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Conserved domains on  [gi|1907114144|ref|XP_036015476|]
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ATPase family AAA domain-containing protein 2 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
459-569 2.87e-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: 188.72  E-value: 2.87e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 459 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPD 538
Cdd:cd05528     2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1907114144 539 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 569
Cdd:cd05528    82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
1-74 4.74e-46

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd19517:

Pssm-ID: 422963 [Multi-domain]  Cd Length: 170  Bit Score: 162.29  E-value: 4.74e-46
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907114144   1 MRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 74
Cdd:cd19517    97 MQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRRPGRFDREFYF 170
CDC48 super family cl36852
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
3-172 1.74e-45

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.


The actual alignment was detected with superfamily member TIGR01243:

Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 175.10  E-value: 1.74e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNAR 82
Cdd:TIGR01243 272 PSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRAR 351
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  83 KEILKIHTRDwNPKPVDMFLEELAEHCVGYCGADIKSICAEAALCALRRRYPQIYTTSEKLQLD---LSSITISAKDFEA 159
Cdd:TIGR01243 352 KEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKINFEAEEIPaevLKELKVTMKDFME 430
                         170
                  ....*....|...
gi 1907114144 160 ALQKIRPASQRAV 172
Cdd:TIGR01243 431 ALKMVEPSAIREV 443
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
3-406 1.70e-42

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


:

Pssm-ID: 223540 [Multi-domain]  Cd Length: 494  Bit Score: 162.30  E-value: 1.70e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLdSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNAR 82
Cdd:COG0464    77 PSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGL-KRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGR 155
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  83 KEILKIHTRdWNPKPVDMFLEELAEHCVGYCGADIKSICAEAALCALRRrypqiyttseKLQLDLSSITISAKDFEAALQ 162
Cdd:COG0464   156 LEILQIHTR-LMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRR----------AIDLVGEYIGVTEDDFEEALK 224
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 163 KIRPASQRAVTSPGQALSAIVKplLQNTVHRILDAlqkvfphvevgtnkslnsdvscpfLESDLAYSDddtpsvyengLS 242
Cdd:COG0464   225 KVLPSRGVLFEDEDVTLDDIGG--LEEAKEELKEA------------------------IETPLKRPE----------LF 268
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 243 QKENLnflhlnrnacyqpmSFRPRLLIVGEPGFGQsSHLAPAVihALE-KFTVYTLDIPVLFGISTTSPEEACSQMIREA 321
Cdd:COG0464   269 RKLGL--------------RPPKGVLLYGPPGTGK-TLLAKAV--ALEsRSRFISVKGSELLSKWVGESEKNIRELFEKA 331
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 322 KRTAPSIVYVPHIHLWWEIVGPT-------LKATFTTLLQTIPSFAPVLLLATSEKPySALPEEVqeLFTHDYGEIFNVQ 394
Cdd:COG0464   332 RKLAPSIIFIDEIDSLASGRGPSedgsgrrVVGQLLTELDGIEKAEGVLVIAATNRP-DDLDPAL--LRPGRFDRLIYVP 408
                         410
                  ....*....|..
gi 1907114144 395 LPDKEERTKFFE 406
Cdd:COG0464   409 LPDLEERLEIFK 420
 
Name Accession Description Interval E-value
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
459-569 2.87e-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: 188.72  E-value: 2.87e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 459 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPD 538
Cdd:cd05528     2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1907114144 539 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 569
Cdd:cd05528    82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
1-74 4.74e-46

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: 162.29  E-value: 4.74e-46
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907114144   1 MRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 74
Cdd:cd19517    97 MQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRRPGRFDREFYF 170
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
3-172 1.74e-45

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: 175.10  E-value: 1.74e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNAR 82
Cdd:TIGR01243 272 PSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRAR 351
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  83 KEILKIHTRDwNPKPVDMFLEELAEHCVGYCGADIKSICAEAALCALRRRYPQIYTTSEKLQLD---LSSITISAKDFEA 159
Cdd:TIGR01243 352 KEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKINFEAEEIPaevLKELKVTMKDFME 430
                         170
                  ....*....|...
gi 1907114144 160 ALQKIRPASQRAV 172
Cdd:TIGR01243 431 ALKMVEPSAIREV 443
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
3-406 1.70e-42

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


Pssm-ID: 223540 [Multi-domain]  Cd Length: 494  Bit Score: 162.30  E-value: 1.70e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLdSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNAR 82
Cdd:COG0464    77 PSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGL-KRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGR 155
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  83 KEILKIHTRdWNPKPVDMFLEELAEHCVGYCGADIKSICAEAALCALRRrypqiyttseKLQLDLSSITISAKDFEAALQ 162
Cdd:COG0464   156 LEILQIHTR-LMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRR----------AIDLVGEYIGVTEDDFEEALK 224
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 163 KIRPASQRAVTSPGQALSAIVKplLQNTVHRILDAlqkvfphvevgtnkslnsdvscpfLESDLAYSDddtpsvyengLS 242
Cdd:COG0464   225 KVLPSRGVLFEDEDVTLDDIGG--LEEAKEELKEA------------------------IETPLKRPE----------LF 268
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 243 QKENLnflhlnrnacyqpmSFRPRLLIVGEPGFGQsSHLAPAVihALE-KFTVYTLDIPVLFGISTTSPEEACSQMIREA 321
Cdd:COG0464   269 RKLGL--------------RPPKGVLLYGPPGTGK-TLLAKAV--ALEsRSRFISVKGSELLSKWVGESEKNIRELFEKA 331
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 322 KRTAPSIVYVPHIHLWWEIVGPT-------LKATFTTLLQTIPSFAPVLLLATSEKPySALPEEVqeLFTHDYGEIFNVQ 394
Cdd:COG0464   332 RKLAPSIIFIDEIDSLASGRGPSedgsgrrVVGQLLTELDGIEKAEGVLVIAATNRP-DDLDPAL--LRPGRFDRLIYVP 408
                         410
                  ....*....|..
gi 1907114144 395 LPDKEERTKFFE 406
Cdd:COG0464   409 LPDLEERLEIFK 420
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
3-176 1.92e-40

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


Pssm-ID: 224143 [Multi-domain]  Cd Length: 406  Bit Score: 153.96  E-value: 1.92e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLAL---MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDK 79
Cdd:COG1222   245 PSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELlnqLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDE 324
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  80 NARKEILKIHTRDWNPKPvDMFLEELAEHCVGYCGADIKSICAEAALCALRRRypqiyttseklqldlsSITISAKDFEA 159
Cdd:COG1222   325 EGRAEILKIHTRKMNLAD-DVDLELLARLTEGFSGADLKAICTEAGMFAIRER----------------RDEVTMEDFLK 387
                         170
                  ....*....|....*..
gi 1907114144 160 ALQKIRPASQRAVTSPG 176
Cdd:COG1222   388 AVEKVVKKKKKLSSTAR 404
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
3-165 8.66e-40

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 151.91  E-value: 8.66e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLApvrSSRQDQIHS---SIVST---LLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSL 76
Cdd:PRK03992  225 PSIIFIDEIDAIA---AKRTDSGTSgdrEVQRTlmqLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPL 301
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  77 PDKNARKEILKIHTRDWNPKP-VDmfLEELAEHCVGYCGADIKSICAEAALCALRRRYPQiyttseklqldlssitISAK 155
Cdd:PRK03992  302 PDEEGRLEILKIHTRKMNLADdVD--LEELAELTEGASGADLKAICTEAGMFAIRDDRTE----------------VTME 363
                         170
                  ....*....|
gi 1907114144 156 DFEAALQKIR 165
Cdd:PRK03992  364 DFLKAIEKVM 373
26Sp45 TIGR01242
26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an ...
3-132 2.05e-33

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: 132.62  E-value: 2.05e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVR---SSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDK 79
Cdd:TIGR01242 216 PSIIFIDEIDAIAAKRtdsGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDF 295
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907114144  80 NARKEILKIHTRDWNPKPvDMFLEELAEHCVGYCGADIKSICAEAALCALRRR 132
Cdd:TIGR01242 296 EGRLEILKIHTRKMKLAE-DVDLEAIAKMTEGASGADLKAICTEAGMFAIREE 347
ftsH CHL00176
cell division protein; Validated
3-136 3.22e-28

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 120.93  E-value: 3.22e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSR----QDQiHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPD 78
Cdd:CHL00176  276 PCIVFIDEIDAVGRQRGAGigggNDE-REQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPD 354
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  79 KNARKEILKIHTRDwnpKPV--DMFLEELAEHCVGYCGADIKSICAEAALCALRRRYPQI 136
Cdd:CHL00176  355 REGRLDILKVHARN---KKLspDVSLELIARRTPGFSGADLANLLNEAAILTARRKKATI 411
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
1-76 1.35e-22

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: 394963 [Multi-domain]  Cd Length: 130  Bit Score: 93.81  E-value: 1.35e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907114144   1 MRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFSL 76
Cdd:pfam00004  56 LAPCVIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
BROMO smart00297
bromo domain;
454-564 2.28e-17

bromo domain;


Pssm-ID: 197636  Cd Length: 107  Bit Score: 78.09  E-value: 2.28e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  454 EEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNAL 533
Cdd:smart00297   1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80
                           90       100       110
                   ....*....|....*....|....*....|.
gi 1907114144  534 EYNPDrdpgDRLIRHRACALRDTAYAIIKEE 564
Cdd:smart00297  81 TYNGP----DSEVYKDAKKLEKFFEKKLREL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
481-537 2.90e-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: 395352  Cd Length: 84  Bit Score: 71.58  E-value: 2.90e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907114144 481 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNP 537
Cdd:pfam00439  17 FLEPVDPDEYPDYYSVIKRPMDLSTIKKKLENGEYKSLAEFEADVKLMFSNARTYNG 73
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
102-136 6.13e-10

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


Pssm-ID: 407720 [Multi-domain]  Cd Length: 45  Bit Score: 55.25  E-value: 6.13e-10
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1907114144 102 LEELAEHCVGYCGADIKSICAEAALCALRRRYPQI 136
Cdd:pfam17862   4 LEELAERTEGFSGADLEALCREAALAALRRGREAV 38
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
474-584 1.80e-08

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 57.51  E-value: 1.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 474 IDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNpdrDPGDRLIRHRacal 553
Cdd:COG5076   162 GRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVYVDA---- 234
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1907114144 554 rdtayAIIKEELDEDFEQLCEEIQESRKKRG 584
Cdd:COG5076   235 -----KELEKYFLKLIEEIPEEMLELSIKPG 260
ycf46 CHL00195
Ycf46; Provisional
265-406 8.08e-05

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 46.17  E-value: 8.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 265 PR-LLIVGEPGFGQSshLAPAVIHALEKFTVYTLDIPVLFGISTTSPEEACSQMIREAKRTAPSIvyvphihLWW-EI-- 340
Cdd:CHL00195  259 PRgLLLVGIQGTGKS--LTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCI-------LWIdEIdk 329
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907114144 341 ----------VGPTLK--ATFTTLLQTIPSfaPVLLLATSEKPYSaLPEEVqeLFTHDYGEIFNVQLPDKEERTKFFE 406
Cdd:CHL00195  330 afsnseskgdSGTTNRvlATFITWLSEKKS--PVFVVATANNIDL-LPLEI--LRKGRFDEIFFLDLPSLEEREKIFK 402
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
1-78 9.03e-05

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: 43.52  E-value: 9.03e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907114144    1 MRPAIIFFDEIDGLAPVRSSRQDQihssiVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPgRFDREFLFSLPD 78
Cdd:smart00382  77 LKPDVLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
 
Name Accession Description Interval E-value
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
459-569 2.87e-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: 188.72  E-value: 2.87e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 459 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPD 538
Cdd:cd05528     2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1907114144 539 RDPGDRLIRHRACALRDTAYAIIKEELDEDF 569
Cdd:cd05528    82 RDPADKLIRSRACELRDEVHAMIEAELDPLF 112
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
1-74 4.74e-46

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: 162.29  E-value: 4.74e-46
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907114144   1 MRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 74
Cdd:cd19517    97 MQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRRPGRFDREFYF 170
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
3-172 1.74e-45

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: 175.10  E-value: 1.74e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNAR 82
Cdd:TIGR01243 272 PSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRAR 351
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  83 KEILKIHTRDwNPKPVDMFLEELAEHCVGYCGADIKSICAEAALCALRRRYPQIYTTSEKLQLD---LSSITISAKDFEA 159
Cdd:TIGR01243 352 KEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKINFEAEEIPaevLKELKVTMKDFME 430
                         170
                  ....*....|...
gi 1907114144 160 ALQKIRPASQRAV 172
Cdd:TIGR01243 431 ALKMVEPSAIREV 443
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
3-406 1.70e-42

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


Pssm-ID: 223540 [Multi-domain]  Cd Length: 494  Bit Score: 162.30  E-value: 1.70e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLdSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNAR 82
Cdd:COG0464    77 PSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGL-KRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGR 155
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  83 KEILKIHTRdWNPKPVDMFLEELAEHCVGYCGADIKSICAEAALCALRRrypqiyttseKLQLDLSSITISAKDFEAALQ 162
Cdd:COG0464   156 LEILQIHTR-LMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRR----------AIDLVGEYIGVTEDDFEEALK 224
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 163 KIRPASQRAVTSPGQALSAIVKplLQNTVHRILDAlqkvfphvevgtnkslnsdvscpfLESDLAYSDddtpsvyengLS 242
Cdd:COG0464   225 KVLPSRGVLFEDEDVTLDDIGG--LEEAKEELKEA------------------------IETPLKRPE----------LF 268
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 243 QKENLnflhlnrnacyqpmSFRPRLLIVGEPGFGQsSHLAPAVihALE-KFTVYTLDIPVLFGISTTSPEEACSQMIREA 321
Cdd:COG0464   269 RKLGL--------------RPPKGVLLYGPPGTGK-TLLAKAV--ALEsRSRFISVKGSELLSKWVGESEKNIRELFEKA 331
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 322 KRTAPSIVYVPHIHLWWEIVGPT-------LKATFTTLLQTIPSFAPVLLLATSEKPySALPEEVqeLFTHDYGEIFNVQ 394
Cdd:COG0464   332 RKLAPSIIFIDEIDSLASGRGPSedgsgrrVVGQLLTELDGIEKAEGVLVIAATNRP-DDLDPAL--LRPGRFDRLIYVP 408
                         410
                  ....*....|..
gi 1907114144 395 LPDKEERTKFFE 406
Cdd:COG0464   409 LPDLEERLEIFK 420
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
3-167 2.10e-41

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: 162.77  E-value: 2.10e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNA 81
Cdd:TIGR01243 547 PAIIFFDEIDAIAPARGARFDTsVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEA 626
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  82 RKEILKIHTRDWnPKPVDMFLEELAEHCVGYCGADIKSICAEAALCALRRRYPQIytTSEKLQLDLSSIT----ISAKDF 157
Cdd:TIGR01243 627 RKEIFKIHTRSM-PLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGSP--AKEKLEVGEEEFLkdlkVEMRHF 703
                         170
                  ....*....|
gi 1907114144 158 EAALQKIRPA 167
Cdd:TIGR01243 704 LEALKKVKPS 713
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
3-176 1.92e-40

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


Pssm-ID: 224143 [Multi-domain]  Cd Length: 406  Bit Score: 153.96  E-value: 1.92e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLAL---MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDK 79
Cdd:COG1222   245 PSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELlnqLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDE 324
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  80 NARKEILKIHTRDWNPKPvDMFLEELAEHCVGYCGADIKSICAEAALCALRRRypqiyttseklqldlsSITISAKDFEA 159
Cdd:COG1222   325 EGRAEILKIHTRKMNLAD-DVDLELLARLTEGFSGADLKAICTEAGMFAIRER----------------RDEVTMEDFLK 387
                         170
                  ....*....|....*..
gi 1907114144 160 ALQKIRPASQRAVTSPG 176
Cdd:COG1222   388 AVEKVVKKKKKLSSTAR 404
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
3-166 2.09e-40

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


Pssm-ID: 223540 [Multi-domain]  Cd Length: 494  Bit Score: 156.14  E-value: 2.09e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNAR 82
Cdd:COG0464   336 PSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEER 415
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  83 KEILKIHTRDWNPKPV-DMFLEELAEHCVGYCGADIKSICAEAALCALRRRYPqiyttseklqldlssITISAKDFEAAL 161
Cdd:COG0464   416 LEIFKIHLRDKKPPLAeDVDLEELAEITEGYSGADIAALVREAALEALREARR---------------REVTLDDFLDAL 480

                  ....*
gi 1907114144 162 QKIRP 166
Cdd:COG0464   481 KKIKP 485
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
3-165 8.66e-40

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 151.91  E-value: 8.66e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLApvrSSRQDQIHS---SIVST---LLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSL 76
Cdd:PRK03992  225 PSIIFIDEIDAIA---AKRTDSGTSgdrEVQRTlmqLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPL 301
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  77 PDKNARKEILKIHTRDWNPKP-VDmfLEELAEHCVGYCGADIKSICAEAALCALRRRYPQiyttseklqldlssitISAK 155
Cdd:PRK03992  302 PDEEGRLEILKIHTRKMNLADdVD--LEELAELTEGASGADLKAICTEAGMFAIRDDRTE----------------VTME 363
                         170
                  ....*....|
gi 1907114144 156 DFEAALQKIR 165
Cdd:PRK03992  364 DFLKAIEKVM 373
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
3-74 1.06e-36

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: 135.50  E-value: 1.06e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 74
Cdd:cd19503    94 PSIIFIDEIDALAPKREEDQREVERRVVAQLLTLMDGMSSRGKVVVIAATNRPDAIDPALRRPGRFDREVEI 165
26Sp45 TIGR01242
26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an ...
3-132 2.05e-33

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: 132.62  E-value: 2.05e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVR---SSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDK 79
Cdd:TIGR01242 216 PSIIFIDEIDAIAAKRtdsGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDF 295
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907114144  80 NARKEILKIHTRDWNPKPvDMFLEELAEHCVGYCGADIKSICAEAALCALRRR 132
Cdd:TIGR01242 296 EGRLEILKIHTRKMKLAE-DVDLEAIAKMTEGASGADLKAICTEAGMFAIREE 347
FtsH_fam TIGR01241
ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct ...
3-164 2.84e-30

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: 125.86  E-value: 2.84e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGlapVRSSRQDQI---HSSIVSTL---LALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSL 76
Cdd:TIGR01241 148 PCIIFIDEIDA---VGRQRGAGLgggNDEREQTLnqlLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDL 224
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  77 PDKNARKEILKIHTRDWNPKPvDMFLEELAEHCVGYCGADIKSICAEAALCALRRRYPqiyttseklqldlssiTISAKD 156
Cdd:TIGR01241 225 PDIKGREEILKVHAKNKKLAP-DVDLKAVARRTPGFSGADLANLLNEAALLAARKNKT----------------EITMND 287

                  ....*...
gi 1907114144 157 FEAALQKI 164
Cdd:TIGR01241 288 IEEAIDRV 295
ftsH CHL00176
cell division protein; Validated
3-136 3.22e-28

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 120.93  E-value: 3.22e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSR----QDQiHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPD 78
Cdd:CHL00176  276 PCIVFIDEIDAVGRQRGAGigggNDE-REQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPD 354
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  79 KNARKEILKIHTRDwnpKPV--DMFLEELAEHCVGYCGADIKSICAEAALCALRRRYPQI 136
Cdd:CHL00176  355 REGRLDILKVHARN---KKLspDVSLELIARRTPGFSGADLANLLNEAAILTARRKKATI 411
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
3-71 6.18e-28

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: 110.60  E-value: 6.18e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDRE 71
Cdd:cd19519    94 PAIIFIDEIDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDRE 162
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
3-164 1.25e-27

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


Pssm-ID: 223541 [Multi-domain]  Cd Length: 596  Bit Score: 118.96  E-value: 1.25e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEID------GLAPvrSSRQDQIHSSIvSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSL 76
Cdd:COG0465   243 PCIIFIDEIDavgrqrGAGL--GGGNDEREQTL-NQLLVEMDGFGGNEGVIVIAATNRPDVLDPALLRPGRFDRQILVEL 319
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  77 PDKNARKEILKIHTRD-WNPKPVDmfLEELAEHCVGYCGADIKSICAEAALCALRRRYPQiyttseklqldlssitISAK 155
Cdd:COG0465   320 PDIKGREQILKVHAKNkPLAEDVD--LKKIARGTPGFSGADLANLLNEAALLAARRNKKE----------------ITMR 381

                  ....*....
gi 1907114144 156 DFEAALQKI 164
Cdd:COG0465   382 DIEEAIDRV 390
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
3-136 1.92e-27

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 116.41  E-value: 1.92e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALM---DGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDK 79
Cdd:PTZ00361  277 PSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLnqlDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDE 356
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907114144  80 NARKEILKIHTRDWNPKPvDMFLEELAEHCVGYCGADIKSICAEAALCALRRRYPQI 136
Cdd:PTZ00361  357 KTKRRIFEIHTSKMTLAE-DVDLEEFIMAKDELSGADIKAICTEAGLLALRERRMKV 412
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
3-70 8.26e-24

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: 98.51  E-value: 8.26e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 70
Cdd:cd19511    87 PCIIFFDEIDSLAPRRGQSDSsGVTDRVVSQLLTELDGIESLKGVVVIAATNRPDMIDPALLRPGRLDK 155
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
3-164 3.21e-23

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


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 102.92  E-value: 3.21e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQ---DQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDK 79
Cdd:PTZ00454  239 PSIIFIDEVDSIATKRFDAQtgaDREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR 318
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  80 NARKEILKIHTRDWNPKPvDMFLEELAEHCVGYCGADIKSICAEAALCALRR-RYpqiyttseklqldlssiTISAKDFE 158
Cdd:PTZ00454  319 RQKRLIFQTITSKMNLSE-EVDLEDFVSRPEKISAADIAAICQEAGMQAVRKnRY-----------------VILPKDFE 380

                  ....*.
gi 1907114144 159 AALQKI 164
Cdd:PTZ00454  381 KGYKTV 386
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
3-170 8.79e-23

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 103.96  E-value: 8.79e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTL---LALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDK 79
Cdd:PRK10733  245 PCIIFIDEIDAVGRQRGAGLGGGHDEREQTLnqmLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDV 324
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  80 NARKEILKIHTRDWnPKPVDMFLEELAEHCVGYCGADIKSICAEAALCALR--RRypqiyttseklqldlssiTISAKDF 157
Cdd:PRK10733  325 RGREQILKVHMRRV-PLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARgnKR------------------VVSMVEF 385
                         170
                  ....*....|...
gi 1907114144 158 EAALQKIRPASQR 170
Cdd:PRK10733  386 EKAKDKIMMGAER 398
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
1-76 1.35e-22

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: 394963 [Multi-domain]  Cd Length: 130  Bit Score: 93.81  E-value: 1.35e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907114144   1 MRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFSL 76
Cdd:pfam00004  56 LAPCVIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
1-173 1.98e-22

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


Pssm-ID: 224144 [Multi-domain]  Cd Length: 368  Bit Score: 99.89  E-value: 1.98e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   1 MRPAIIFFDEIDGLAPVR---SSRQDQihSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRrpGRFDREFLFSLP 77
Cdd:COG1223   209 AAPCIVFIDELDAIALDRryqELRGDV--SEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIR--SRFEEEIEFKLP 284
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  78 DKNARKEILKIHTRDWnPKPVDMFLEELAEHCVGYCGADIKSICAEAALcalrrrYPQIYTTSEKlqldlssitISAKDF 157
Cdd:COG1223   285 NDEERLEILEYYAKKF-PLPVDADLRYLAAKTKGMSGRDIKEKVLKTAL------HRAIAEDREK---------VEREDI 348
                         170
                  ....*....|....*.
gi 1907114144 158 EAALQKIRPASQRAVT 173
Cdd:COG1223   349 EKALKKERKRRAPRPK 364
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
1-74 2.90e-22

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: 93.89  E-value: 2.90e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907114144   1 MRPAIIFFDEIDGLAPVRSSRQDQIHSS-IVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 74
Cdd:cd19481    84 LAPCILFIDEIDAIGRKRDSSGESGELRrVLNQLLTELDGVNSRSKVLVIAATNRPDLLDPALLRPGRFDEVIEF 158
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
3-70 1.51e-21

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: 92.17  E-value: 1.51e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 70
Cdd:cd19529    87 PCVIFFDEIDSIAPRRGTTGDSgVTERVVNQLLTELDGLEEMNGVVVIAATNRPDIIDPALLRAGRFDR 155
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
3-71 1.92e-21

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: 92.08  E-value: 1.92e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL----DSRGEIVVIGATNRLDSIDPALRRPGRFDRE 71
Cdd:cd19518    94 PCIVFIDEIDAITPKRESAQREMERRIVSQLLTCMDELnnekTAGGPVLVIGATNRPDSLDPALRRAGRFDRE 166
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
3-70 2.01e-20

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: 88.70  E-value: 2.01e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 70
Cdd:cd19530    90 PCVIFFDEVDALVPKRGDGGSWASERVVNQLLTEMDGLEERSNVFVIAATNRPDIIDPAMLRPGRLDK 157
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
459-561 6.22e-20

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


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 85.50  E-value: 6.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 459 RELRIFLRNVthRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPD 538
Cdd:cd04369     3 KKLRSLLDAL--KKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGP 80
                          90       100
                  ....*....|....*....|...
gi 1907114144 539 RDPgdrlIRHRACALRDTAYAII 561
Cdd:cd04369    81 GSP----IYKDAKKLEKLFEKLL 99
pup_AAA TIGR03689
proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some ...
2-141 7.37e-20

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: 94.01  E-value: 7.37e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   2 RPAIIFFDEIDGLAPVRSS-RQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKN 80
Cdd:TIGR03689 289 RPVIVFFDEMDSLFRTRGSgVSSDVETTVVPQLLAEIDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAE 368
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907114144  81 ARKEILKIHTRDWNPKPvdmflEELAEHcvgycgadikSICAEAALCALRRR-YPQIYTTSE 141
Cdd:TIGR03689 369 AAADIFAKYLTDDLPLP-----EDLAAH----------DGDREATAAALIQRvVDALYARSE 415
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
3-70 3.13e-19

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: 85.85  E-value: 3.13e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLAL---MDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 70
Cdd:cd19502    97 PSIIFIDEIDAIGAKRFDSGTGGDREVQRTMLELlnqLDGFDPRGNIKVIMATNRPDILDPALLRPGRFDR 167
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
481-576 1.15e-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  Cd Length: 101  Bit Score: 81.83  E-value: 1.15e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 481 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDrdpgdrlirhracalrDTAYAI 560
Cdd:cd05509    22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGP----------------DTEYYK 85
                          90
                  ....*....|....*.
gi 1907114144 561 IKEELDEDFEQLCEEI 576
Cdd:cd05509    86 CANKLEKFFWKKLKEL 101
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
2-70 1.65e-18

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: 83.33  E-value: 1.65e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907114144   2 RPAIIFFDEIDGLAPVRSSRQDQ--IHSSIVSTLLALMDGLDSRGE-IVVIGATNRLDSIDPALRRPGRFDR 70
Cdd:cd19527    85 KPCVIFFDELDSLAPSRGNSGDSggVMDRVVSQLLAELDGMSSSGQdVFVIGATNRPDLLDPALLRPGRFDK 156
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
3-71 1.96e-18

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: 83.44  E-value: 1.96e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTL---LALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDRE 71
Cdd:cd19501    97 PCIVFIDEIDAVGRKRGAGLGGGHDEREQTLnqlLVEMDGFESNTGVIVIAATNRPDVLDPALLRPGRFDRQ 168
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
461-561 1.42e-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: 78.60  E-value: 1.42e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 461 LRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNpDRD 540
Cdd:cd05512     2 LEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN-AKD 80
                          90       100
                  ....*....|....*....|..
gi 1907114144 541 PgdrlIRHRACA-LRDTAYAII 561
Cdd:cd05512    81 T----IFYRAAVrLRDQGGAIL 98
BROMO smart00297
bromo domain;
454-564 2.28e-17

bromo domain;


Pssm-ID: 197636  Cd Length: 107  Bit Score: 78.09  E-value: 2.28e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144  454 EEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNAL 533
Cdd:smart00297   1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80
                           90       100       110
                   ....*....|....*....|....*....|.
gi 1907114144  534 EYNPDrdpgDRLIRHRACALRDTAYAIIKEE 564
Cdd:smart00297  81 TYNGP----DSEVYKDAKKLEKFFEKKLREL 107
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
5-69 8.42e-17

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: 79.07  E-value: 8.42e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907114144   5 IIFFDEIDGLAPVRSSRQDQ--IHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFD 69
Cdd:cd19504   106 IIIFDEIDAICKQRGSMAGStgVHDTVVNQLLSKIDGVEQLNNILVIGMTNRKDLIDEALLRPGRLE 172
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
3-70 6.96e-16

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: 76.01  E-value: 6.96e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSS---IVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 70
Cdd:cd19528    87 PCVLFFDELDSIAKARGGNIGDAGGAadrVINQILTEMDGMNTKKNVFIIGATNRPDIIDPAILRPGRLDQ 157
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
481-536 1.33e-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  Cd Length: 112  Bit Score: 73.45  E-value: 1.33e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907114144 481 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 536
Cdd:cd05511    21 FHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYN 76
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
481-537 2.90e-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: 395352  Cd Length: 84  Bit Score: 71.58  E-value: 2.90e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907114144 481 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNP 537
Cdd:pfam00439  17 FLEPVDPDEYPDYYSVIKRPMDLSTIKKKLENGEYKSLAEFEADVKLMFSNARTYNG 73
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
2-70 5.13e-15

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: 73.23  E-value: 5.13e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907114144   2 RPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 70
Cdd:cd19526    86 KPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDK 154
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
480-541 4.06e-14

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


Pssm-ID: 99930  Cd Length: 102  Bit Score: 68.84  E-value: 4.06e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907114144 480 VFTKPVDP--DEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRDP 541
Cdd:cd05498    23 PFYKPVDPeaLGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHP 86
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
471-537 5.30e-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: 5.30e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907114144 471 RLAIDKRFRVFTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNP 537
Cdd:cd05506    11 KLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNP 79
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
481-562 6.37e-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  Cd Length: 112  Bit Score: 65.93  E-value: 6.37e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 481 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNpdRDPGDRLIRHrACALRDTAYAI 560
Cdd:cd05510    29 FLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYN--SDPSHPLRRH-ANFMKKKAEHL 105

                  ..
gi 1907114144 561 IK 562
Cdd:cd05510   106 LK 107
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
479-536 2.35e-12

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


Pssm-ID: 99932  Cd Length: 103  Bit Score: 63.87  E-value: 2.35e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 479 RVFTKPVDPDE--VPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 536
Cdd:cd05500    23 RPFLVPVDPVKlnIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFN 82
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
480-541 1.18e-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: 61.92  E-value: 1.18e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907114144 480 VFTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRDP 541
Cdd:cd05499    23 PFLDPVDPValNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTD 86
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
1-73 1.72e-11

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: 63.14  E-value: 1.72e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907114144   1 MRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL--DSRGEIVVIGATNRLDSIDPALRRpgRFDREFL 73
Cdd:cd19509    90 LQPSIIFIDEIDSLLSERGSGEHEASRRVKTEFLVQMDGVlnKPEDRVLVLGATNRPWELDEAFLR--RFEKRIY 162
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
481-540 2.51e-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: 61.26  E-value: 2.51e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 481 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRD 540
Cdd:cd05504    33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHT 92
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
481-536 9.84e-11

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


Pssm-ID: 99945  Cd Length: 98  Bit Score: 58.96  E-value: 9.84e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907114144 481 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 536
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 ...
481-539 1.89e-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: 1.89e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907114144 481 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDR 539
Cdd:cd05496    26 FRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNK 84
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
102-136 6.13e-10

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


Pssm-ID: 407720 [Multi-domain]  Cd Length: 45  Bit Score: 55.25  E-value: 6.13e-10
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1907114144 102 LEELAEHCVGYCGADIKSICAEAALCALRRRYPQI 136
Cdd:pfam17862   4 LEELAERTEGFSGADLEALCREAALAALRRGREAV 38
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
481-541 6.76e-10

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


Pssm-ID: 99935  Cd Length: 97  Bit Score: 56.61  E-value: 6.76e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907114144 481 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRDP 541
Cdd:cd05503    21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSE 81
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
481-536 9.37e-10

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: 9.37e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907114144 481 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 536
Cdd:cd05505    21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYY 76
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
460-537 3.18e-09

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


Pssm-ID: 99927  Cd Length: 108  Bit Score: 55.14  E-value: 3.18e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 460 ELRIFLRNVTHRLAIDKRFRV-FTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 536
Cdd:cd05495     3 ELRQALMPTLEKLYKQDPESLpFRQPVDPKllGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYN 82

                  .
gi 1907114144 537 P 537
Cdd:cd05495    83 R 83
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
470-538 3.44e-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: 3.44e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 470 HRLAIdkrfrVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN-PD 538
Cdd:cd05515    21 RRLSL-----IFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNePD 85
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
481-546 5.38e-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: 54.35  E-value: 5.38e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907114144 481 FTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPdrdPGDRLI 546
Cdd:cd05497    26 FQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNK---PGDDVV 90
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
1-68 1.23e-08

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: 55.12  E-value: 1.23e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907114144   1 MRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRG--EIVVIGATNRLDSIDPALRR--PGRF 68
Cdd:cd19520    93 LQPSIIFIDEIDSFLRQRSSTDHEATAMMKAEFMSLWDGLSTDGncRVIVMGATNRPQDLDEAILRrmPKRF 164
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
3-76 1.27e-08

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: 54.46  E-value: 1.27e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907114144   3 PAIIFFDEIDGLAPvrssrqdQIHSSIVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSL 76
Cdd:cd00009    85 PGVLFIDEIDSLSR-------GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151
ycf46 CHL00195
Ycf46; Provisional
3-124 1.44e-08

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 58.11  E-value: 1.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIV-STLLALMDglDSRGEIVVIGATNRLDSIDPALRRPGRFDREFLFSLPDKNA 81
Cdd:CHL00195  319 PCILWIDEIDKAFSNSESKGDSGTTNRVlATFITWLS--EKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEE 396
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1907114144  82 RKEILKIHTRDWNPKPVDMF-LEELAEHCVGYCGADIKSICAEA 124
Cdd:CHL00195  397 REKIFKIHLQKFRPKSWKKYdIKKLSKLSNKFSGAEIEQSIIEA 440
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
474-584 1.80e-08

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 57.51  E-value: 1.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 474 IDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNpdrDPGDRLIRHRacal 553
Cdd:COG5076   162 GRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVYVDA---- 234
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1907114144 554 rdtayAIIKEELDEDFEQLCEEIQESRKKRG 584
Cdd:COG5076   235 -----KELEKYFLKLIEEIPEEMLELSIKPG 260
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
489-536 2.07e-08

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


Pssm-ID: 99947  Cd Length: 107  Bit Score: 52.82  E-value: 2.07e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1907114144 489 EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 536
Cdd:cd05516    36 ELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFN 83
Bromodomain_1 cd05494
Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated ...
452-582 2.81e-08

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


Pssm-ID: 99926  Cd Length: 114  Bit Score: 52.45  E-value: 2.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 452 EQEEDTFRELRIFLRNvthrlaidKRFRVFTKPVDPDE--VPDYVTVIKQPMDLSsviSKIDLHkyltVKDYLKDIDLIC 529
Cdd:cd05494     3 EALERVLRELKRHRRN--------EDAWPFLEPVNPPRrgAPDYRDVIKRPMSFG---TKVNNI----VETGARDLEDLQ 67
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907114144 530 SNAleynpdRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESRKK 582
Cdd:cd05494    68 IVQ------EDPADKQIDDEGRRSPSNIYAVEALEQLIVFQCKQVKGLKQKRH 114
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
3-64 1.52e-07

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: 52.30  E-value: 1.52e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGE--IVVIGATNRLDSIDPALRR 64
Cdd:cd19525   115 PAVIFIDEIDSLLSQRGEGEHESSRRIKTEFLVQLDGATTSSEdrILVVGATNRPQEIDEAARR 178
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
2-70 3.61e-07

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: 51.02  E-value: 3.61e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907114144   2 RPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL--DSRGeIVVIGATNRLDSIDPALRRpgRFDR 70
Cdd:cd19521    99 KPSIIFIDEVDSLCGTRGEGESEASRRIKTELLVQMNGVgnDSQG-VLVLGATNIPWQLDSAIRR--RFEK 166
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
480-540 4.52e-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: 48.90  E-value: 4.52e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907114144 480 VFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN-PDRD 540
Cdd:cd05507    23 VFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNsSDHD 84
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
477-536 4.69e-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  Cd Length: 104  Bit Score: 48.78  E-value: 4.69e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 477 RFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 536
Cdd:cd05522    24 LTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYN 83
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
1-64 5.27e-07

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: 50.23  E-value: 5.27e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907114144   1 MRPAIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDSRGE--IVVIGATNRLDSIDPA-LRR 64
Cdd:cd19524    91 LQPSIIFIDEVDSLLSERSEGEHEASRRLKTEFLIEFDGVQSNGDdrVLVMGATNRPQELDDAvLRR 157
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
479-536 9.87e-07

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


Pssm-ID: 99948  Cd Length: 103  Bit Score: 47.82  E-value: 9.87e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907114144 479 RVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 536
Cdd:cd05517    25 ELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN 82
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
442-538 1.08e-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  Cd Length: 109  Bit Score: 48.06  E-value: 1.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 442 LTAEEVKRLEeqeedtfrelRIFLRNVTHRLAIDkrfrvFTKPVDPdEVPDYVTVIKQPMDLSSVISKIDL---HKYLTV 518
Cdd:cd05502     1 LSPIDQRKCE----------RLLLELYCHELSLP-----FHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPkspQHYSSP 64
                          90       100
                  ....*....|....*....|
gi 1907114144 519 KDYLKDIDLICSNALEYNPD 538
Cdd:cd05502    65 EEFVADVRLMFKNCYKFNEE 84
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
489-536 4.57e-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  Cd Length: 103  Bit Score: 45.90  E-value: 4.57e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1907114144 489 EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 536
Cdd:cd05518    35 DYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82
RecA-like_fidgetin cd19523
ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. ...
3-73 5.30e-06

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: 47.19  E-value: 5.30e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIhSSIVSTLLALMDGLDSRGE--IVVIGATNRLDSIDPALRRpgRFDREFL 73
Cdd:cd19523    93 PSVLFISDLDALLSSQDDEASPV-GRLQVELLAQLDGVLGSGEdgVLVVCTTSKPEEIDESLRR--YFSKRLL 162
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
491-537 5.98e-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: 5.98e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1907114144 491 PDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNP 537
Cdd:cd05520    37 PDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNV 83
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
3-64 5.56e-05

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: 44.59  E-value: 5.56e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   3 PAIIFFDEIDGLAPVRSSRQDQIHSSIV-STLLALMDGL-------DSRGEIVVIGATNRLDSIDPALRR 64
Cdd:cd19522    93 PTTIFIDEIDSICSRRGTSEEHEASRRVkSELLVQMDGVggasendDPSKMVMVLAATNFPWDIDEALRR 162
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
481-536 7.25e-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: 42.37  E-value: 7.25e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907114144 481 FTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 536
Cdd:cd05508    23 FLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYN 78
ycf46 CHL00195
Ycf46; Provisional
265-406 8.08e-05

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 46.17  E-value: 8.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 265 PR-LLIVGEPGFGQSshLAPAVIHALEKFTVYTLDIPVLFGISTTSPEEACSQMIREAKRTAPSIvyvphihLWW-EI-- 340
Cdd:CHL00195  259 PRgLLLVGIQGTGKS--LTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCI-------LWIdEIdk 329
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907114144 341 ----------VGPTLK--ATFTTLLQTIPSfaPVLLLATSEKPYSaLPEEVqeLFTHDYGEIFNVQLPDKEERTKFFE 406
Cdd:CHL00195  330 afsnseskgdSGTTNRvlATFITWLSEKKS--PVFVVATANNIDL-LPLEI--LRKGRFDEIFFLDLPSLEEREKIFK 402
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
4-70 8.41e-05

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: 43.49  E-value: 8.41e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907114144   4 AIIFFDEID-----GLAPVRSSRQDQIHSSI-VSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPGRFDR 70
Cdd:cd19510    77 SIILLEDIDaafesREHNKKNPSAYGGLSRVtFSGLLNALDGVASSEERIVFMTTNHIERLDPALIRPGRVDM 149
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
1-78 9.03e-05

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: 43.52  E-value: 9.03e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907114144    1 MRPAIIFFDEIDGLAPVRSSRQDQihssiVSTLLALMDGLDSRGEIVVIGATNRLDSIDPALRRPgRFDREFLFSLPD 78
Cdd:smart00382  77 LKPDVLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
491-535 1.04e-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  Cd Length: 113  Bit Score: 42.32  E-value: 1.04e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1907114144 491 PDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEY 535
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 ...
451-537 2.15e-04

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


Pssm-ID: 99958  Cd Length: 128  Bit Score: 41.94  E-value: 2.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144 451 EEQEEDTFRELRIFLRNVthRLAIDKRFRVftkPVD-PDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLIC 529
Cdd:cd05529    23 DEERERLISGLDKLLLSL--QLEIAEYFEY---PVDlRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLIL 97

                  ....*...
gi 1907114144 530 SNALEYNP 537
Cdd:cd05529    98 SNAETFNE 105
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
1-72 1.00e-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: 40.43  E-value: 1.00e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907114144   1 MRPAIIFFDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDglDSRGEIVVIGATNRLDSIDPALRRPGRFDREF 72
Cdd:cd19507    89 IAPCVLWIDEIEKGFSNADSKGDSgTSSRVLGTFLTWLQ--EKKKPVFVVATANNVQSLPPELLRKGRFDEIF 159
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
476-536 2.05e-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: 2.05e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907114144 476 KRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYN 536
Cdd:cd05519    22 KLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYN 82
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
490-562 3.17e-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  Cd Length: 106  Bit Score: 37.75  E-value: 3.17e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907114144 490 VPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLKDIDLICSNALEYNPDRDPGDRlirhRACALRDtAYAIIK 562
Cdd:cd05525    38 NPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGR----DVCRLRK-AYYQAK 105
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
2-68 3.91e-03

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


Pssm-ID: 400191 [Multi-domain]  Cd Length: 135  Bit Score: 38.43  E-value: 3.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907114144   2 RPAIIFFDEIdglapvrssrqDQIHSSIVSTLLALMD----GLDSRGEIV--------VIGATNRLD----SIDPALRRp 65
Cdd:pfam07728  66 EGEIAVLDEI-----------NRANPDVLNSLLSLLDerrlLLPDGGELVkaapdgfrLIATMNPLDrglnELSPALRS- 133

                  ...
gi 1907114144  66 gRF 68
Cdd:pfam07728 134 -RF 135
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.19
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
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