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Conserved domains on  [gi|66812984|ref|XP_640671|]
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bromodomain-containing protein [Dictyostelium discoideum AX4]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
740-909 8.31e-111

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: 348.73  E-value: 8.31e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  740 SIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVGGQKVSFFMRKGADCLSKWV 819
Cdd:cd19517    1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  820 GEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRR 899
Cdd:cd19517   81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160
                        170
                 ....*....|
gi 66812984  900 PGRFDRELLF 909
Cdd:cd19517  161 PGRFDREFYF 170
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
1290-1404 2.87e-47

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: 164.84  E-value: 2.87e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1290 VRQLRILLREMVSKIIFDKKYLSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYYH 1369
Cdd:cd05528    1 LRELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80
                         90       100       110
                 ....*....|....*....|....*....|....*
gi 66812984 1370 FNDSnslEAIKANSRSKQLQDEVLSMVENIDPTLI 1404
Cdd:cd05528   81 DRDP---ADKLIRSRACELRDEVHAMIEAELDPLF 112
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
1095-1172 1.57e-04

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 cd19518:

Pssm-ID: 422963 [Multi-domain]  Cd Length: 169  Bit Score: 44.32  E-value: 1.57e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66812984 1095 QNFSVYRPR-LLIHGEQGMGQIQLANSLLYHLEeFPIFSIDISALISDPTSKTvEESCIRILSEAKKASPSIIYIPNID 1172
Cdd:cd19518   27 QHLGVEPPRgVLLHGPPGCGKTMLANAIAGELK-VPFLKISATEIVSGVSGES-EEKIRELFDQAISNAPCIVFIDEID 103
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
937-973 6.34e-04

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: 39.07  E-value: 6.34e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 66812984    937 LLEISDQLAGYCGADIKSLCSESVLCSLRTTYPQIYK 973
Cdd:pfam17862    4 LEELAERTEGFSGADLEALCREAALAALRRGREAVTQ 40
Activator_LAG-3 super family cl29315
Transcriptional activator LAG-3; The C.elegans Notch pathway, involved in the control of ...
195-288 6.45e-03

Transcriptional activator LAG-3; The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1.


The actual alignment was detected with superfamily member pfam11498:

Pssm-ID: 151935  Cd Length: 476  Bit Score: 41.10  E-value: 6.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    195 QQLKKQQ------PQENIGLGKFQHQIQQE-LQNKQHQKHIRYQQQQMKLEEEQKKFQPQRpQRQRVPPKSFSFEATLNG 267
Cdd:pfam11498  323 AQLAQQQnkmrllQQQEMEMQRIEQQRQQQiMHQHQQQQQQEHQQQQMLLQQQQQMHQLQQ-HHQMNGGGQFATQAHQHA 401
                           90       100
                   ....*....|....*....|..
gi 66812984    268 -YDDDIDEIHSNNRQRKKQNTN 288
Cdd:pfam11498  402 aYLQQMQHMRLQEQIQHQQQQA 423
 
Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
740-909 8.31e-111

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: 348.73  E-value: 8.31e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  740 SIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVGGQKVSFFMRKGADCLSKWV 819
Cdd:cd19517    1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  820 GEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRR 899
Cdd:cd19517   81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160
                        170
                 ....*....|
gi 66812984  900 PGRFDRELLF 909
Cdd:cd19517  161 PGRFDREFYF 170
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
735-1008 8.14e-77

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 271.40  E-value: 8.14e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    735 KIGFSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADC 814
Cdd:TIGR01243  174 KVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGA-----YFISINGPEI 248
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    815 LSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQVIVIGATNRIDSID 894
Cdd:TIGR01243  249 MSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALD 328
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    895 PALRRPGRFDRELLFTLPSKEARHRILTIHTENwLPKPSSQLLLEISDQLAGYCGADIKSLCSESVLCSLRTTYPQ--IY 972
Cdd:TIGR01243  329 PALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREgkIN 407
                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 66812984    973 KTSNKLQLSV-DNILVEKSHFQDAMKLITPSSKRNLI 1008
Cdd:TIGR01243  408 FEAEEIPAEVlKELKVTMKDFMEALKMVEPSAIREVL 444
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
727-1002 9.07e-72

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: 249.74  E-value: 9.07e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  727 SEPLSIDNKIGFSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSF 806
Cdd:COG0464  230 RGVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRS-----RF 304
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  807 FMRKGADCLSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQVIVIGA 886
Cdd:COG0464  305 ISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAA 384
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  887 TNRIDSIDPALRRPGRFDRELLFTLPSKEARHRILTIHTENWLPKPSSQLLL-EISDQLAGYCGADIKSLCSESVLCSLR 965
Cdd:COG0464  385 TNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLeELAEITEGYSGADIAALVREAALEALR 464
                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 66812984  966 TTYPqiyktsnklqlsvdnILVEKSHFQDAMKLITPS 1002
Cdd:COG0464  465 EARR---------------REVTLDDFLDALKKIKPS 486
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
735-958 4.54e-63

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 220.86  E-value: 4.54e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   735 KIGFSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNvggqkVSFFMRKGADC 814
Cdd:PRK03992  127 NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN-----ATFIRVVGSEL 201
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   815 LSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRS------SRQDQihnsivST---LLALMDGLDNRGQVIVIG 885
Cdd:PRK03992  202 VQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTdsgtsgDREVQ------RTlmqLLAEMDGFDPRGNVKIIA 275
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 66812984   886 ATNRIDSIDPALRRPGRFDRELLFTLPSKEARHRILTIHTENWLPKPSSQlLLEISDQLAGYCGADIKSLCSE 958
Cdd:PRK03992  276 ATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVD-LEELAELTEGASGADLKAICTE 347
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
776-911 9.85e-50

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: 172.39  E-value: 9.85e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    776 VLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADCLSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSS 855
Cdd:pfam00004    1 LLLYGPPGTGKTTLAKAVAKELGA-----PFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGS 75
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 66812984    856 RQDQIHNSIVSTLLALMDGLDNR-GQVIVIGATNRIDSIDPALRrpGRFDRELLFTL 911
Cdd:pfam00004   76 GGDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
1290-1404 2.87e-47

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: 164.84  E-value: 2.87e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1290 VRQLRILLREMVSKIIFDKKYLSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYYH 1369
Cdd:cd05528    1 LRELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80
                         90       100       110
                 ....*....|....*....|....*....|....*
gi 66812984 1370 FNDSnslEAIKANSRSKQLQDEVLSMVENIDPTLI 1404
Cdd:cd05528   81 DRDP---ADKLIRSRACELRDEVHAMIEAELDPLF 112
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
772-912 3.12e-20

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 88.97  E-value: 3.12e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984     772 PPKGVLFYGPPGTGKTLLARALVNECNVGGQKVSFF------------MRKGADCLSKWVGEAERQLRLLFEQAKAMQPS 839
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIdgedileevldqLLLIIVGGKKASGSGELRLRLALALARKLKPD 80
                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 66812984     840 IIFFDEIDGLAPVRSSRQDQihnsiVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRRPgRFDRELLFTLP 912
Cdd:smart00382   81 VLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLI 147
BROMO smart00297
bromo domain;
1286-1380 1.74e-14

bromo domain;


Pssm-ID: 197636  Cd Length: 107  Bit Score: 71.16  E-value: 1.74e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    1286 DRQLVRQLRILLREMVSKIIFDKKYLSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTE 1365
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80
                            90
                    ....*....|....*
gi 66812984    1366 LYYHFNDSNSLEAIK 1380
Cdd:smart00297   81 TYNGPDSEVYKDAKK 95
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
1297-1378 5.75e-14

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


Pssm-ID: 395352  Cd Length: 84  Bit Score: 68.88  E-value: 5.75e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   1297 LREMVSKIIFDKKYLSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYyhfNDSNSL 1376
Cdd:pfam00439    1 CLEILDKLMEHPLAAPFLEPVDPDEYPDYYSVIKRPMDLSTIKKKLENGEYKSLAEFEADVKLMFSNARTY---NGPGSV 77

                   ..
gi 66812984   1377 EA 1378
Cdd:pfam00439   78 IY 79
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
1225-1398 4.40e-07

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 54.04  E-value: 4.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1225 SSKFEISKLTKRSIKDFYENIVNDI-----KEVGITIKKALTVKIQESQQLPiVPFQSDSVRELKKDRQLVRQLRILLRE 1299
Cdd:COG5076   63 SIVDDREPGSMANVNDDLENVGGITyspfeKNRPESLRFDEIVFLAIESVTP-ESGLGSLLMAHLKTSVKKRKTPKIEDE 141
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1300 MVSKIIF------------DKKYLS--FFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTE 1365
Cdd:COG5076  142 LLYADNKaiakfkkqlflrDGRFLSsiFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCK 221
                        170       180       190
                 ....*....|....*....|....*....|....*
gi 66812984 1366 LyYHFNDSNSLEAIKA--NSRSKQLQDEVLSMVEN 1398
Cdd:COG5076  222 L-YNGPDSSVYVDAKEleKYFLKLIEEIPEEMLEL 255
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
1095-1172 1.57e-04

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: 44.32  E-value: 1.57e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66812984 1095 QNFSVYRPR-LLIHGEQGMGQIQLANSLLYHLEeFPIFSIDISALISDPTSKTvEESCIRILSEAKKASPSIIYIPNID 1172
Cdd:cd19518   27 QHLGVEPPRgVLLHGPPGCGKTMLANAIAGELK-VPFLKISATEIVSGVSGES-EEKIRELFDQAISNAPCIVFIDEID 103
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
937-973 6.34e-04

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: 39.07  E-value: 6.34e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 66812984    937 LLEISDQLAGYCGADIKSLCSESVLCSLRTTYPQIYK 973
Cdd:pfam17862    4 LEELAERTEGFSGADLEALCREAALAALRRGREAVTQ 40
Activator_LAG-3 pfam11498
Transcriptional activator LAG-3; The C.elegans Notch pathway, involved in the control of ...
195-288 6.45e-03

Transcriptional activator LAG-3; The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1.


Pssm-ID: 151935  Cd Length: 476  Bit Score: 41.10  E-value: 6.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    195 QQLKKQQ------PQENIGLGKFQHQIQQE-LQNKQHQKHIRYQQQQMKLEEEQKKFQPQRpQRQRVPPKSFSFEATLNG 267
Cdd:pfam11498  323 AQLAQQQnkmrllQQQEMEMQRIEQQRQQQiMHQHQQQQQQEHQQQQMLLQQQQQMHQLQQ-HHQMNGGGQFATQAHQHA 401
                           90       100
                   ....*....|....*....|..
gi 66812984    268 -YDDDIDEIHSNNRQRKKQNTN 288
Cdd:pfam11498  402 aYLQQMQHMRLQEQIQHQQQQA 423
 
Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
740-909 8.31e-111

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: 348.73  E-value: 8.31e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  740 SIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVGGQKVSFFMRKGADCLSKWV 819
Cdd:cd19517    1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  820 GEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRR 899
Cdd:cd19517   81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160
                        170
                 ....*....|
gi 66812984  900 PGRFDRELLF 909
Cdd:cd19517  161 PGRFDREFYF 170
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
740-909 2.82e-84

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: 273.01  E-value: 2.82e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  740 SIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADCLSKWV 819
Cdd:cd19503    1 DIGGLDEQIASLKELIELPLKYPELFRALGLKPPRGVLLHGPPGTGKTLLARAVANEAGA-----NFLSISGPSIVSKYL 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  820 GEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRR 899
Cdd:cd19503   76 GESEKNLREIFEEARSHAPSIIFIDEIDALAPKREEDQREVERRVVAQLLTLMDGMSSRGKVVVIAATNRPDAIDPALRR 155
                        170
                 ....*....|
gi 66812984  900 PGRFDRELLF 909
Cdd:cd19503  156 PGRFDREVEI 165
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
735-1008 8.14e-77

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 271.40  E-value: 8.14e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    735 KIGFSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADC 814
Cdd:TIGR01243  174 KVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGA-----YFISINGPEI 248
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    815 LSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQVIVIGATNRIDSID 894
Cdd:TIGR01243  249 MSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALD 328
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    895 PALRRPGRFDRELLFTLPSKEARHRILTIHTENwLPKPSSQLLLEISDQLAGYCGADIKSLCSESVLCSLRTTYPQ--IY 972
Cdd:TIGR01243  329 PALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREgkIN 407
                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 66812984    973 KTSNKLQLSV-DNILVEKSHFQDAMKLITPSSKRNLI 1008
Cdd:TIGR01243  408 FEAEEIPAEVlKELKVTMKDFMEALKMVEPSAIREVL 444
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
727-1002 9.07e-72

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: 249.74  E-value: 9.07e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  727 SEPLSIDNKIGFSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSF 806
Cdd:COG0464  230 RGVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRS-----RF 304
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  807 FMRKGADCLSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQVIVIGA 886
Cdd:COG0464  305 ISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAA 384
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  887 TNRIDSIDPALRRPGRFDRELLFTLPSKEARHRILTIHTENWLPKPSSQLLL-EISDQLAGYCGADIKSLCSESVLCSLR 965
Cdd:COG0464  385 TNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLeELAEITEGYSGADIAALVREAALEALR 464
                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 66812984  966 TTYPqiyktsnklqlsvdnILVEKSHFQDAMKLITPS 1002
Cdd:COG0464  465 EARR---------------REVTLDDFLDALKKIKPS 486
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
725-1019 1.05e-70

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: 253.29  E-value: 1.05e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    725 KDSEPLSIDN------KIGFSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNEcn 798
Cdd:TIGR01243  433 KMVEPSAIREvlvevpNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATE-- 510
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    799 vggQKVSFFMRKGADCLSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQ-IHNSIVSTLLALMDGLDN 877
Cdd:TIGR01243  511 ---SGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTsVTDRIVNQLLTEMDGIQE 587
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    878 RGQVIVIGATNRIDSIDPALRRPGRFDRELLFTLPSKEARHRILTIHTENwLPKPSSQLLLEISDQLAGYCGADIKSLCS 957
Cdd:TIGR01243  588 LSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRS-MPLAEDVDLEELAEMTEGYTGADIEAVCR 666
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 66812984    958 ESVLCSLRTTYPQIYKtsNKLQLSVDNIL----VEKSHFQDAMKLITPSSKRNLISFSNPLSSILK 1019
Cdd:TIGR01243  667 EAAMAALRESIGSPAK--EKLEVGEEEFLkdlkVEMRHFLEALKKVKPSVSKEDMLRYERLAKELK 730
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
741-907 6.62e-66

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: 220.39  E-value: 6.62e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  741 IGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADCLSKWVG 820
Cdd:cd19519    2 IGGCRKQLAQIREMVELPLRHPELFKAIGIKPPRGILLYGPPGTGKTLIARAVANETGA-----FFFLINGPEIMSKLAG 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  821 EAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRRP 900
Cdd:cd19519   77 ESESNLRKAFEEAEKNAPAIIFIDEIDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRF 156

                 ....*..
gi 66812984  901 GRFDREL 907
Cdd:cd19519  157 GRFDREI 163
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
736-965 3.76e-65

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


Pssm-ID: 224143 [Multi-domain]  Cd Length: 406  Bit Score: 227.53  E-value: 3.76e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  736 IGFSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVGGQKVSffmrkGADCL 815
Cdd:COG1222  148 VTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVV-----GSELV 222
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  816 SKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLAL---MDGLDNRGQVIVIGATNRIDS 892
Cdd:COG1222  223 QKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELlnqLDGFDPRGNVKVIMATNRPDI 302
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  893 IDPALRRPGRFDRELLFTLPSKEARHRILTIHTE--------NWlpkpssQLLLEISDqlaGYCGADIKSLCSESVLCSL 964
Cdd:COG1222  303 LDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRkmnladdvDL------ELLARLTE---GFSGADLKAICTEAGMFAI 373

                 .
gi 66812984  965 R 965
Cdd:COG1222  374 R 374
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
735-958 4.54e-63

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 220.86  E-value: 4.54e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   735 KIGFSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNvggqkVSFFMRKGADC 814
Cdd:PRK03992  127 NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN-----ATFIRVVGSEL 201
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   815 LSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRS------SRQDQihnsivST---LLALMDGLDNRGQVIVIG 885
Cdd:PRK03992  202 VQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTdsgtsgDREVQ------RTlmqLLAEMDGFDPRGNVKIIA 275
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 66812984   886 ATNRIDSIDPALRRPGRFDRELLFTLPSKEARHRILTIHTENWLPKPSSQlLLEISDQLAGYCGADIKSLCSE 958
Cdd:PRK03992  276 ATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVD-LEELAELTEGASGADLKAICTE 347
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
751-905 3.22e-62

second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase domains; This subfamily includes the second of two ATPase domains of the molecular chaperone CDC48 in yeast and p97 or VCP in metazoans, Peroxisomal biogenesis factor 1 (PEX1) and -6 (PEX6), Valosin-containing protein-like ATPase (VAT), and nuclear VCP-like protein (NVL). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 209.45  E-value: 3.22e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  751 LKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECnvggqKVSFFMRKGADCLSKWVGEAERQLRLLF 830
Cdd:cd19511    5 LKEAVEWPLKHPDAFKRLGIRPPKGVLLYGPPGCGKTLLAKALASEA-----GLNFISVKGPELFSKYVGESERAVREIF 79
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 66812984  831 EQAKAMQPSIIFFDEIDGLAPVRSSRQD-QIHNSIVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRRPGRFDR 905
Cdd:cd19511   80 QKARQAAPCIIFFDEIDSLAPRRGQSDSsGVTDRVVSQLLTELDGIESLKGVVVIAATNRPDMIDPALLRPGRLDK 155
26Sp45 TIGR01242
26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an ...
735-965 6.83e-62

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: 216.59  E-value: 6.83e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    735 KIGFSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNvggqkVSFFMRKGADC 814
Cdd:TIGR01242  118 NVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN-----ATFIRVVGSEL 192
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    815 LSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVR---SSRQDQIHNSIVSTLLALMDGLDNRGQVIVIGATNRID 891
Cdd:TIGR01242  193 VRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRtdsGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPD 272
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 66812984    892 SIDPALRRPGRFDRELLFTLPSKEARHRILTIHTENWLPKPSSQlLLEISDQLAGYCGADIKSLCSESVLCSLR 965
Cdd:TIGR01242  273 ILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVD-LEAIAKMTEGASGADLKAICTEAGMFAIR 345
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
749-908 7.54e-57

second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ATPase domains; The Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), is an archaeal homolog of the ubiquitous Cdc48/p97. It is a protein unfoldase that functions in concert with the 20S proteasome by unfolding proteasome substrates and passing them on for degradation. VAT forms a homohexamer, each monomer contains two tandem ATPase domains, referred to as D1 and D2, and an N-terminal domain. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410937 [Multi-domain]  Cd Length: 159  Bit Score: 194.25  E-value: 7.54e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  749 QLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNvggqkVSFFMRKGADCLSKWVGEAERQLRL 828
Cdd:cd19529    3 QELKEAVEWPLLKPEVFKRLGIRPPKGILLYGPPGTGKTLLAKAVATESN-----ANFISVKGPELLSKWVGESEKAIRE 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  829 LFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQ-IHNSIVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRRPGRFDREL 907
Cdd:cd19529   78 IFRKARQVAPCVIFFDEIDSIAPRRGTTGDSgVTERVVNQLLTELDGLEEMNGVVVIAATNRPDIIDPALLRAGRFDRLI 157

                 .
gi 66812984  908 L 908
Cdd:cd19529  158 Y 158
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
738-909 2.10e-56

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: 193.32  E-value: 2.10e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  738 FSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNvggqkVSFFMRKGADCLSK 817
Cdd:cd19502    2 YEDIGGLDEQIREIREVVELPLKHPELFEELGIEPPKGVLLYGPPGTGKTLLAKAVANHTD-----ATFIRVVGSELVQK 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  818 WVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLAL---MDGLDNRGQVIVIGATNRIDSID 894
Cdd:cd19502   77 YIGEGARLVRELFEMAREKAPSIIFIDEIDAIGAKRFDSGTGGDREVQRTMLELlnqLDGFDPRGNIKVIMATNRPDILD 156
                        170
                 ....*....|....*
gi 66812984  895 PALRRPGRFDRELLF 909
Cdd:cd19502  157 PALLRPGRFDRKIEF 171
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
740-907 2.27e-52

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: 181.83  E-value: 2.27e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  740 SIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECnvggqKVSFFMRKGADCLSKWV 819
Cdd:cd19518    1 DIGGMDSTLKELCELLIHPILPPEYFQHLGVEPPRGVLLHGPPGCGKTMLANAIAGEL-----KVPFLKISATEIVSGVS 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  820 GEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGL----DNRGQVIVIGATNRIDSIDP 895
Cdd:cd19518   76 GESEEKIRELFDQAISNAPCIVFIDEIDAITPKRESAQREMERRIVSQLLTCMDELnnekTAGGPVLVIGATNRPDSLDP 155
                        170
                 ....*....|..
gi 66812984  896 ALRRPGRFDREL 907
Cdd:cd19518  156 ALRRAGRFDREI 167
pup_AAA TIGR03689
proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some ...
736-933 3.07e-52

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: 193.00  E-value: 3.07e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    736 IGFSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNE-----CNVGGQKVSFFMRK 810
Cdd:TIGR03689  179 VTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVANSlaariGAEGGGKSYFLNIK 258
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    811 GADCLSKWVGEAERQLRLLFEQAKAM----QPSIIFFDEIDGLAPVR-SSRQDQIHNSIVSTLLALMDGLDNRGQVIVIG 885
Cdd:TIGR03689  259 GPELLNKYVGETERQIRLIFQRAREKasegRPVIVFFDEMDSLFRTRgSGVSSDVETTVVPQLLAEIDGVESLDNVIVIG 338
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 66812984    886 ATNRIDSIDPALRRPGRFDRELLFTLPSKEARHRILTIHTENWLPKPS 933
Cdd:TIGR03689  339 ASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFAKYLTDDLPLPE 386
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
738-990 1.28e-51

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 189.21  E-value: 1.28e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   738 FSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNvggqkVSFFMRKGADCLSK 817
Cdd:PTZ00361  182 YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETS-----ATFLRVVGSELIQK 256
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   818 WVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLAL---MDGLDNRGQVIVIGATNRIDSID 894
Cdd:PTZ00361  257 YLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELlnqLDGFDSRGDVKVIMATNRIESLD 336
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   895 PALRRPGRFDRELLFTLPSKEARHRILTIHTENWLPKPSSQL--LLEISDQLagyCGADIKSLCSESVLCSLRTTYPQIy 972
Cdd:PTZ00361  337 PALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLeeFIMAKDEL---SGADIKAICTEAGLLALRERRMKV- 412
                         250
                  ....*....|....*...
gi 66812984   973 kTSNKLQLSVDNILVEKS 990
Cdd:PTZ00361  413 -TQADFRKAKEKVLYRKK 429
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
751-905 5.06e-51

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


Pssm-ID: 410936 [Multi-domain]  Cd Length: 161  Bit Score: 177.70  E-value: 5.06e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  751 LKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECnvggqKVSFFMRKGADCLSKWVGEAERQLRLLF 830
Cdd:cd19528    5 LQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC-----QANFISVKGPELLTMWFGESEANVRDIF 79
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 66812984  831 EQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNS---IVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRRPGRFDR 905
Cdd:cd19528   80 DKARAAAPCVLFFDELDSIAKARGGNIGDAGGAadrVINQILTEMDGMNTKKNVFIIGATNRPDIIDPAILRPGRLDQ 157
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
751-909 7.54e-51

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: 176.70  E-value: 7.54e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  751 LKEMLMLPLLYPEVFnKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADCLSKWVGEAERQLRLLF 830
Cdd:cd19481    5 LREAVEAPRRGSRLR-RYGLGLPKGILLYGPPGTGKTLLAKALAGELGL-----PLIVVKLSSLLSKYVGESEKNLRKIF 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  831 EQAKAMQPSIIFFDEIDGLAPVRSSRQDQIH-NSIVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRRPGRFDRELLF 909
Cdd:cd19481   79 ERARRLAPCILFIDEIDAIGRKRDSSGESGElRRVLNQLLTELDGVNSRSKVLVIAATNRPDLLDPALLRPGRFDEVIEF 158
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
756-1003 7.14e-50

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: 185.80  E-value: 7.14e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  756 MLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNEcnvggqKVSFFMRKGADCLSKWVGEAERQLRLLFEQAKA 835
Cdd:COG0464    1 ELPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE------GAEFLSINGPEILSKYVGESELRLRELFEEAEK 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  836 MQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLdNRGQVIVIGATNRIDSIDPALRRPGRFDRELLFTLPSKE 915
Cdd:COG0464   75 LAPSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGL-KRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEA 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  916 ARHRILTIHTENwLPKPSSQLLLEISDQLAGYCGADIKSLCSESVLCSLRTTYPQIyktSNKLQLSVDNilvekshFQDA 995
Cdd:COG0464  154 GRLEILQIHTRL-MFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRRAIDLV---GEYIGVTEDD-------FEEA 222

                 ....*...
gi 66812984  996 MKLITPSS 1003
Cdd:COG0464  223 LKKVLPSR 230
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
776-911 9.85e-50

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: 172.39  E-value: 9.85e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    776 VLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADCLSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSS 855
Cdd:pfam00004    1 LLLYGPPGTGKTTLAKAVAKELGA-----PFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGS 75
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 66812984    856 RQDQIHNSIVSTLLALMDGLDNR-GQVIVIGATNRIDSIDPALRrpGRFDRELLFTL 911
Cdd:pfam00004   76 GGDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
746-908 1.05e-49

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: 173.83  E-value: 1.05e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  746 KHIQLLKEMLML-PLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECnvggqKVSFFMRKGADCLSKWVGEAER 824
Cdd:cd19530    2 DHVREELTMSILrPIKRPDIYKALGIDLPTGVLLYGPPGCGKTLLAKAVANES-----GANFISVKGPELLNKYVGESER 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  825 QLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRRPGRFD 904
Cdd:cd19530   77 AVRQVFQRARASAPCVIFFDEVDALVPKRGDGGSWASERVVNQLLTEMDGLEERSNVFVIAATNRPDIIDPAMLRPGRLD 156

                 ....
gi 66812984  905 RELL 908
Cdd:cd19530  157 KTLY 160
FtsH_fam TIGR01241
ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct ...
733-1005 1.48e-48

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: 181.71  E-value: 1.48e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    733 DNKIGFSSIGGLDKHIQLLKEMLMLpLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGA 812
Cdd:TIGR01241   49 KPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGV-----PFFSISGS 122
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    813 DCLSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGlapVRSSRQDQI---HNSIVSTL---LALMDGLDNRGQVIVIGA 886
Cdd:TIGR01241  123 DFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDA---VGRQRGAGLgggNDEREQTLnqlLVEMDGFGTNTGVIVIAA 199
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    887 TNRIDSIDPALRRPGRFDRELLFTLPSKEARHRILTIHTENwLPKPSSQLLLEISDQLAGYCGADIKSLCSESVLCSLRT 966
Cdd:TIGR01241  200 TNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKN-KKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARK 278
                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 66812984    967 TYPQIykTSNKLQLSVDNIL--VEKSHfqdamKLITPSSKR 1005
Cdd:TIGR01241  279 NKTEI--TMNDIEEAIDRVIagPEKKS-----RVISEKEKK 312
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
741-908 6.93e-48

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: 168.68  E-value: 6.93e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  741 IGGLDKHIQLLKEMLMLPLLYPEVFnKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADCLSKWVG 820
Cdd:cd19509    1 IAGLDDAKEALKEAVILPSLRPDLF-PGLRGPPRGILLYGPPGTGKTLLARAVASESGS-----TFFSISASSLVSKWVG 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  821 EAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNR--GQVIVIGATNRIDSIDPALR 898
Cdd:cd19509   75 ESEKIVRALFALARELQPSIIFIDEIDSLLSERGSGEHEASRRVKTEFLVQMDGVLNKpeDRVLVLGATNRPWELDEAFL 154
                        170
                 ....*....|
gi 66812984  899 RpgRFDRELL 908
Cdd:cd19509  155 R--RFEKRIY 162
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
736-906 1.90e-47

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: 167.79  E-value: 1.90e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  736 IGFSSIGGLDKHIQLLKEMLMLpLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADCL 815
Cdd:cd19501    1 VTFKDVAGCEEAKEELKEVVEF-LKNPEKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGV-----PFFSISGSDFV 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  816 SKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTL---LALMDGLDNRGQVIVIGATNRIDS 892
Cdd:cd19501   75 EMFVGVGASRVRDLFEQAKKNAPCIVFIDEIDAVGRKRGAGLGGGHDEREQTLnqlLVEMDGFESNTGVIVIAATNRPDV 154
                        170
                 ....*....|....
gi 66812984  893 IDPALRRPGRFDRE 906
Cdd:cd19501  155 LDPALLRPGRFDRQ 168
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
1290-1404 2.87e-47

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: 164.84  E-value: 2.87e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1290 VRQLRILLREMVSKIIFDKKYLSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYYH 1369
Cdd:cd05528    1 LRELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80
                         90       100       110
                 ....*....|....*....|....*....|....*
gi 66812984 1370 FNDSnslEAIKANSRSKQLQDEVLSMVENIDPTLI 1404
Cdd:cd05528   81 DRDP---ADKLIRSRACELRDEVHAMIEAELDPLF 112
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
749-908 1.48e-45

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: 161.83  E-value: 1.48e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  749 QLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADCLSKWVGEAERQLRL 828
Cdd:cd19526    3 KALEETIEWPSKYPKIFASSPLRLRSGILLYGPPGCGKTLLASAIASECGL-----NFISVKGPELLNKYIGASEQNVRD 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  829 LFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRRPGRFDRELL 908
Cdd:cd19526   78 LFSRAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDKLVY 157
ftsH CHL00176
cell division protein; Validated
705-986 1.71e-44

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 172.93  E-value: 1.71e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   705 EFGVGKRGSSGPLPINLSGNKDSEPLSIDNKIGFSSIGGLDKHIQLLKEMLMLpLLYPEVFNKFKIQPPKGVLFYGPPGT 784
Cdd:CHL00176  149 QRSSNFKGGPGQNLMNFGKSKARFQMEADTGITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGT 227
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   785 GKTLLARALVNECNVggqkvSFFMRKGADCLSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSR-------Q 857
Cdd:CHL00176  228 GKTLLAKAIAGEAEV-----PFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGigggndeR 302
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   858 DQIHNSivstLLALMDGLDNRGQVIVIGATNRIDSIDPALRRPGRFDRELLFTLPSKEARHRILTIHTENwlpKPSSQ-- 935
Cdd:CHL00176  303 EQTLNQ----LLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARN---KKLSPdv 375
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 66812984   936 LLLEISDQLAGYCGADIKSLCSESVLCSLRTTYPQIykTSNKLQLSVDNIL 986
Cdd:CHL00176  376 SLELIARRTPGFSGADLANLLNEAAILTARRKKATI--TMKEIDTAIDRVI 424
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
753-907 6.68e-44

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: 157.29  E-value: 6.68e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  753 EMLMLPLLYPEVFNKfKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADCLSKWVGEAERQLRLLFEQ 832
Cdd:cd19527    7 DTIQLPLEHPELFSS-GLRKRSGILLYGPPGTGKTLLAKAIATECSL-----NFLSVKGPELINMYIGESEANVREVFQK 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 66812984  833 AKAMQPSIIFFDEIDGLAPVRSSRQDQ--IHNSIVSTLLALMDGLDNRGQ-VIVIGATNRIDSIDPALRRPGRFDREL 907
Cdd:cd19527   81 ARDAKPCVIFFDELDSLAPSRGNSGDSggVMDRVVSQLLAELDGMSSSGQdVFVIGATNRPDLLDPALLRPGRFDKLL 158
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
730-965 1.15e-43

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


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 164.55  E-value: 1.15e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   730 LSIDNK--IGFSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNEcnvggQKVSFF 807
Cdd:PTZ00454  134 LQMSEKpdVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHH-----TTATFI 208
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   808 MRKGADCLSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQ---DQIHNSIVSTLLALMDGLDNRGQVIVI 884
Cdd:PTZ00454  209 RVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQtgaDREVQRILLELLNQMDGFDQTTNVKVI 288
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   885 GATNRIDSIDPALRRPGRFDRELLFTLPSKEARHRILTIHTE--NWLPKPSSQLLLEISDQLagyCGADIKSLCSESVLC 962
Cdd:PTZ00454  289 MATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSkmNLSEEVDLEDFVSRPEKI---SAADIAAICQEAGMQ 365

                  ...
gi 66812984   963 SLR 965
Cdd:PTZ00454  366 AVR 368
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
762-1003 9.03e-42

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


Pssm-ID: 224144 [Multi-domain]  Cd Length: 368  Bit Score: 158.44  E-value: 9.03e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  762 PEVFNKFKiqpPKGVLFYGPPGTGKTLLARALVNECnvggqKVSFFMRKGADCLSKWVGEAERQLRLLFEQAKAMQPSII 841
Cdd:COG1223  143 PERFGDWA---PKNVLFYGPPGTGKTMMAKALANEA-----KVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCIV 214
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  842 FFDEIDGLAPVR---SSRQDQihNSIVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRrpGRFDRELLFTLPSKEARH 918
Cdd:COG1223  215 FIDELDAIALDRryqELRGDV--SEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIR--SRFEEEIEFKLPNDEERL 290
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  919 RILTIHTENwLPKPSSQLLLEISDQLAGYCGADIKslcsESVLcslrttypqiyKTSNKLQLSVDNILVEKSHFQDAMKL 998
Cdd:COG1223  291 EILEYYAKK-FPLPVDADLRYLAAKTKGMSGRDIK----EKVL-----------KTALHRAIAEDREKVEREDIEKALKK 354

                 ....*
gi 66812984  999 ITPSS 1003
Cdd:COG1223  355 ERKRR 359
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
740-903 1.14e-41

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: 151.04  E-value: 1.14e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  740 SIGGLDKHIQLLKEMLMLPLLYPEVFNKFKI-QPPKGVLFYGPPGTGKTLLARALVNE--CNVGGQKVSFFMrkgadclS 816
Cdd:cd19520    1 DIGGLDEVITELKELVILPLQRPELFDNSRLlQPPKGVLLYGPPGCGKTMLAKATAKEagARFINLQVSSLT-------D 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  817 KWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRG--QVIVIGATNRIDSID 894
Cdd:cd19520   74 KWYGESQKLVAAVFSLASKLQPSIIFIDEIDSFLRQRSSTDHEATAMMKAEFMSLWDGLSTDGncRVIVMGATNRPQDLD 153
                        170
                 ....*....|.
gi 66812984  895 PALRR--PGRF 903
Cdd:cd19520  154 EAILRrmPKRF 164
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
705-971 1.26e-41

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


Pssm-ID: 223541 [Multi-domain]  Cd Length: 596  Bit Score: 163.26  E-value: 1.26e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  705 EFGVGKRGSSGPLPINLSGNKDSEPLSIDNKIGFSSIGGLDKHIQLLKEmLMLPLLYPEVFNKFKIQPPKGVLFYGPPGT 784
Cdd:COG0465  116 FFRRQAQGGGGGGAFSFGKSKAKLYLEDQVKVTFADVAGVDEAKEELSE-LVDFLKNPKKYQALGAKIPKGVLLVGPPGT 194
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  785 GKTLLARALVNECNVggqkvSFFMRKGADCLSKWVGEAERQLRLLFEQAKAMQPSIIFFDEID------GLAPvrSSRQD 858
Cdd:COG0465  195 GKTLLAKAVAGEAGV-----PFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDavgrqrGAGL--GGGND 267
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  859 QIHNSIvSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRRPGRFDRELLFTLPSKEARHRILTIHTENwlpKPSSQL-- 936
Cdd:COG0465  268 EREQTL-NQLLVEMDGFGGNEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKN---KPLAEDvd 343
                        250       260       270
                 ....*....|....*....|....*....|....*
gi 66812984  937 LLEISDQLAGYCGADIKSLCSESVLCSLRTTYPQI 971
Cdd:COG0465  344 LKKIARGTPGFSGADLANLLNEAALLAARRNKKEI 378
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
735-965 7.18e-40

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 158.66  E-value: 7.18e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   735 KIGFSSIGGLDKHIQLLKEMLMLpLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECnvggqKVSFFMRKGADC 814
Cdd:PRK10733  148 KTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA-----KVPFFTISGSDF 221
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   815 LSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTL---LALMDGLDNRGQVIVIGATNRID 891
Cdd:PRK10733  222 VEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLnqmLVEMDGFEGNEGIIVIAATNRPD 301
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 66812984   892 SIDPALRRPGRFDRELLFTLPSKEARHRILTIHTENwLPKPSSQLLLEISDQLAGYCGADIKSLCSESVLCSLR 965
Cdd:PRK10733  302 VLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRR-VPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAAR 374
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
727-907 1.24e-39

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: 145.90  E-value: 1.24e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  727 SEPLSIDNKIGFSSIGGLDKHIQLLKEMLMLPLLYPEVFNKFKiQPPKGVLFYGPPGTGKTLLARALVNECnvggqKVSF 806
Cdd:cd19525   10 SEIMDHGPPINWADIAGLEFAKKTIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQS-----GATF 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  807 FMRKGADCLSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRG--QVIVI 884
Cdd:cd19525   84 FSISASSLTSKWVGEGEKMVRALFSVARCKQPAVIFIDEIDSLLSQRGEGEHESSRRIKTEFLVQLDGATTSSedRILVV 163
                        170       180
                 ....*....|....*....|...
gi 66812984  885 GATNRIDSIDPALRRpgRFDREL 907
Cdd:cd19525  164 GATNRPQEIDEAARR--RLVKRL 184
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
741-899 4.07e-37

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: 137.67  E-value: 4.07e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  741 IGGLDKHIQLLKEMLMLPLLYPEVFNKFKiQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADCLSKWVG 820
Cdd:cd19524    2 IAGQDLAKQALQEMVILPSLRPELFTGLR-APARGLLLFGPPGNGKTMLAKAVAAESNA-----TFFNISAASLTSKYVG 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  821 EAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRG--QVIVIGATNRIDSIDPA-L 897
Cdd:cd19524   76 EGEKLVRALFAVARELQPSIIFIDEVDSLLSERSEGEHEASRRLKTEFLIEFDGVQSNGddRVLVMGATNRPQELDDAvL 155

                 ..
gi 66812984  898 RR 899
Cdd:cd19524  156 RR 157
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
741-899 3.97e-36

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: 135.11  E-value: 3.97e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  741 IGGLDKHIQLLKEMLMLPLLYPEVFNKFKiQPPKGVLFYGPPGTGKTLLARALVNECnvggqKVSFFMRKGADCLSKWVG 820
Cdd:cd19522    2 IADLEEAKKLLEEAVVLPMWMPEFFKGIR-RPWKGVLMVGPPGTGKTLLAKAVATEC-----GTTFFNVSSSTLTSKYRG 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  821 EAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVR-SSRQDQIHNSIVSTLLALMDGL-------DNRGQVIVIGATNRIDS 892
Cdd:cd19522   76 ESEKLVRLLFEMARFYAPTTIFIDEIDSICSRRgTSEEHEASRRVKSELLVQMDGVggasendDPSKMVMVLAATNFPWD 155

                 ....*..
gi 66812984  893 IDPALRR 899
Cdd:cd19522  156 IDEALRR 162
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
741-904 5.12e-36

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: 135.31  E-value: 5.12e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  741 IGGLDKHIQ-LLKEMLMLPLLYPEVFNKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVGGQKVSffmrKGADCLSKWV 819
Cdd:cd19504    2 IGGLDKEFSdIFRRAFASRVFPPEIVEQLGCKHVKGILLYGPPGTGKTLMARQIGKMLNAREPKIV----NGPEILNKYV 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  820 GEAERQLRLLFEQAKAMQPS--------IIFFDEIDGLAPVRSSRQDQ--IHNSIVSTLLALMDGLDNRGQVIVIGATNR 889
Cdd:cd19504   78 GESEANIRKLFADAEEEQRRlgansglhIIIFDEIDAICKQRGSMAGStgVHDTVVNQLLSKIDGVEQLNNILVIGMTNR 157
                        170
                 ....*....|....*
gi 66812984  890 IDSIDPALRRPGRFD 904
Cdd:cd19504  158 KDLIDEALLRPGRLE 172
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
735-907 1.99e-35

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


Pssm-ID: 410929 [Multi-domain]  Cd Length: 170  Bit Score: 133.06  E-value: 1.99e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  735 KIGFSSIGGLDKHIQLLKEMLMLPLLYPEVFnKFKIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADC 814
Cdd:cd19521    3 NVKWEDVAGLEGAKEALKEAVILPVKFPHLF-TGNRKPWSGILLYGPPGTGKSYLAKAVATEANS-----TFFSVSSSDL 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  815 LSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQ-VIVIGATNRIDSI 893
Cdd:cd19521   77 VSKWMGESEKLVKQLFAMARENKPSIIFIDEVDSLCGTRGEGESEASRRIKTELLVQMNGVGNDSQgVLVLGATNIPWQL 156
                        170
                 ....*....|....
gi 66812984  894 DPALRRpgRFDREL 907
Cdd:cd19521  157 DSAIRR--RFEKRI 168
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
769-911 1.03e-27

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 110.31  E-value: 1.03e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  769 KIQPPKGVLFYGPPGTGKTLLARALVNECnvGGQKVSFFMRKGADCLSKWVGEAERQ---LRLLFEQAKAMQPSIIFFDE 845
Cdd:cd00009   15 ELPPPKNLLLYGPPGTGKTTLARAIANEL--FRPGAPFLYLNASDLLEGLVVAELFGhflVRLLFELAEKAKPGVLFIDE 92
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 66812984  846 IDGLAPvrssrqdQIHNSIVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRRPGRFDRELLFTL 911
Cdd:cd00009   93 IDSLSR-------GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151
RecA-like_fidgetin cd19523
ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. ...
741-908 3.20e-27

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


Pssm-ID: 410931 [Multi-domain]  Cd Length: 163  Bit Score: 109.59  E-value: 3.20e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  741 IGGLDKHIQLLKEMLMLPLLYPEVFNKFkIQPPKGVLFYGPPGTGKTLLARALVNECNVggqkvSFFMRKGADCLSKWVG 820
Cdd:cd19523    2 IAGLGALKAAIKEEVLWPLLRPDAFSGL-LRLPRSILLFGPRGTGKTLLGRCLASQLGA-----TFLRLRGSTLVAKWAG 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  821 EAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIhNSIVSTLLALMDGLDNRG--QVIVIGATNRIDSIDPALR 898
Cdd:cd19523   76 EGEKILQASFLAARCRQPSVLFISDLDALLSSQDDEASPV-GRLQVELLAQLDGVLGSGedGVLVVCTTSKPEEIDESLR 154
                        170
                 ....*....|
gi 66812984  899 RpgRFDRELL 908
Cdd:cd19523  155 R--YFSKRLL 162
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
772-912 3.12e-20

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 88.97  E-value: 3.12e-20
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984     772 PPKGVLFYGPPGTGKTLLARALVNECNVGGQKVSFF------------MRKGADCLSKWVGEAERQLRLLFEQAKAMQPS 839
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIdgedileevldqLLLIIVGGKKASGSGELRLRLALALARKLKPD 80
                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 66812984     840 IIFFDEIDGLAPVRSSRQDQihnsiVSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRRPgRFDRELLFTLP 912
Cdd:smart00382   81 VLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLI 147
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
741-905 3.82e-18

ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of photosynthesis in cyanobacteria, especially in CO2 uptake and utilization. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410915 [Multi-domain]  Cd Length: 161  Bit Score: 83.19  E-value: 3.82e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  741 IGGLDKhiqlLKEMLML--PLLYPEVFNkFKIQPPKGVLFYGPPGTGKTLLARALVNECN-------VGgqkvSFFmrkg 811
Cdd:cd19507    2 VGGLDN----LKDWLKKrkAAFSKQASA-YGLPTPKGLLLVGIQGTGKSLTAKAIAGVWQlpllrldMG----RLF---- 68
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  812 adclSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQ-IHNSIVSTLLALMDglDNRGQVIVIGATNRI 890
Cdd:cd19507   69 ----GGLVGESESRLRQMIQTAEAIAPCVLWIDEIEKGFSNADSKGDSgTSSRVLGTFLTWLQ--EKKKPVFVVATANNV 142
                        170
                 ....*....|....*
gi 66812984  891 DSIDPALRRPGRFDR 905
Cdd:cd19507  143 QSLPPELLRKGRFDE 157
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
1300-1381 4.89e-16

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: 75.76  E-value: 4.89e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1300 MVSKIIFDKKYLS----FFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYyhfNDSNS 1375
Cdd:cd05511    4 ILDEIVNELKNLPdswpFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLY---NGPDS 80

                 ....*.
gi 66812984 1376 LEAIKA 1381
Cdd:cd05511   81 VYTKKA 86
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
1291-1392 6.34e-15

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: 72.02  E-value: 6.34e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1291 RQLRILLREMVSKIifdKKYLSFFRD-VNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTelyYH 1369
Cdd:cd04369    3 KKLRSLLDALKKLK---RDLSEPFLEpVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNA---KT 76
                         90       100
                 ....*....|....*....|...
gi 66812984 1370 FNDSNSLEAIKANSRSKQLQDEV 1392
Cdd:cd04369   77 YNGPGSPIYKDAKKLEKLFEKLL 99
BROMO smart00297
bromo domain;
1286-1380 1.74e-14

bromo domain;


Pssm-ID: 197636  Cd Length: 107  Bit Score: 71.16  E-value: 1.74e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    1286 DRQLVRQLRILLREMVSKIIFDKKYLSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTE 1365
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80
                            90
                    ....*....|....*
gi 66812984    1366 LYYHFNDSNSLEAIK 1380
Cdd:smart00297   81 TYNGPDSEVYKDAKK 95
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
1297-1378 5.75e-14

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


Pssm-ID: 395352  Cd Length: 84  Bit Score: 68.88  E-value: 5.75e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   1297 LREMVSKIIFDKKYLSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYyhfNDSNSL 1376
Cdd:pfam00439    1 CLEILDKLMEHPLAAPFLEPVDPDEYPDYYSVIKRPMDLSTIKKKLENGEYKSLAEFEADVKLMFSNARTY---NGPGSV 77

                   ..
gi 66812984   1377 EA 1378
Cdd:pfam00439   78 IY 79
ycf46 CHL00195
Ycf46; Provisional
773-953 1.93e-13

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 75.06  E-value: 1.93e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   773 PKGVLFYGPPGTGKTLLARALVNECNVGGQKVSFfmrkgADCLSKWVGEAERQLRLLFEQAKAMQPSIIFFDEIDGLAPV 852
Cdd:CHL00195  259 PRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDV-----GKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSN 333
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   853 RSSRQDQ-IHNSIVSTLLALMDglDNRGQVIVIGATNRIDSIDPALRRPGRFDRELLFTLPSKEARHRILTIHTENWLPK 931
Cdd:CHL00195  334 SESKGDSgTTNRVLATFITWLS--EKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPK 411
                         170       180
                  ....*....|....*....|....*.
gi 66812984   932 PSS----QLLLEISDQlagYCGADIK 953
Cdd:CHL00195  412 SWKkydiKKLSKLSNK---FSGAEIE 434
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
1288-1382 2.63e-12

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: 64.50  E-value: 2.63e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1288 QLVRQLRILLREMVSkiifDKKYLSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELY 1367
Cdd:cd05509    1 PLYTQLKKVLDSLKN----HKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLY 76
                         90
                 ....*....|....*
gi 66812984 1368 yhfNDSNSLEAIKAN 1382
Cdd:cd05509   77 ---NGPDTEYYKCAN 88
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
774-905 1.42e-11

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: 64.30  E-value: 1.42e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  774 KGVLFYGPPGTGKTLLARALVNECNVGGQKVSffmrkgadcLSKWVGEAERQLRLLfeqAKAMQPSIIFFDEID-----G 848
Cdd:cd19510   24 RGYLLYGPPGTGKSSFIAALAGELDYDICDLN---------LSEVVLTDDRLNHLL---NTAPKQSIILLEDIDaafesR 91
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 66812984  849 LAPVRSSRQDQIHNSI-VSTLLALMDGLDNRGQVIVIGATNRIDSIDPALRRPGRFDR 905
Cdd:cd19510   92 EHNKKNPSAYGGLSRVtFSGLLNALDGVASSEERIVFMTTNHIERLDPALIRPGRVDM 149
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
1294-1375 2.18e-11

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: 62.01  E-value: 2.18e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1294 RILLREMVSKiifdKKYLSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELyyhFNDS 1373
Cdd:cd05503    6 ETILDEMEAH----EDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCET---FNED 78

                 ..
gi 66812984 1374 NS 1375
Cdd:cd05503   79 DS 80
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
1296-1367 2.77e-11

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: 61.53  E-value: 2.77e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 66812984 1296 LLREMvskiiFDKKYLS----FFRDVNAEQ--FPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELY 1367
Cdd:cd05498    8 ILKEL-----FSKKHKAyawpFYKPVDPEAlgLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKY 80
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
1296-1373 1.30e-10

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


Pssm-ID: 99936  Cd Length: 115  Bit Score: 60.10  E-value: 1.30e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 66812984 1296 LLREMVSKIIFDKKYLSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYYHFNDS 1373
Cdd:cd05504   16 ALEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTS 93
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
1299-1387 1.62e-09

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


Pssm-ID: 99937  Cd Length: 97  Bit Score: 56.39  E-value: 1.62e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1299 EMVSKIIFDKKYLSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYYHfNDSNSLEA 1378
Cdd:cd05505    7 EILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYE-NGSYVLSC 85

                 ....*....
gi 66812984 1379 IkanSRSKQ 1387
Cdd:cd05505   86 M---RKTEQ 91
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
776-897 2.64e-09

ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as Thyroid hormone receptor interactor 13 (TRIP13) and 16E1BP) is a key regulator of specific chromosomal events, like the control of G2/prophase processes such as DNA break formation and recombination, checkpoint signaling, and chromosome synapsis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion


Pssm-ID: 410916  Cd Length: 199  Bit Score: 58.61  E-value: 2.64e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  776 VLFYGPPGTGKTLLARALVNECNVggqKVSFFMRKG-------ADCLSKWVGEAERQLRLLFEQAKAM--QPSIIFF--- 843
Cdd:cd19508   55 VLLHGPPGTGKTSLCKALAQKLSI---RLSSRYRYGqlieinsHSLFSKWFSESGKLVTKMFQKIQELidDKDALVFvli 131
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 66812984  844 DEIDGLAPVRSSRQDQIHNS----IVSTLLALMDGLDNRGQVIVIGATNRIDSIDPAL 897
Cdd:cd19508  132 DEVESLAAARSASSSGTEPSdairVVNAVLTQIDRIKRYHNNVILLTSNLLEKIDVAF 189
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
1293-1367 7.60e-09

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: 54.71  E-value: 7.60e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 66812984 1293 LRILLREMVSKIIFDKKYLSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELY 1367
Cdd:cd05512    2 LEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAY 76
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
1320-1378 2.38e-08

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: 53.40  E-value: 2.38e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 66812984 1320 EQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYYH-----FNDSNSLEA 1378
Cdd:cd05522   35 AREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNEndsqeYKDAVLLEK 98
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
1312-1375 3.23e-08

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: 53.11  E-value: 3.23e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 66812984 1312 SFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTelyYHFNDSNS 1375
Cdd:cd05520   26 PFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENA---KRYNVPNS 86
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
1311-1363 3.35e-08

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


Pssm-ID: 99946  Cd Length: 105  Bit Score: 53.08  E-value: 3.35e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 66812984 1311 LSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTN 1363
Cdd:cd05515   25 LIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDN 77
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
1282-1368 5.59e-08

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: 52.72  E-value: 5.59e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1282 ELKKDRQLVRQLRILLREMvSKIIFDkkylSFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIV 1361
Cdd:cd05524    3 PIAVCQELYDTIRNYKSED-GRILCE----SFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLI 77

                 ....*..
gi 66812984 1362 TNTELYY 1368
Cdd:cd05524   78 NNAKAYY 84
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
1316-1371 1.21e-07

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: 51.52  E-value: 1.21e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 66812984 1316 DVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTelyYHFN 1371
Cdd:cd05499   29 DPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNC---YTFN 81
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
1321-1381 1.49e-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: 51.29  E-value: 1.49e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 66812984 1321 QFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYYH-----FNDSNSLEAIKA 1381
Cdd:cd05517   35 LYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEpgsqvYKDANAIKKIFT 100
RecA-like_Ycf2 cd19505
ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; ...
772-905 1.60e-07

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


Pssm-ID: 410913 [Multi-domain]  Cd Length: 161  Bit Score: 52.76  E-value: 1.60e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  772 PPKGVLFYGPPGTGKTLLARALVNECNVGGQKVS----------FFMRKGADCLSKWvGEAERQLRLLFEQAKAMQPSII 841
Cdd:cd19505   11 PSKGILLIGSIETGRSYLIKSLAANSYVPLIRISlnkllynkpdFGNDDWIDGMLIL-KESLHRLNLQFELAKAMSPCII 89
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 66812984  842 FFDEIDGLapvRSSRQDQIHNSIVSTLLALM-------DGLDNRGQVIVIGATNRIDSIDPALRRPGRFDR 905
Cdd:cd19505   90 WIPNIHEL---NVNRSTQNLEEDPKLLLGLLlnylsrdFEKSSTRNILVIASTHIPQKVDPALIAPNRLDT 157
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
1313-1367 2.49e-07

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: 50.90  E-value: 2.49e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 66812984 1313 FFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELY 1367
Cdd:cd05510   29 FLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLY 83
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
1225-1398 4.40e-07

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 54.04  E-value: 4.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1225 SSKFEISKLTKRSIKDFYENIVNDI-----KEVGITIKKALTVKIQESQQLPiVPFQSDSVRELKKDRQLVRQLRILLRE 1299
Cdd:COG5076   63 SIVDDREPGSMANVNDDLENVGGITyspfeKNRPESLRFDEIVFLAIESVTP-ESGLGSLLMAHLKTSVKKRKTPKIEDE 141
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1300 MVSKIIF------------DKKYLS--FFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTE 1365
Cdd:COG5076  142 LLYADNKaiakfkkqlflrDGRFLSsiFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCK 221
                        170       180       190
                 ....*....|....*....|....*....|....*
gi 66812984 1366 LyYHFNDSNSLEAIKA--NSRSKQLQDEVLSMVEN 1398
Cdd:COG5076  222 L-YNGPDSSVYVDAKEleKYFLKLIEEIPEEMLEL 255
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
1314-1368 6.10e-07

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


Pssm-ID: 99934  Cd Length: 109  Bit Score: 49.60  E-value: 6.10e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 66812984 1314 FRDVNAEQFPEYYELIKNPMSLQRISQNLDSYE---YISLESFLKDIDLIVTNTELYY 1368
Cdd:cd05502   25 FHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSpqhYSSPEEFVADVRLMFKNCYKFN 82
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
773-919 7.27e-07

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


Pssm-ID: 400187 [Multi-domain]  Cd Length: 168  Bit Score: 51.04  E-value: 7.27e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    773 PKGV-LFYGPPGTGKTLLARALVNECNVGGQKV-----SFFMRKGAdcLSKWVGEAERQLR-----LLFEQAKAMQPSII 841
Cdd:pfam07724    2 PIGSfLFLGPTGVGKTELAKALAELLFGDERALiridmSEYMEEHS--VSRLIGAPPGYVGyeeggQLTEAVRRKPYSIV 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    842 FFDEIdglapvrssrqDQIHNSIVSTLLALMDG---LDNRGQ------VIVIGATNrIDSIDP--ALRRPGRFDRELLFT 910
Cdd:pfam07724   80 LIDEI-----------EKAHPGVQNDLLQILEGgtlTDKQGRtvdfknTLFIMTGN-FGSEKIsdASRLGDSPDYELLKE 147

                   ....*....
gi 66812984    911 LPSKEARHR 919
Cdd:pfam07724  148 EVMDLLKKG 156
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
778-955 8.00e-07

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


Pssm-ID: 225165 [Multi-domain]  Cd Length: 436  Bit Score: 53.39  E-value: 8.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  778 FYGPPGTGKTLLARALVNECNVGGQKVS--FFMRKgadclskwvgeaerQLRLLFEQAKAMQPS----IIFFDEIDGLap 851
Cdd:COG2256   53 LWGPPGTGKTTLARLIAGTTNAAFEALSavTSGVK--------------DLREIIEEARKNRLLgrrtILFLDEIHRF-- 116
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  852 vRSSRQDqihnsivsTLLALMDgldnRGQVIVIGAT--NRIDSIDPALRrpgrfDRELLFTLPS------KEARHRILTi 923
Cdd:COG2256  117 -NKAQQD--------ALLPHVE----NGTIILIGATteNPSFELNPALL-----SRARVFELKPlssediKKLLKRALL- 177
                        170       180       190
                 ....*....|....*....|....*....|..
gi 66812984  924 HTENWLPKPSSQLLLEISDQLAGYCGADIKSL 955
Cdd:COG2256  178 DEERGLGGQIIVLDEEALDYLVRLSNGDARRA 209
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
776-898 8.12e-07

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 53.55  E-value: 8.12e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   776 VLFYGPPGTGKTLLARALVNECN---------VGGQKvsffmrkgadclskwvgeaerQLRLLFEQAKAM----QPSIIF 842
Cdd:PRK13342   39 MILWGPPGTGKTTLARIIAGATDapfealsavTSGVK---------------------DLREVIEEARQRrsagRRTILF 97
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 66812984   843 FDEIDGLApvrSSRQDqihnsivsTLLALMDgldnRGQVIVIGAT--NRIDSIDPALR 898
Cdd:PRK13342   98 IDEIHRFN---KAQQD--------ALLPHVE----DGTITLIGATteNPSFEVNPALL 140
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
1323-1367 1.40e-06

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: 48.46  E-value: 1.40e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 66812984 1323 PEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELY 1367
Cdd:cd05500   37 PHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTF 81
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
1323-1367 3.41e-06

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: 47.42  E-value: 3.41e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 66812984 1323 PEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELY 1367
Cdd:cd05516   38 PEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTF 82
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
1292-1367 4.08e-06

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: 47.05  E-value: 4.08e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66812984 1292 QLRILLREMVSKIIFDKKYLSFFR---DVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELY 1367
Cdd:cd05495    3 ELRQALMPTLEKLYKQDPESLPFRqpvDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLY 81
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
1322-1377 4.63e-06

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: 46.95  E-value: 4.63e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 66812984 1322 FPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYYH-----FNDSNSLE 1377
Cdd:cd05519   36 YPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQegsivYEDAVEME 96
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
774-909 1.05e-05

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


Pssm-ID: 410920 [Multi-domain]  Cd Length: 150  Bit Score: 47.14  E-value: 1.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  774 KGVLFYGPPGTGKTLLARALVNECNVG-----GQKVSFFMRKGADCLSK---WVGEAERQLrllfeqakamqpsIIFFDE 845
Cdd:cd19512   23 RNILFYGPPGTGKTLFAKKLALHSGMDyaimtGGDVAPMGREGVTAIHKvfdWANTSRRGL-------------LLFVDE 89
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 66812984  846 IDGLAPVRSSrqDQIHNSIVSTLLALM--DGLDNRGQVIVIgATNRIDSIDPALRrpGRFDRELLF 909
Cdd:cd19512   90 ADAFLRKRST--EKISEDLRAALNAFLyrTGEQSNKFMLVL-ASNQPEQFDWAIN--DRIDEMVEF 150
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
1290-1381 1.27e-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: 45.45  E-value: 1.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1290 VRQLRILLREMVSKIIFDKKYLsFFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTeLYYH 1369
Cdd:cd05508    1 VDQLSKLLKFALERMKQPGAEP-FLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNA-IIYN 78
                         90
                 ....*....|..
gi 66812984 1370 FNDSNSLEAIKA 1381
Cdd:cd05508   79 GGDHKLTQAAKA 90
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
1292-1367 2.13e-05

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: 45.11  E-value: 2.13e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66812984 1292 QLRILLREMVsKIIFDKKYLSFFR---DVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELY 1367
Cdd:cd05497    5 QLQYLLKVVL-KALWKHKFAWPFQqpvDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIY 82
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteristic of the ...
773-923 2.37e-05

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


Pssm-ID: 404141 [Multi-domain]  Cd Length: 166  Bit Score: 46.36  E-value: 2.37e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    773 PKGVLFYGPPGTGKTLLARALVNEcnVGGQKVSFFMRKGADCLSKWVGeAERQLRL-LFEQAKAMQPSIIF---FDEIDG 848
Cdd:pfam13191   23 PPLVLLTGEAGTGKTSLLRELLRA--LERDGVYVLRGKCDECLRPSAL-LEALTREgLLRQLLDELESSLLeawRDRILE 99
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 66812984    849 LAPVRSSRQDQIHNSIVSTLLALMDGLDNRGQ--VIVIgatNRIDSIDPAlrrpgrfDRELLFTLPSKEARHRILTI 923
Cdd:pfam13191  100 ELAPVPELAGDLAERLLDLLLRLLDLLARDERplVLVL---DDLQWADEA-------SLQLLAALLRLLESLPLLVV 166
PRK04195 PRK04195
replication factor C large subunit; Provisional
769-849 3.30e-05

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 48.38  E-value: 3.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984   769 KIQPPKGVLFYGPPGTGKTLLARALVN-------ECNVGGQkvsffmRKgADCLSKWVGEAERQlRLLFEQAKamqpSII 841
Cdd:PRK04195   35 KGKPKKALLLYGPPGVGKTSLAHALANdygweviELNASDQ------RT-ADVIERVAGEAATS-GSLFGARR----KLI 102

                  ....*...
gi 66812984   842 FFDEIDGL 849
Cdd:PRK04195  103 LLDEVDGI 110
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
1302-1379 3.45e-05

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


Pssm-ID: 99949  Cd Length: 103  Bit Score: 44.36  E-value: 3.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1302 SKIIFDKKYLSFFRDVNAEQ-------------FPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYY 1368
Cdd:cd05518    3 KRMLALFLYVLEYREGSGRRlcdlfmekpskkdYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82
                         90
                 ....*....|....*.
gi 66812984 1369 H-----FNDSNSLEAI 1379
Cdd:cd05518   83 EegsqvYEDANILEKV 98
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
777-893 5.95e-05

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


Pssm-ID: 410907 [Multi-domain]  Cd Length: 178  Bit Score: 45.63  E-value: 5.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  777 LFYGPPGTGKTLLARALVNECNVGGQKV-----SFFMRKGADCLSK-----WVGEAERQlrLLFEQAKAMQPSIIFFDEI 846
Cdd:cd19499   45 LFLGPTGVGKTELAKALAELLFGDEDNLiridmSEYMEKHSVSRLIgappgYVGYTEGG--QLTEAVRRKPYSVVLLDEI 122
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 66812984  847 DGLAPVrssrqdqIHNSIvstLLALMDG--LDNRG------QVIVIGATN--------RIDSI 893
Cdd:cd19499  123 EKAHPD-------VQNLL---LQVLDDGrlTDSHGrtvdfkNTIIIMTSNhfrpeflnRIDEI 175
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
1321-1390 1.06e-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: 43.86  E-value: 1.06e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1321 QFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTElyyHFNDSNSLEAIKANSRSKQLQD 1390
Cdd:cd05529   57 WYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAE---TFNEPNSEIAKKAKRLSDWLLR 123
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
1305-1397 1.07e-04

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: 43.12  E-value: 1.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1305 IFDKKYLS-FFRDVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYYHFNDSNSLEAikans 1383
Cdd:cd05507   15 LASHRYASvFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMA----- 89
                         90
                 ....*....|....
gi 66812984 1384 rsKQLQDEVLSMVE 1397
Cdd:cd05507   90 --VEMQREVMSQIQ 101
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
1316-1367 1.18e-04

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: 42.70  E-value: 1.18e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 66812984 1316 DVNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELY 1367
Cdd:cd05506   26 DVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRY 77
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
1095-1172 1.57e-04

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: 44.32  E-value: 1.57e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66812984 1095 QNFSVYRPR-LLIHGEQGMGQIQLANSLLYHLEeFPIFSIDISALISDPTSKTvEESCIRILSEAKKASPSIIYIPNID 1172
Cdd:cd19518   27 QHLGVEPPRgVLLHGPPGCGKTMLANAIAGELK-VPFLKISATEIVSGVSGES-EEKIRELFDQAISNAPCIVFIDEID 103
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
1291-1367 2.81e-04

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: 42.44  E-value: 2.81e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 66812984 1291 RQLRILLREMvskiiFDKKYLSFFRD-VNAEQFPEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELY 1367
Cdd:cd05496    8 KQCKELVNLM-----WDCEDSEPFRQpVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSY 80
MoxR COG0714
MoxR-like ATPase [General function prediction only];
776-921 3.53e-04

MoxR-like ATPase [General function prediction only];


Pssm-ID: 223786 [Multi-domain]  Cd Length: 329  Bit Score: 44.73  E-value: 3.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  776 VLFYGPPGTGKTLLARALVNECNVGGQKVSF--FMRkGADCLSKWVGEAERQL--------RLLFEQAKAmqpsIIFFDE 845
Cdd:COG0714   46 VLLEGPPGVGKTLLARALARALGLPFVRIQCtpDLL-PSDLLGTYAYAALLLEpgefrfvpGPLFAAVRV----ILLLDE 120
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  846 IDGLAPvrssrqdqihnSIVSTLLALMD-------GLDN---RGQVIVIGATNRIDSID-----PALRRpgRFDRELLFT 910
Cdd:COG0714  121 INRAPP-----------EVQNALLEALEerqvtvpGLTTirlPPPFIVIATQNPGEYEGtyplpEALLD--RFLLRIYVD 187
                        170
                 ....*....|.
gi 66812984  911 LPSKEARHRIL 921
Cdd:COG0714  188 YPDSEEEERII 198
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
1088-1172 3.84e-04

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: 43.05  E-value: 3.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984 1088 FINNLMIQNFSVYRPR-LLIHGEQGMGQIQLANSLLYHLEEfPIFSIDISALISDPTSKTvEESCIRILSEAKKASPSII 1166
Cdd:cd19503   20 LKYPELFRALGLKPPRgVLLHGPPGTGKTLLARAVANEAGA-NFLSISGPSIVSKYLGES-EKNLREIFEEARSHAPSII 97

                 ....*.
gi 66812984 1167 YIPNID 1172
Cdd:cd19503   98 FIDEID 103
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
1324-1372 5.06e-04

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 40.87  E-value: 5.06e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 66812984 1324 EYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYYHFND 1372
Cdd:cd05501   32 DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDDD 80
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
937-973 6.34e-04

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: 39.07  E-value: 6.34e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 66812984    937 LLEISDQLAGYCGADIKSLCSESVLCSLRTTYPQIYK 973
Cdd:pfam17862    4 LEELAERTEGFSGADLEALCREAALAALRRGREAVTQ 40
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
776-800 7.42e-04

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 43.58  E-value: 7.42e-04
                          10        20
                  ....*....|....*....|....*
gi 66812984   776 VLFYGPPGTGKTLLARALVNECNVG 800
Cdd:PRK00080   54 VLLYGPPGLGKTTLANIIANEMGVN 78
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, ...
776-850 8.15e-04

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


Pssm-ID: 224140 [Multi-domain]  Cd Length: 408  Bit Score: 43.74  E-value: 8.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  776 VLFYGPPGTGKTLLARALVNECNvggqkVSFFMrkgADCLS----KWVGEAERQ--LRLL----FEQAKAmQPSIIFFDE 845
Cdd:COG1219  100 ILLIGPTGSGKTLLAQTLAKILN-----VPFAI---ADATTlteaGYVGEDVENilLKLLqaadYDVERA-ERGIIYIDE 170

                 ....*
gi 66812984  846 IDGLA 850
Cdd:COG1219  171 IDKIA 175
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
776-850 8.61e-04

ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent protease ClpXP. In ClpXP, ClpX ATPase serves to specifically recognize, unfold, and translocate protein substrates into the chamber of ClpP protease for degradation. This RecA-like_ClpX domain subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410905 [Multi-domain]  Cd Length: 251  Bit Score: 42.97  E-value: 8.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  776 VLFYGPPGTGKTLLARALVNECNvggqkVSFFMrkgADCLS----KWVGEAERQ--LRLL----FEQAKAmQPSIIFFDE 845
Cdd:cd19497   53 ILLIGPTGSGKTLLAQTLAKILD-----VPFAI---ADATTlteaGYVGEDVENilLKLLqaadYDVERA-QRGIVYIDE 123

                 ....*
gi 66812984  846 IDGLA 850
Cdd:cd19497  124 IDKIA 128
RuvB_N pfam05496
Holliday junction DNA helicase ruvB N-terminus; The RuvB protein makes up part of the RuvABC ...
776-800 1.14e-03

Holliday junction DNA helicase ruvB N-terminus; The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.


Pssm-ID: 398900  Cd Length: 159  Bit Score: 41.33  E-value: 1.14e-03
                           10        20
                   ....*....|....*....|....*
gi 66812984    776 VLFYGPPGTGKTLLARALVNECNVG 800
Cdd:pfam05496   36 VLLYGPPGLGKTTLANIIANEMGVN 60
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
773-846 1.17e-03

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


Pssm-ID: 224401 [Multi-domain]  Cd Length: 254  Bit Score: 42.78  E-value: 1.17e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 66812984  773 PKGVLFYGPPGTGKTLLARALVNECNVGGQKVSFFmrKGADCLSKWvGEAERQLRLLFEQAKAM-QPSIIFFDEI 846
Cdd:COG1484  105 GENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFI--TAPDLLSKL-KAAFDEGRLEEKLLRELkKVDLLIIDDI 176
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit [Replication, ...
776-799 2.61e-03

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


Pssm-ID: 225164 [Multi-domain]  Cd Length: 332  Bit Score: 42.16  E-value: 2.61e-03
                         10        20
                 ....*....|....*....|....
gi 66812984  776 VLFYGPPGTGKTLLARALVNECNV 799
Cdd:COG2255   55 VLLFGPPGLGKTTLAHIIANELGV 78
ABC_ATPase cd00267
ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large ...
764-899 2.67e-03

ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213179 [Multi-domain]  Cd Length: 157  Bit Score: 40.31  E-value: 2.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  764 VFNKFKIQPPKG--VLFYGPPGTGKTLLARALVNECNVGGQKVSFFmrkGADCLSKWVGEAERQLRLLFE---------- 831
Cdd:cd00267   14 ALDNVSLTLKAGeiVALVGPNGSGKSTLLRAIAGLLKPTSGEILID---GKDIAKLPLEELRRRIGYVPQlsggqrqrva 90
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 66812984  832 --QAKAMQPSIIFFDEID-GLapvrssrqDQIHNSIVSTLLALMdgldNRGQVIVIGATNRIDSIDPALRR 899
Cdd:cd00267   91 laRALLLNPDLLLLDEPTsGL--------DPASRERLLELLREL----AEEGRTVIIVTHDPELAELAADR 149
RecA-like_IQCA1 cd19506
ATPase domain of IQ and AAA domain-containing protein 1 (IQCA1); IQCA1 (also known as dynein ...
749-889 4.65e-03

ATPase domain of IQ and AAA domain-containing protein 1 (IQCA1); IQCA1 (also known as dynein regulatory complex subunit 11, DRC11 and IQCA) is an ATPase subunit of the nexin-dynein regulatory complex (N-DRC). The 9 + 2 axoneme of most motile cilia and flagella consists of nine outer doublet microtubules arranged in a ring surrounding a central pair of two singlet microtubules. The N-DRC complex maintains alignment between outer doublet microtubules and limits microtubule sliding in motile axonemes. 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: 410914 [Multi-domain]  Cd Length: 160  Bit Score: 39.82  E-value: 4.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984  749 QLLKEMLMLPLLYPEVFNKFKIQppKGVLFYGPPGTGKTLLARALVNEcnVGGqkvSFFMRKGADCLSKWVGEAERQ--L 826
Cdd:cd19506    4 QLLTLYGILPLGSQAVHEKAPLV--KSLLLAGPSGVGKKMLVHAICTE--TGA---NLFNLSPSNIAGKYPGKNGLQmmL 76
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 66812984  827 RLLFEQAKAMQPSIIFFDEIDGLAPVRSSRQDQIHN--SIVSTLLALMDGLDNRGQVIVIGATNR 889
Cdd:cd19506   77 HLVLKVARQLQPSVIWIGDAEKTFYKKVPKTEKQLDpkRLKKDLPKILKSLKPEDRVLIVGTTSR 141
Mg_chelatase pfam01078
Magnesium chelatase, subunit ChlI; Magnesium-chelatase is a three-component enzyme that ...
776-793 5.75e-03

Magnesium chelatase, subunit ChlI; Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa.


Pssm-ID: 307292  Cd Length: 207  Bit Score: 40.21  E-value: 5.75e-03
                           10
                   ....*....|....*...
gi 66812984    776 VLFYGPPGTGKTLLARAL 793
Cdd:pfam01078   25 LLMIGPPGSGKTMLAKRL 42
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
1323-1369 6.05e-03

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: 37.77  E-value: 6.05e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 66812984 1323 PEYYELIKNPMSLQRISQNLDSYEYISLESFLKDIDLIVTNTELYYH 1369
Cdd:cd05513   32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNK 78
Activator_LAG-3 pfam11498
Transcriptional activator LAG-3; The C.elegans Notch pathway, involved in the control of ...
195-288 6.45e-03

Transcriptional activator LAG-3; The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1.


Pssm-ID: 151935  Cd Length: 476  Bit Score: 41.10  E-value: 6.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66812984    195 QQLKKQQ------PQENIGLGKFQHQIQQE-LQNKQHQKHIRYQQQQMKLEEEQKKFQPQRpQRQRVPPKSFSFEATLNG 267
Cdd:pfam11498  323 AQLAQQQnkmrllQQQEMEMQRIEQQRQQQiMHQHQQQQQQEHQQQQMLLQQQQQMHQLQQ-HHQMNGGGQFATQAHQHA 401
                           90       100
                   ....*....|....*....|..
gi 66812984    268 -YDDDIDEIHSNNRQRKKQNTN 288
Cdd:pfam11498  402 aYLQQMQHMRLQEQIQHQQQQA 423
 
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.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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