKI 671
Cdd:COG0464   374 ---------------LGREPVTTEDLLEALERE 391
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 402-671 9.08e-71

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 242.82  E-value: 9.08e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  402 MQLDSS--VRFDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrvAFF 479
Cdd:PRK03992  120 MEVIESpnVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATF 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  480 MR-KGADCLSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLApvrSSRQDQIHS---SIVST---LLALMDGLDSRGE 552
Cdd:PRK03992  194 IRvVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIA---AKRTDSGTSgdrEVQRTlmqLLAEMDGFDPRGN 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  553 IVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKDARKEILKIHTRDWNPKP-VDmfLEELAENCVGYCGADIKSICAEA 631
Cdd:PRK03992  271 VKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADdVD--LEELAELTEGASGADLKAICTEA 348

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 199560855  632 ALCALRRRYPQiyttseklqldlssinISAKDFETAMQKI 671
Cdd:PRK03992  349 GMFAIRDDRTE----------------VTMEDFLKAIEKV 372
26Sp45 TIGR01242
26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an ...
 408-639 4.45e-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: 222.37  E-value: 4.45e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   408 VRFDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrvAFFMR-KGADC 486
Cdd:TIGR01242  119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATFIRvVGSEL 192

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   487 LSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVR---SSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLD 563
Cdd:TIGR01242  193 VRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRtdsGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPD 272

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 199560855   564 SIDPALRRPGRFDREFLFSLPDKDARKEILKIHTRDWNPKPvDMFLEELAENCVGYCGADIKSICAEAALCALRRR 639
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 ...
 413-578 1.42e-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: 1.42e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  413 VGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKWVG 492
Cdd:cd19519     2 IGGCRKQLAQIREMVELPLRHPELFKAIGIKPPRGILLYGPPGTGKTLIARAVANETG-----AFFFLINGPEIMSKLAG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  493 ESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRP 572
Cdd:cd19519    77 ESESNLRKAFEEAEKNAPAIIFIDEIDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRF 156


                  ....*.
gi 199560855  573 GRFDRE 578
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 ...
 422-577 3.18e-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: 209.06  E-value: 3.18e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  422 ALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsrgdkRVAFFMRKGADCLSKWVGESERQLRLL 501
Cdd:cd19511     4 ELKEAVEWPLKHPDAFKRLGIRPPKGVLLYGPPGCGKTLLAKALASEA-----GLNFISVKGPELFSKYVGESERAVREI 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 199560855  502 FDQAYQMRPAIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 577
Cdd:cd19511    79 FQKARQAAPCIIFFDEIDSLAPRRGQSDSsGVTDRVVSQLLTELDGIESLKGVVVIAATNRPDMIDPALLRPGRLDK 155
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 375-643 1.95e-57

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 205.78  E-value: 1.95e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  375 LNFRKDEIRGIYKDRMKIGANLADVDPMQLDSsvrFDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPP 454
Cdd:PTZ00361  150 LHNKTHSVVGILLDEVDPLVSVMKVDKAPLES---YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPP 226

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  455 GTGKTLVARALANECSrgdkrvAFFMR-KGADCLSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIH 533
Cdd:PTZ00361  227 GTGKTLLAKAVANETS------ATFLRvVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGE 300

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  534 SSIVSTLLAL---MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKDARKEILKIHTRDWNPKPvDMFLE 610
Cdd:PTZ00361  301 KEIQRTMLELlnqLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAE-DVDLE 379

                         250       260       270
                  ....*....|....*....|....*....|...
gi 199560855  611 ELAENCVGYCGADIKSICAEAALCALRRRYPQI 643
Cdd:PTZ00361  380 EFIMAKDELSGADIKAICTEAGLLALRERRMKV 412
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 423-577 7.46e-57

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: 193.87  E-value: 7.46e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  423 LKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANEcsrgdKRVAFFMRKGADCLSKWVGESERQLRLLF 502
Cdd:cd19529     5 LKEAVEWPLLKPEVFKRLGIRPPKGILLYGPPGTGKTLLAKAVATE-----SNANFISVKGPELLSKWVGESEKAIREIF 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 199560855  503 DQAYQMRPAIIFFDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 577
Cdd:cd19529    80 RKARQVAPCVIFFDEIDSIAPRRGTTGDSgVTERVVNQLLTELDGLEEMNGVVVIAATNRPDIIDPALLRAGRFDR 155
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 972-1082 2.44e-56

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: 190.26  E-value: 2.44e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  972 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPD 1051
Cdd:cd05528     2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 199560855 1052 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 1082
Cdd:cd05528    82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112
FtsH_fam TIGR01241
ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct ...
 402-672 1.39e-54

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: 199.05  E-value: 1.39e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   402 MQLDSSVRFDSVGGLSSHIAALKEMVLFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMR 481
Cdd:TIGR01241   46 NEEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAG-----VPFFSI 119

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   482 KGADCLSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGlapVRSSRQDQI---HSSIVSTL---LALMDGLDSRGEIVV 555
Cdd:TIGR01241  120 SGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDA---VGRQRGAGLgggNDEREQTLnqlLVEMDGFGTNTGVIV 196

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   556 IGATNRLDSIDPALRRPGRFDREFLFSLPDKDARKEILKIHTRDWNPKPvDMFLEELAENCVGYCGADIKSICAEAALCA 635
Cdd:TIGR01241  197 IAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAP-DVDLKAVARRTPGFSGADLANLLNEAALLA 275

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 199560855   636 LRRRYPQiyttseklqldlssinISAKDFETAMQKII 672
Cdd:TIGR01241  276 ARKNKTE----------------ITMNDIEEAIDRVI 296
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 410-577 6.41e-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: 180.23  E-value: 6.41e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  410 FDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrvAFFMR-KGADCLS 488
Cdd:cd19502     2 YEDIGGLDEQIREIREVVELPLKHPELFEELGIEPPKGVLLYGPPGTGKTLLAKAVANHTD------ATFIRvVGSELVQ 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  489 KWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLAL---MDGLDSRGEIVVIGATNRLDSI 565
Cdd:cd19502    76 KYIGEGARLVRELFEMAREKAPSIIFIDEIDAIGAKRFDSGTGGDREVQRTMLELlnqLDGFDPRGNIKVIMATNRPDIL 155

                         170
                  ....*....|..
gi 199560855  566 DPALRRPGRFDR 577
Cdd:cd19502   156 DPALLRPGRFDR 167
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 423-577 1.85e-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: 178.47  E-value: 1.85e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  423 LKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKWVGESERQLRLLF 502
Cdd:cd19528     5 LQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQ-----ANFISVKGPELLTMWFGESEANVRDIF 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 199560855  503 DQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSS---IVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 577
Cdd:cd19528    80 DKARAAAPCVLFFDELDSIAKARGGNIGDAGGAadrVINQILTEMDGMNTKKNVFIIGATNRPDIIDPAILRPGRLDQ 157
pup_AAA TIGR03689
proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some ...
 408-696 2.83e-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: 2.83e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   408 VRFDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANE-CSR----GDKRVAFFMRK 482
Cdd:TIGR03689  179 VTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVANSlAARigaeGGGKSYFLNIK 258

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   483 GADCLSKWVGESERQLRLLFDQAYQM----RPAIIFFDEIDGLAPVRSS-RQDQIHSSIVSTLLALMDGLDSRGEIVVIG 557
Cdd:TIGR03689  259 GPELLNKYVGETERQIRLIFQRAREKasegRPVIVFFDEMDSLFRTRGSgVSSDVETTVVPQLLAEIDGVESLDNVIVIG 338

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   558 ATNRLDSIDPALRRPGRFDREFLFSLPDKDARKEILKIHTRDWNPKPvdmflEELAENcvgycgadikSICAEAALCALR 637
Cdd:TIGR03689  339 ASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFAKYLTDDLPLP-----EDLAAH----------DGDREATAAALI 403

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   638 RR-YPQIYTTSEKLQ-LDLSSINISA-----KDF--------------ETAMQKIIPASQRAVTSPgQALSAIVKPLLQN 696
Cdd:TIGR03689  404 QRvVDALYARSEANRyVEVTYANGSTevlyfADFvsgamlanivdrakKRAIKDHITGGQVGLRAE-HLLAAVEDEFREN 482
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 412-578 3.68e-51

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: 177.98  E-value: 3.68e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  412 SVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsrgdkRVAFFMRKGADCLSKWV 491
Cdd:cd19518     1 DIGGMDSTLKELCELLIHPILPPEYFQHLGVEPPRGVLLHGPPGCGKTMLANAIAGEL-----KVPFLKISATEIVSGVS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  492 GESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL----DSRGEIVVIGATNRLDSIDP 567
Cdd:cd19518    76 GESEEKIRELFDQAISNAPCIVFIDEIDAITPKRESAQREMERRIVSQLLTCMDELnnekTAGGPVLVIGATNRPDSLDP 155

                         170
                  ....*....|.
gi 199560855  568 ALRRPGRFDRE 578
Cdd:cd19518   156 ALRRAGRFDRE 166
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
408-672 4.61e-50

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


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 187.94  E-value: 4.61e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  408 VRFDSVGGLSSHIAALKEMVLFpLLYPEVFEKF--KIqpPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFF------ 479
Cdd:COG0465   139 VTFDDVAGVDEAKEELQEIVDF-LKDPEKFTRLgaKI--PKGVLLVGPPGTGKTLLAKAVAGEAG-----VPFFsisgsd 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  480 ---MRKGadclskwVGESeRqLRLLFDQAYQMRPAIIFFDEIDGLAPVRSS--------RqDQihssivsTL---LALMD 545
Cdd:COG0465   211 fveMFVG-------VGAS-R-VRDLFEQAKKNAPCIIFIDEIDAVGRQRGAglggghdeR-EQ-------TLnqlLVEMD 273

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  546 GLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKDARKEILKIHTRDwnpKP----VDmfLEELAENCVGYCG 621
Cdd:COG0465   274 GFEGNEGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDVKGREAILKVHARK---KPlapdVD--LEVIARRTPGFSG 348

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 199560855  622 ADIKSICAEAALCALRRRYPQiyttseklqldlssinISAKDFETAMQKII 672
Cdd:COG0465   349 ADLANLVNEAALLAARRNKKA----------------VTMEDFEEAIDRVI 383
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
435-631 1.22e-49

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 176.61  E-value: 1.22e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  435 EVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsrgdkRVAFFMRKGADCLSKWVGESERQLRLLFDQAYQmRPAIIF 514
Cdd:COG1223    25 ENLRKFGLWPPRKILFYGPPGTGKTMLAEALAGEL-----KLPLLTVRLDSLIGSYLGETARNLRKLFDFARR-APCVIF 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  515 FDEIDGLAPVRSSRQD--QIHsSIVSTLLALMDGLDSrgEIVVIGATNRLDSIDPALRRpgRFDREFLFSLPDKDARKEI 592
Cdd:COG1223    99 FDEFDAIAKDRGDQNDvgEVK-RVVNALLQELDGLPS--GSVVIAATNHPELLDSALWR--RFDEVIEFPLPDKEERKEI 173

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 199560855  593 LKIHTRDWnPKPVDMFLEELAENCVGYCGADIKSICAEA 631
Cdd:COG1223   174 LELNLKKF-PLPFELDLKKLAKKLEGLSGADIEKVLKTA 211
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 420-581 6.87e-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: 170.93  E-value: 6.87e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  420 IAALKEMVLFPLLYPEVfEKFKIQPPRGCLFYGPPGTGKTLVARALANECsrgdkRVAFFMRKGADCLSKWVGESERQLR 499
Cdd:cd19481     2 KASLREAVEAPRRGSRL-RRYGLGLPKGILLYGPPGTGKTLLAKALAGEL-----GLPLIVVKLSSLLSKYVGESEKNLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  500 LLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSS-IVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDRE 578
Cdd:cd19481    76 KIFERARRLAPCILFIDEIDAIGRKRDSSGESGELRrVLNQLLTELDGVNSRSKVLVIAATNRPDLLDPALLRPGRFDEV 155


                  ...
gi 199560855  579 FLF 581
Cdd:cd19481   156 IEF 158
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 396-677 1.42e-48

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


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 178.80  E-value: 1.42e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  396 LADVDPMQLDSSVR-----------FDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARA 464
Cdd:PTZ00454  119 VVDILPPEADSSIQllqmsekpdvtYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKA 198

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  465 LANECSrgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQ---DQIHSSIVSTLL 541
Cdd:PTZ00454  199 VAHHTT-----ATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQtgaDREVQRILLELL 273

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  542 ALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKDARKEILKIHTRDWNPKPvDMFLEELAENCVGYCG 621
Cdd:PTZ00454  274 NQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSE-EVDLEDFVSRPEKISA 352

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 199560855  622 ADIKSICAEAALCALRR-RYPqiyttseklqldlssinISAKDFETAMQKIIPASQR 677
Cdd:PTZ00454  353 ADIAAICQEAGMQAVRKnRYV-----------------ILPKDFEKGYKTVVRKTDR 392
ftsH CHL00176
cell division protein; Validated
 384-672 4.55e-48

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 182.94  E-value: 4.55e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  384 GIYKDRMKIGANLADVDpMQLDSSVRFDSVGGLSSHIAALKEMVLFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVAR 463
Cdd:CHL00176  157 GPGQNLMNFGKSKARFQ-MEADTGITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAK 234

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  464 ALANECSrgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSR----QDQiHSSIVST 539
Cdd:CHL00176  235 AIAGEAE-----VPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGigggNDE-REQTLNQ 308

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  540 LLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKDARKEILKIHTRDwnpKPV--DMFLEELAENCV 617
Cdd:CHL00176  309 LLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARN---KKLspDVSLELIARRTP 385

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 199560855  618 GYCGADIKSICAEAALCALRRRYPQiyttseklqldlssinISAKDFETAMQKII 672
Cdd:CHL00176  386 GFSGADLANLLNEAAILTARRKKAT----------------ITMKEIDTAIDRVI 424
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 449-583 7.25e-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: 167.00  E-value: 7.25e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   449 LFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSR 528
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKELG-----APFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSG 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 199560855   529 QDQIHSSIVSTLLALMDGLDSR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFSL 583
Cdd:pfam00004   77 GDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 423-577 3.95e-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: 163.04  E-value: 3.95e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  423 LKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsrgdkRVAFFMRKGADCLSKWVGESERQLRLLF 502
Cdd:cd19530     8 LTMSILRPIKRPDIYKALGIDLPTGVLLYGPPGCGKTLLAKAVANES-----GANFISVKGPELLNKYVGESERAVRQVF 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 199560855  503 DQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 577
Cdd:cd19530    83 QRARASAPCVIFFDEVDALVPKRGDGGSWASERVVNQLLTEMDGLEERSNVFVIAATNRPDIIDPAMLRPGRLDK 157
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 408-578 1.97e-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: 161.63  E-value: 1.97e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  408 VRFDSVGGLSSHIAALKEMVLFpLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsrgdkRVAFFMRKGADCL 487
Cdd:cd19501     1 VTFKDVAGCEEAKEELKEVVEF-LKNPEKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA-----GVPFFSISGSDFV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  488 SKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTL---LALMDGLDSRGEIVVIGATNRLDS 564
Cdd:cd19501    75 EMFVGVGASRVRDLFEQAKKNAPCIVFIDEIDAVGRKRGAGLGGGHDEREQTLnqlLVEMDGFESNTGVIVIAATNRPDV 154

                         170
                  ....*....|....
gi 199560855  565 IDPALRRPGRFDRE 578
Cdd:cd19501   155 LDPALLRPGRFDRQ 168
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 413-580 7.29e-45

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: 159.83  E-value: 7.29e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  413 VGGLSSHIAALKEMVLFPLLYPEVFeKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKWVG 492
Cdd:cd19509     1 IAGLDDAKEALKEAVILPSLRPDLF-PGLRGPPRGILLYGPPGTGKTLLARAVASESG-----STFFSISASSLVSKWVG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  493 ESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL--DSRGEIVVIGATNRLDSIDPALR 570
Cdd:cd19509    75 ESEKIVRALFALARELQPSIIFIDEIDSLLSERGSGEHEASRRVKTEFLVQMDGVlnKPEDRVLVLGATNRPWELDEAFL 154

                         170
                  ....*....|
gi 199560855  571 RpgRFDREFL 580
Cdd:cd19509   155 R--RFEKRIY 162
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 425-577 1.39e-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: 1.39e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  425 EMVLFPLLYPEVFEKfKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKWVGESERQLRLLFDQ 504
Cdd:cd19527     7 DTIQLPLEHPELFSS-GLRKRSGILLYGPPGTGKTLLAKAIATECS-----LNFLSVKGPELINMYIGESEANVREVFQK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 199560855  505 AYQMRPAIIFFDEIDGLAPVRSSRQDQ--IHSSIVSTLLALMDGLDSRGE-IVVIGATNRLDSIDPALRRPGRFDR 577
Cdd:cd19527    81 ARDAKPCVIFFDELDSLAPSRGNSGDSggVMDRVVSQLLAELDGMSSSGQdVFVIGATNRPDLLDPALLRPGRFDK 156
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
375-677 5.51e-42

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 164.82  E-value: 5.51e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  375 LNFRKDEIRGIYKDRMKiganladvdpmqldssVRFDSVGGLSSHIAALKEMVLFpLLYPEVFEKFKIQPPRGCLFYGPP 454
Cdd:PRK10733  132 MSFGKSKARMLTEDQIK----------------TTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPP 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  455 GTGKTLVARALAnecsrGDKRVAFFMRKGADCLSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHS 534
Cdd:PRK10733  195 GTGKTLLAKAIA-----GEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHD 269

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  535 SIVSTL---LALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKDARKEILKIHTRDWnPKPVDMFLEE 611
Cdd:PRK10733  270 EREQTLnqmLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRV-PLAPDIDAAI 348

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 199560855  612 LAENCVGYCGADIKSICAEAALCALR--RRYpqiyttseklqldlssinISAKDFETAMQKIIPASQR 677
Cdd:PRK10733  349 IARGTPGFSGADLANLVNEAALFAARgnKRV------------------VSMVEFEKAKDKIMMGAER 398
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 421-577 2.01e-40

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


Pssm-ID: 410934 [Multi-domain]  Cd Length: 158  Bit Score: 146.80  E-value: 2.01e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  421 AALKEMVLFPLLYPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKWVGESERQLRL 500
Cdd:cd19526     3 KALEETIEWPSKYPKIFASSPLRLRSGILLYGPPGCGKTLLASAIASECG-----LNFISVKGPELLNKYIGASEQNVRD 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 199560855  501 LFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 577
Cdd:cd19526    78 LFSRAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDK 154
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 412-575 3.93e-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: 140.64  E-value: 3.93e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  412 SVGGLSSHIAALKEMVLFPLLYPEVFEKFKI-QPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKW 490
Cdd:cd19520     1 DIGGLDEVITELKELVILPLQRPELFDNSRLlQPPKGVLLYGPPGCGKTMLAKATAKEAG-----ARFINLQVSSLTDKW 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  491 VGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRG--EIVVIGATNRLDSIDPA 568
Cdd:cd19520    76 YGESQKLVAAVFSLASKLQPSIIFIDEIDSFLRQRSSTDHEATAMMKAEFMSLWDGLSTDGncRVIVMGATNRPQDLDEA 155


                  ....*....
gi 199560855  569 LRR--PGRF 575
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; ...
 402-571 5.51e-36

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


Pssm-ID: 410933 [Multi-domain]  Cd Length: 186  Bit Score: 135.12  E-value: 5.51e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  402 MQLDSSVRFDSVGGLSSHIAALKEMVLFPLLYPEVFEKFKiQPPRGCLFYGPPGTGKTLVARALANECsrgdkRVAFFMR 481
Cdd:cd19525    13 MDHGPPINWADIAGLEFAKKTIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQS-----GATFFSI 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  482 KGADCLSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGE--IVVIGAT 559
Cdd:cd19525    87 SASSLTSKWVGEGEKMVRALFSVARCKQPAVIFIDEIDSLLSQRGEGEHESSRRIKTEFLVQLDGATTSSEdrILVVGAT 166

                         170
                  ....*....|..
gi 199560855  560 NRLDSIDPALRR 571
Cdd:cd19525   167 NRPQEIDEAARR 178
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 407-577 1.56e-35

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: 133.06  E-value: 1.56e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  407 SVRFDSVGGLSSHIAALKEMVLFPLLYPEVFeKFKIQPPRGCLFYGPPGTGKTLVARALANECSRgdkrvAFFMRKGADC 486
Cdd:cd19521     3 NVKWEDVAGLEGAKEALKEAVILPVKFPHLF-TGNRKPWSGILLYGPPGTGKSYLAKAVATEANS-----TFFSVSSSDL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  487 LSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL--DSRGeIVVIGATNRLDS 564
Cdd:cd19521    77 VSKWMGESEKLVKQLFAMARENKPSIIFIDEVDSLCGTRGEGESEASRRIKTELLVQMNGVgnDSQG-VLVLGATNIPWQ 155

                         170
                  ....*....|...
gi 199560855  565 IDPALRRpgRFDR 577
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; ...
 413-576 1.91e-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: 1.91e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  413 VGGLSSHIAALKEMV----LFPllyPEVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSRGDKRVAffmrKGADCLS 488
Cdd:cd19504     2 IGGLDKEFSDIFRRAfasrVFP---PEIVEQLGCKHVKGILLYGPPGTGKTLMARQIGKMLNAREPKIV----NGPEILN 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  489 KWVGESERQLRLLFDQAYQMRPA--------IIFFDEIDGLAPVRSSRQDQ--IHSSIVSTLLALMDGLDSRGEIVVIGA 558
Cdd:cd19504    75 KYVGESEANIRKLFADAEEEQRRlgansglhIIIFDEIDAICKQRGSMAGStgVHDTVVNQLLSKIDGVEQLNNILVIGM 154

                         170
                  ....*....|....*...
gi 199560855  559 TNRLDSIDPALRRPGRFD 576
Cdd:cd19504   155 TNRKDLIDEALLRPGRLE 172
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 413-571 1.99e-32

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: 124.19  E-value: 1.99e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  413 VGGLSSHIAALKEMVLFPLLYPEVFEKFKiQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKWVG 492
Cdd:cd19524     2 IAGQDLAKQALQEMVILPSLRPELFTGLR-APARGLLLFGPPGNGKTMLAKAVAAESN-----ATFFNISAASLTSKYVG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  493 ESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGE--IVVIGATNRLDSIDPA-L 569
Cdd:cd19524    76 EGEKLVRALFAVARELQPSIIFIDEVDSLLSERSEGEHEASRRLKTEFLIEFDGVQSNGDdrVLVMGATNRPQELDDAvL 155


                  ..
gi 199560855  570 RR 571
Cdd:cd19524   156 RR 157
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 413-571 6.02e-32

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: 122.79  E-value: 6.02e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  413 VGGLSSHIAALKEMVLFPLLYPEVFEKFKiQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKWVG 492
Cdd:cd19522     2 IADLEEAKKLLEEAVVLPMWMPEFFKGIR-RPWKGVLMVGPPGTGKTLLAKAVATECG-----TTFFNVSSSTLTSKYRG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  493 ESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIHSSIV-STLLALMDGL-------DSRGEIVVIGATNRLDS 564
Cdd:cd19522    76 ESEKLVRLLFEMARFYAPTTIFIDEIDSICSRRGTSEEHEASRRVkSELLVQMDGVggasendDPSKMVMVLAATNFPWD 155


                  ....*..
gi 199560855  565 IDPALRR 571
Cdd:cd19522   156 IDEALRR 162
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 435-583 4.28e-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: 108.39  E-value: 4.28e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  435 EVFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSRgdKRVAFFMRKGADCLSKWVGESERQ---LRLLFDQAYQMRPA 511
Cdd:cd00009     9 ALREALELPPPKNLLLYGPPGTGKTTLARAIANELFR--PGAPFLYLNASDLLEGLVVAELFGhflVRLLFELAEKAKPG 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 199560855  512 IIFFDEIDGLAPvrssrqdQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSL 583
Cdd:cd00009    87 VLFIDEIDSLSR-------GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151
RecA-like_fidgetin cd19523
ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. ...
 413-580 4.98e-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: 108.43  E-value: 4.98e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  413 VGGLSSHIAALKEMVLFPLLYPEVFEKFkIQPPRGCLFYGPPGTGKTLVARALANECSrgdkrVAFFMRKGADCLSKWVG 492
Cdd:cd19523     2 IAGLGALKAAIKEEVLWPLLRPDAFSGL-LRLPRSILLFGPRGTGKTLLGRCLASQLG-----ATFLRLRGSTLVAKWAG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  493 ESERQLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSRQDQIhSSIVSTLLALMDGLDSRGE--IVVIGATNRLDSIDPALR 570
Cdd:cd19523    76 EGEKILQASFLAARCRQPSVLFISDLDALLSSQDDEASPV-GRLQVELLAQLDGVLGSGEdgVLVVCTTSKPEEIDESLR 154

                         170
                  ....*....|
gi 199560855  571 RpgRFDREFL 580
Cdd:cd19523   155 R--YFSKRLL 162
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 972-1074 4.49e-20

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


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 86.27  E-value: 4.49e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  972 RELRIFLRNVthRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPD 1051
Cdd:cd04369     3 KKLRSLLDAL--KKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGP 80

                          90       100
                  ....*....|....*....|...
gi 199560855 1052 RDPgdrlIRHRACALRDTAYAII 1074
Cdd:cd04369    81 GSP----IYKDAKKLEKLFEKLL 99
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 444-585 4.82e-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: 88.20  E-value: 4.82e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855    444 PPRGCLFYGPPGTGKTLVARALANECSRGDKRVAFF------------MRKGADCLSKWVGESERQLRLLFDQAYQMRPA 511
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIdgedileevldqLLLIIVGGKKASGSGELRLRLALALARKLKPD 80

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 199560855    512 IIFFDEIDGLAPVRSSRQDQihssiVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPgRFDREFLFSLPD 585
Cdd:smart00382   81 VLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 994-1089 1.21e-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: 82.22  E-value: 1.21e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  994 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDrdpgdrlirhracalrDTAYAI 1073
Cdd:cd05509    22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGP----------------DTEYYK 85

                          90
                  ....*....|....*.
gi 199560855 1074 IKEELDEDFEQLCEEI 1089
Cdd:cd05509    86 CANKLEKFFWKKLKEL 101
ycf46 CHL00195
Ycf46; Provisional
 445-676 3.27e-18

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 89.69  E-value: 3.27e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  445 PRGCLFYGPPGTGKTLVARALANECS----RGDKRVAFfmrkgadclSKWVGESERQLRLLFDQAYQMRPAIIFFDEIDG 520
Cdd:CHL00195  259 PRGLLLVGIQGTGKSLTAKAIANDWQlpllRLDVGKLF---------GGIVGESESRMRQMIRIAEALSPCILWIDEIDK 329

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  521 LAPVRSSRQDQIHSSIV-STLLALMDglDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKDARKEILKIHTRD 599
Cdd:CHL00195  330 AFSNSESKGDSGTTNRVlATFITWLS--EKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQK 407

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 199560855  600 WNPKPVDMF-LEELAENCVGYCGADIKSICAEAALCALrrrypqiyttSEKLQLdlssiniSAKDFETAMQKIIPASQ 676
Cdd:CHL00195  408 FRPKSWKKYdIKKLSKLSNKFSGAEIEQSIIEAMYIAF----------YEKREF-------TTDDILLALKQFIPLAQ 468
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 438-579 8.23e-18

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: 82.03  E-value: 8.23e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  438 EKFKIQPPRGCLFYGPPGTGKTLVARALANECSRGDKRV---AFFmrkgadclSKWVGESERQLRLLFDQAYQMRPAIIF 514
Cdd:cd19507    24 SAYGLPTPKGLLLVGIQGTGKSLTAKAIAGVWQLPLLRLdmgRLF--------GGLVGESESRLRQMIQTAEAIAPCVLW 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 199560855  515 FDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDglDSRGEIVVIGATNRLDSIDPALRRPGRFDREF 579
Cdd:cd19507    96 IDEIEKGFSNADSKGDSgTSSRVLGTFLTWLQ--EKKKPVFVVATANNVQSLPPELLRKGRFDEIF 159
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 974-1074 1.27e-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: 79.37  E-value: 1.27e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  974 LRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNpDRD 1053
Cdd:cd05512     2 LEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN-AKD 80

                          90       100
                  ....*....|....*....|..
gi 199560855 1054 PgdrlIRHRACA-LRDTAYAII 1074
Cdd:cd05512    81 T----IFYRAAVrLRDQGGAIL 98
BROMO smart00297
bromo domain;
967-1077 2.38e-17

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 78.86  E-value: 2.38e-17
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855    967 EEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNAL 1046
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100       110
                    ....*....|....*....|....*....|.
gi 199560855   1047 EYNPDrdpgDRLIRHRACALRDTAYAIIKEE 1077
Cdd:smart00297   81 TYNGP----DSEVYKDAKKLEKFFEKKLREL 107
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 994-1049 1.86e-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: 73.84  E-value: 1.86e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 199560855  994 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 1049
Cdd:cd05511    21 FHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYN 76
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 994-1050 5.46e-15

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: 71.19  E-value: 5.46e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 199560855   994 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNP 1050
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 ...
 993-1054 5.41e-14

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


Pssm-ID: 99930  Cd Length: 102  Bit Score: 69.23  E-value: 5.41e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 199560855  993 VFTKPVDP--DEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRDP 1054
Cdd:cd05498    23 PFYKPVDPeaLGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHP 86
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 994-1075 7.66e-13

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: 66.31  E-value: 7.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  994 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNpdRDPGDRLIRHrACALRDTAYAI 1073
Cdd:cd05510    29 FLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYN--SDPSHPLRRH-ANFMKKKAEHL 105


                  ..
gi 199560855 1074 IK 1075
Cdd:cd05510   106 LK 107
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 984-1050 9.08e-13

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: 9.08e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 199560855  984 RLAIDKRFRVFTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNP 1050
Cdd:cd05506    11 KLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNP 79
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 446-577 1.14e-12

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: 66.99  E-value: 1.14e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  446 RGCLFYGPPGTGKTLVARALANEcsrgdkrvaffMRKGADCLS-KWVGESERQLRLLFDQAYQmrPAIIFFDEID----- 519
Cdd:cd19510    24 RGYLLYGPPGTGKSSFIAALAGE-----------LDYDICDLNlSEVVLTDDRLNHLLNTAPK--QSIILLEDIDaafes 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 199560855  520 GLAPVRSSRQDQIHSSI-VSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 577
Cdd:cd19510    91 REHNKKNPSAYGGLSRVtFSGLLNALDGVASSEERIVFMTTNHIERLDPALIRPGRVDM 149
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 989-1049 2.85e-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: 64.26  E-value: 2.85e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 199560855  989 KRFRV---FTKPVDPDE--VPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 1049
Cdd:cd05500    17 KRLKDarpFLVPVDPVKlnIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFN 82
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
 449-569 4.52e-12

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: 66.70  E-value: 4.52e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  449 LFYGPPGTGKTLVARALANECSrgdKRVAFFMRKG-------ADCLSKWVGESERQLRLLFDQAYQM---RPAIIF--FD 516
Cdd:cd19508    56 LLHGPPGTGKTSLCKALAQKLS---IRLSSRYRYGqlieinsHSLFSKWFSESGKLVTKMFQKIQELiddKDALVFvlID 132

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 199560855  517 EIDGLAPVRSSRQDQIHSS----IVSTLLALMDGLDSRGEIVVIGATNRLDSIDPAL 569
Cdd:cd19508   133 EVESLAAARSASSSGTEPSdairVVNAVLTQIDRIKRYHNNVILLTSNLLEKIDVAF 189
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 993-1054 1.33e-11

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: 62.30  E-value: 1.33e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 199560855  993 VFTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRDP 1054
Cdd:cd05499    23 PFLDPVDPValNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTD 86
T7SS_EccA TIGR03922
type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the ...
 449-598 2.93e-11

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


Pssm-ID: 188437 [Multi-domain]  Cd Length: 557  Bit Score: 67.95  E-value: 2.93e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   449 LFYGPPGTGKTLVARALANE-CSRGD-KRVAFFMRKGADCLSKWVGESERQLRLLFDQAYQmrpAIIFFDEIDGLAPVRS 526
Cdd:TIGR03922  316 LFAGPPGTGKTTIARVVAKIyCGLGVlRKPLVREVSRADLIGQYIGESEAKTNEIIDSALG---GVLFLDEAYTLVETGY 392

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 199560855   527 SRQDQIHSSIVSTLLALMDglDSRGEIVVIGA--TNRLD---SIDPALRRpgRFDR--EFLFSLPDkdarkEILKIHTR 598
Cdd:TIGR03922  393 GQKDPFGLEAIDTLLARME--NDRDRLVVIGAgyRKDLDkflEVNEGLRS--RFTRviEFPSYSPD-----ELVEIARR 462
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 994-1053 3.79e-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: 61.64  E-value: 3.79e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  994 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRD 1053
Cdd:cd05504    33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHT 92
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 994-1049 1.37e-10

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


Pssm-ID: 99945  Cd Length: 98  Bit Score: 59.35  E-value: 1.37e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 199560855  994 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 1049
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 ...
 994-1052 3.09e-10

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: 59.01  E-value: 3.09e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 199560855  994 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDR 1052
Cdd:cd05496    26 FRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNK 84
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 994-1054 1.02e-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: 57.00  E-value: 1.02e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 199560855  994 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRDP 1054
Cdd:cd05503    21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSE 81
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 994-1049 1.50e-09

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


Pssm-ID: 99937  Cd Length: 97  Bit Score: 56.39  E-value: 1.50e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 199560855  994 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 1049
Cdd:cd05505    21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYY 76
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 973-1050 2.28e-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: 56.30  E-value: 2.28e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  973 ELRIFLRNVTHRLAIDKRFRV-FTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 1049
Cdd:cd05495     3 ELRQALMPTLEKLYKQDPESLpFRQPVDPKllGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYN 82


                  .
gi 199560855 1050 P 1050
Cdd:cd05495    83 R 83
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 609-643 2.96e-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: 53.70  E-value: 2.96e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 199560855   609 LEELAENCVGYCGADIKSICAEAALCALRRRYPQI 643
Cdd:pfam17862    4 LEELAERTEGFSGADLEALCREAALAALRRGLEAV 38
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 994-1059 5.69e-09

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: 55.12  E-value: 5.69e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 199560855  994 FTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPdrdPGDRLI 1059
Cdd:cd05497    26 FQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNK---PGDDVV 90
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 983-1051 5.92e-09

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: 55.00  E-value: 5.92e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  983 HRLAIdkrfrVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN-PD 1051
Cdd:cd05515    21 RRLSL-----IFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNePD 85
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 987-1097 2.41e-08

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 57.89  E-value: 2.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  987 IDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNpdrDPGDRLIRHRacal 1066
Cdd:COG5076   162 GRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVYVDA---- 234

                          90       100       110
                  ....*....|....*....|....*....|.
gi 199560855 1067 rdtayAIIKEELDEDFEQLCEEIQESRKKRG 1097
Cdd:COG5076   235 -----KELEKYFLKLIEEIPEEMLELSIKPG 260
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 1002-1049 2.77e-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: 53.20  E-value: 2.77e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 199560855 1002 EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 1049
Cdd:cd05516    36 ELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFN 83
RecA-like_Ycf2 cd19505
ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; ...
 444-577 5.56e-08

ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; however, its function remains unclear. The gene encoding YCF2 is the largest known plastid gene in angiosperms and has been used to predict phylogenetic relationships. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410913 [Multi-domain]  Cd Length: 161  Bit Score: 53.53  E-value: 5.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  444 PPRGCLFYGPPGTGKTLVARALA------------NECSrgDKRVAFFMRKGADCLSKWvGESERQLRLLFDQAYQMRPA 511
Cdd:cd19505    11 PSKGILLIGSIETGRSYLIKSLAansyvplirislNKLL--YNKPDFGNDDWIDGMLIL-KESLHRLNLQFELAKAMSPC 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 199560855  512 IIFFDEIDGLApVRSSRQDQIHSSivSTLLALMDGLDSRG-------EIVVIGATNRLDSIDPALRRPGRFDR 577
Cdd:cd19505    88 IIWIPNIHELN-VNRSTQNLEEDP--KLLLGLLLNYLSRDfeksstrNILVIASTHIPQKVDPALIAPNRLDT 157
Bromodomain_1 cd05494
Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated ...
 965-1095 5.78e-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: 52.45  E-value: 5.78e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  965 EQEEDTFRELRIFLRNvthrlaidKRFRVFTKPVDPDE--VPDYVTVIKQPMDLSsviSKIDLHkyltVKDYLKDIDLIC 1042
Cdd:cd05494     3 EALERVLRELKRHRRN--------EDAWPFLEPVNPPRrgAPDYRDVIKRPMSFG---TKVNNI----VETGARDLEDLQ 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 199560855 1043 SNAleynpdRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESRKK 1095
Cdd:cd05494    68 IVQ------EDPADKQIDDEGRRSPSNIYAVEALEQLIVFQCKQVKGLKQKRH 114
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 446-576 1.02e-07

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


Pssm-ID: 410920 [Multi-domain]  Cd Length: 150  Bit Score: 52.53  E-value: 1.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  446 RGCLFYGPPGTGKTLVARALANEC-------SRGDkrVAFFMRKGADCLSK---WVGESERQLrllfdqayqmrpaIIFF 515
Cdd:cd19512    23 RNILFYGPPGTGKTLFAKKLALHSgmdyaimTGGD--VAPMGREGVTAIHKvfdWANTSRRGL-------------LLFV 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 199560855  516 DEIDGLAPVRSSrqDQIHSSIVSTLLALM--DGLDSRgEIVVIGATNRLDSIDPALRrpGRFD 576
Cdd:cd19512    88 DEADAFLRKRST--EKISEDLRAALNAFLyrTGEQSN-KFMLVLASNQPEQFDWAIN--DRID 145
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 448-570 8.31e-07

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 53.16  E-value: 8.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  448 CLFYGPPGTGKTLVARALANECSRgdkrvAFFMrkgadcLSKwVGESERQLRLLFDQAYQMRPA----IIFFDEIDGLAp 523
Cdd:PRK13342   39 MILWGPPGTGKTTLARIIAGATDA-----PFEA------LSA-VTSGVKDLREVIEEARQRRSAgrrtILFIDEIHRFN- 105

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 199560855  524 vrSSRQDqihssivsTLLALMDgldsRGEIVVIGAT--NRLDSIDPALR 570
Cdd:PRK13342  106 --KAQQD--------ALLPHVE----DGTITLIGATteNPSFEVNPALL 140
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 990-1049 9.15e-07

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: 48.78  E-value: 9.15e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  990 RFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 1049
Cdd:cd05522    24 LTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYN 83
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 993-1053 9.44e-07

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


Pssm-ID: 99939  Cd Length: 104  Bit Score: 48.51  E-value: 9.44e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 199560855  993 VFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN-PDRD 1053
Cdd:cd05507    23 VFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNsSDHD 84
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 955-1051 1.13e-06

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: 48.44  E-value: 1.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  955 LTAEEVKRLEeqeedtfrelRIFLRNVTHRLAIDkrfrvFTKPVDPdEVPDYVTVIKQPMDLSSVISKIDLH---KYLTV 1031
Cdd:cd05502     1 LSPIDQRKCE----------RLLLELYCHELSLP-----FHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKspqHYSSP 64

                          90       100
                  ....*....|....*....|
gi 199560855 1032 KDYLKDIDLICSNALEYNPD 1051
Cdd:cd05502    65 EEFVADVRLMFKNCYKFNEE 84
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 992-1049 1.41e-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: 48.20  E-value: 1.41e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 199560855  992 RVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 1049
Cdd:cd05517    25 ELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN 82
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 449-618 4.20e-06

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 50.82  E-value: 4.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  449 LFYGPPGTGKTLVARALANECSRgdkrvAFFMrkgadcLSKwVGESERQLRLLFDQAYQMR----PAIIFFDEIDglapv 524
Cdd:COG2256    53 ILWGPPGTGKTTLARLIANATDA-----EFVA------LSA-VTSGVKDIREVIEEARERRaygrRTILFVDEIH----- 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  525 R--SSRQDqihssivsTLLALMDgldsRGEIVVIGAT---------------------NRLDS------IDPALRRPGRF 575
Cdd:COG2256   116 RfnKAQQD--------ALLPHVE----DGTITLIGATtenpsfevnsallsrcrvfvlKPLSEedleqlLERALADDERG 183

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 199560855  576 D-----------REFLFSLPDKDARK-----EILKIHTRDWNPKPVDmflEELAENCVG 618
Cdd:COG2256   184 LggyklelddeaLEALARLADGDARRalnalELAVLSAPPDGVIEIT---LELVEEALQ 239
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 1002-1049 8.49e-06

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: 45.90  E-value: 8.49e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 199560855 1002 EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 1049
Cdd:cd05518    35 DYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 1004-1050 9.69e-06

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: 45.79  E-value: 9.69e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 199560855 1004 PDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNP 1050
Cdd:cd05520    37 PDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNV 83
ycf46 CHL00195
Ycf46; Provisional
 778-919 2.18e-05

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 48.86  E-value: 2.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  778 PR-LLIVGEPGFGQSshLAPAVIHALEKFTVYTLDIPVLFGISTTSPEEACSQMIREAKRTAPSIvyvphvhLWW-EI-- 853
Cdd:CHL00195  259 PRgLLLVGIQGTGKS--LTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCI-------LWIdEIdk 329

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 199560855  854 ----------VGPTLR--ATFTTLLQNIPSfaPVLLLATSERPYSaLPEEVqeLFTHDYGEIFNVQLPDKEERTKFFE 919
Cdd:CHL00195  330 afsnseskgdSGTTNRvlATFITWLSEKKS--PVFVVATANNIDL-LPLEI--LRKGRFDEIFFLDLPSLEEREKIFK 402
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
443-594 2.48e-05

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


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 48.31  E-value: 2.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  443 QPPRGCLFYGPPGTGKTLVARA----LANECSRGDKRVAF-------------FMRKGADCLSKWVGESERQLRL--LFD 503
Cdd:COG1474    49 ERPSNVLIYGPTGTGKTAVAKYvleeLEEEAEERGVDVRVvyvncrqastryrVLSRILEELGSGEDIPSTGLSTdeLFD 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  504 QAYQM-----RPAIIFFDEIDGLapvrssrQDQIHSSIVSTLLALMDGLDSRGeIVVIGATNRL---DSIDPALRRpgRF 575
Cdd:COG1474   129 RLYEAlderdGVLVVVLDEIDYL-------VDDEGDDLLYQLLRANEELEGAR-VGVIGISNDLeflENLDPRVKS--SL 198

                         170       180
                  ....*....|....*....|
gi 199560855  576 -DREFLFSLPDKDARKEILK 594
Cdd:COG1474   199 gEEEIVFPPYDADELRDILE 218
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
442-479 6.19e-05

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


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 45.93  E-value: 6.19e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 199560855  442 IQPPRGCLFYGPPGTGKTLVARALANECSRGDKRVAFF 479
Cdd:COG1484    96 IERGENLILLGPPGTGKTHLAIALGHEACRAGYRVRFT 133
PRK04195 PRK04195
replication factor C large subunit; Provisional
 441-521 7.45e-05

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 46.84  E-value: 7.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  441 KIQPPRGCLFYGPPGTGKTLVARALANE---------CSrgDKRvaffmrkGADCLSKWVGESERQlRLLFDQAYQmrpa 511
Cdd:PRK04195   35 KGKPKKALLLYGPPGVGKTSLAHALANDygwevielnAS--DQR-------TADVIERVAGEAATS-GSLFGARRK---- 100

                          90
                  ....*....|
gi 199560855  512 IIFFDEIDGL 521
Cdd:PRK04195  101 LILLDEVDGI 110
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 994-1049 9.19e-05

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: 42.76  E-value: 9.19e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 199560855  994 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 1049
Cdd:cd05508    23 FLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYN 78
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 1004-1048 1.56e-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: 42.71  E-value: 1.56e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 199560855 1004 PDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEY 1048
Cdd:cd05524    39 PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAY 83
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 964-1050 2.09e-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: 42.71  E-value: 2.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  964 EEQEEDTFRELRIFLRNVthRLAIDKRFRVftkPVD-PDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLIC 1042
Cdd:cd05529    23 DEERERLISGLDKLLLSL--QLEIAEYFEY---PVDlRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLIL 97


                  ....*...
gi 199560855 1043 SNALEYNP 1050
Cdd:cd05529    98 SNAETFNE 105
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
445-583 3.81e-04

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 43.37  E-value: 3.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  445 PRGC--LFYGPPGTGKTLVARALANE-CSRGDKrVAFFMrkgadclskwVGESERQLR-----LLFD-QAYQMRPAIIFF 515
Cdd:COG0467    18 PRGSstLLSGPPGTGKTTLALQFLAEgLRRGEK-GLYVS----------FEESPEQLLrraesLGLDlEEYIESGLLRII 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 199560855  516 DeidglapVRSSRQDQIHSSIVSTLLALMDGLDSRgeIVVIgatnrlDSIDP---ALRRPGRFdREFLFSL 583
Cdd:COG0467    87 D-------LSPEELGLDLEELLARLREAVEEFGAK--RVVI------DSLSGlllALPDPERL-REFLHRL 141
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 449-565 4.60e-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: 42.55  E-value: 4.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  449 LFYGPPGTGKTLVARALANE-CSRGDKRVAF----FMRKGADCLSK-----WVGESERQlrLLFDQAYQMRPAIIFFDEI 518
Cdd:cd19499    45 LFLGPTGVGKTELAKALAELlFGDEDNLIRIdmseYMEKHSVSRLIgappgYVGYTEGG--QLTEAVRRKPYSVVLLDEI 122

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 199560855  519 dglapvrssrqDQIHSSIVSTLLALMD-G--LDSRGEIVVIGAT--------------NRLDSI 565
Cdd:cd19499   123 -----------EKAHPDVQNLLLQVLDdGrlTDSHGRTVDFKNTiiimtsnhfrpeflNRIDEI 175
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 445-556 1.51e-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: 40.95  E-value: 1.51e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   445 PRGCLFYGPPGTGKTLVARALANECSRgdKRVAFFMRKGADCLSK---WVGESERQLRLLFDQAYQMRPAIIFFDEIDGL 521
Cdd:pfam13191   24 PPSVLLTGEAGTGKTTLLRELLRALER--DGGYFLRGKCDENLPYsplLEALTREGLLRQLLDELESSLLEAWRAALLEA 101

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 199560855   522 APVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVI 556
Cdd:pfam13191  102 LAPVPELPGDLAERLLDLLLRLLDLLARGERPLVL 136
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 758-892 2.51e-03

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: 40.04  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  758 ENLNFLHLNRNACYQPMSFR-----PR-LLIVGEPGFGQSshLAPAVIHALEKFTVYTLDIPVLFGISTTSPEEACSQMI 831
Cdd:cd19507     6 DNLKDWLKKRKAAFSKQASAyglptPKgLLLVGIQGTGKS--LTAKAIAGVWQLPLLRLDMGRLFGGLVGESESRLRQMI 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 199560855  832 REAKRTAPSIVYVPhvhlwwEI------------VGPTLR--ATFTTLLQNipSFAPVLLLATSERpYSALPEEV 892
Cdd:cd19507    84 QTAEAIAPCVLWID------EIekgfsnadskgdSGTSSRvlGTFLTWLQE--KKKPVFVVATANN-VQSLPPEL 149
PRK08116 PRK08116
hypothetical protein; Validated
 433-468 2.70e-03

hypothetical protein; Validated


Pssm-ID: 236153 [Multi-domain]  Cd Length: 268  Bit Score: 41.16  E-value: 2.70e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 199560855  433 YPEVFEKFKIQPpRGCLFYGPPGTGKTLVARALANE 468
Cdd:PRK08116  103 YVKKFEEMKKEN-VGLLLWGSVGTGKTYLAACIANE 137
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 989-1049 3.35e-03

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


Pssm-ID: 99950  Cd Length: 103  Bit Score: 38.47  E-value: 3.35e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 199560855  989 KRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 1049
Cdd:cd05519    22 KLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYN 82
AAA_22 pfam13401
AAA domain;
442-565 5.31e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 38.48  E-value: 5.31e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   442 IQPPRGCLF-YGPPGTGKTLVARALANECSRGDKRVAFFMRKGADCLS---KWV-------GESERQLRLLFDQAYQ--- 507
Cdd:pfam13401    1 IRFGAGILVlTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKdllRALlralglpLSGRLSKEELLAALQQlll 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855   508 --MRPAIIFFDEIDGLapvrssrqdqiHSSIVSTLLALMDGLDSRGEIVVIGaTNRLDSI 565
Cdd:pfam13401   81 alAVAVVLIIDEAQHL-----------SLEALEELRDLLNLSSKLLQLILVG-TPELREL 128
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 1003-1075 5.78e-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: 5.78e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 199560855 1003 VPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRDPGDRlirhRACALRDtAYAIIK 1075
Cdd:cd05525    38 NPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGR----DVCRLRK-AYYQAK 105
RecA-like_superfamily cd01120
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 ...
 449-566 5.90e-03

RecA-like_NTPases; RecA-like NTPases. This superfamily 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: 410865 [Multi-domain]  Cd Length: 119  Bit Score: 38.25  E-value: 5.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  449 LFYGPPGTGKTLVARALANECSRGDKRVAFFMrkGADCLskwvgeserqLRLLFDQAYQMRPAIIFFDEIDGLAPVRSSR 528
Cdd:cd01120     2 LITGPPGSGKTTLLLQFAEQALLSDEPVIFIS--FLDTI----------LEAIEDLIEEKKLDIIIIDSLSSLARASQGD 69

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 199560855  529 QDQIHSSIVSTLLALMdgldSRGEIVVIgATNRLDSID 566
Cdd:cd01120    70 RSSELLEDLAKLLRAA----RNTGITVI-ATIHSDKFD 102
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
448-468 6.26e-03

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 40.50  E-value: 6.26e-03
                          10        20
                  ....*....|....*....|.
gi 199560855  448 CLFYGPPGTGKTLVARALANE 468
Cdd:PRK00080   54 VLLYGPPGLGKTTLANIIANE 74
PRK13341 PRK13341
AAA family ATPase;
449-627 7.72e-03

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 40.81  E-value: 7.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  449 LFYGPPGTGKTLVARALANECSrgdkrvAFFMRKGAdCLSkwvGESErqLRLLFDQAYQMRP-----AIIFFDEIDGLap 523
Cdd:PRK13341   56 ILYGPPGVGKTTLARIIANHTR------AHFSSLNA-VLA---GVKD--LRAEVDRAKERLErhgkrTILFIDEVHRF-- 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  524 vRSSRQDqihssivstllALMDGLDsRGEIVVIGAT--NRLDSIDPALRRPGRFDRefLFSLPDKDARK---EILKIHTR 598
Cdd:PRK13341  122 -NKAQQD-----------ALLPWVE-NGTITLIGATteNPYFEVNKALVSRSRLFR--LKSLSDEDLHQllkRALQDKER 186

                         170       180       190
                  ....*....|....*....|....*....|
gi 199560855  599 DWNPKPVDmfLEELAEN-CVGYCGADIKSI 627
Cdd:PRK13341  187 GYGDRKVD--LEPEAEKhLVDVANGDARSL 214
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
 449-522 7.87e-03

ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent protease ClpXP. In ClpXP, ClpX ATPase serves to specifically recognize, unfold, and translocate protein substrates into the chamber of ClpP protease for degradation. This RecA-like_ClpX domain 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: 410905 [Multi-domain]  Cd Length: 251  Bit Score: 39.89  E-value: 7.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199560855  449 LFYGPPGTGKTLVARALANECSrgdkrVAFFMrkgADCLS----KWVGESERQ--LRLLFDQAYQMRPA---IIFFDEID 519
Cdd:cd19497    54 LLIGPTGSGKTLLAQTLAKILD-----VPFAI---ADATTlteaGYVGEDVENilLKLLQAADYDVERAqrgIVYIDEID 125


                  ...
gi 199560855  520 GLA 522
Cdd:cd19497   126 KIA 128
 
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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