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Conserved domains on  [gi|2462574449|ref|XP_054198595|]
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ATPase family AAA domain-containing protein 2B isoform X10 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 401-570 1.25e-117

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: 358.75  E-value: 1.25e-117
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  401 SIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKKVAFFMRKGADCLSKWV 480
Cdd:cd19517      1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  481 GESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRR 560
Cdd:cd19517     81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160

                          170
                   ....*....|
gi 2462574449  561 PGRFDREFLF 570
Cdd:cd19517    161 PGRFDREFYF 170
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 960-1044 6.77e-46

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: 160.22  E-value: 6.77e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  960 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 1039
Cdd:cd05528      1 LRELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80


                   ....*
gi 2462574449 1040 DKDPG 1044
Cdd:cd05528     81 DRDPA 85
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 595-635 1.52e-10

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


:

Pssm-ID: 465537 [Multi-domain]  Cd Length: 45  Bit Score: 57.16  E-value: 1.52e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2462574449  595 DAFLGELAEKCVGYCGADIKALCTEAALIALRRRYPQIYAS 635
Cdd:pfam17862    1 DVDLEELAERTEGFSGADLEALCREAALAALRRGLEAVTQE 41
COG5076 super family cl34891
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 852-1038 9.69e-09

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


The actual alignment was detected with superfamily member COG5076:

Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 58.66  E-value: 9.69e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  852 LTLLQDIPSFS--PIFLLSTSETMYSELPEEVKcIFRIQYEEV-LYIQRPIEEDRRKFF-QELILNQASMAPPRRKHAAL 927
Cdd:COG5076     42 EEGSKNLFQKQlkRMPKEYITSIVDDREPGSMA-NVNDDLENVgGITYSPFEKNRPESLrFDEIVFLAIESVTPESGLGS 120

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  928 CAMEVLPLalPSPPRQLSESEKSRMEDQEENTLRELR-LFLRDVTKRlatdkrFNIFSKPVDIEEVSDYLEVIKEPMDLS 1006
Cdd:COG5076    121 LLMAHLKT--SVKKRKTPKIEDELLYADNKAIAKFKKqLFLRDGRFL------SSIFLGLPSKREYPDYYEIIKSPMDLL 192

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2462574449 1007 TVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:COG5076    193 TIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN 224
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 759-895 1.73e-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 cd19507:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 161  Bit Score: 43.13  E-value: 1.73e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  759 YHQPTsyrPR-LLLSGERGSGQtSHLAPALLHTLeRFSVHRLDLPALYSVSAKTPEESCAQIFREARRTVPSIVYMPHI- 836
Cdd:cd19507     26 YGLPT---PKgLLLVGIQGTGK-SLTAKAIAGVW-QLPLLRLDMGRLFGGLVGESESRLRQMIQTAEAIAPCVLWIDEIe 100

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574449  837 ---------GDwwEAVSETVRATFLTLLQDipSFSPIFLLSTSETMYSeLPEEVkcIFRIQYEEVLYI 895
Cdd:cd19507    101 kgfsnadskGD--SGTSSRVLGTFLTWLQE--KKKPVFVVATANNVQS-LPPEL--LRKGRFDEIFFV 161
 
Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 401-570 1.25e-117

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: 358.75  E-value: 1.25e-117
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  401 SIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKKVAFFMRKGADCLSKWV 480
Cdd:cd19517      1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  481 GESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRR 560
Cdd:cd19517     81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160

                          170
                   ....*....|
gi 2462574449  561 PGRFDREFLF 570
Cdd:cd19517    161 PGRFDREFYF 170
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 396-632 3.62e-92

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 297.30  E-value: 3.62e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  396 SVRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADC 475
Cdd:COG1222     74 DVTFDDIGGLDEQIEEIREAVELPLKNPELFRKYGIEPPKGVLLYGPPGTGKTLLAKAVAGEL-----GAPFIRVRGSEL 148

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  476 LSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSI 554
Cdd:COG1222    149 VSKYIGEGARNVREVFELAREKAPSIIFIDEIDAIAARRTDDGTsGEVQRTVNQLLAELDGFESRGDVLIIAATNRPDLL 228

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574449  555 DPALRRPGRFDREFLFNLPDQKARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGADIKALCTEAALIALRRRYPQI 632
Cdd:COG1222    229 DPALLRPGRFDRVIEVPLPDEEAREEILKIHLRD-MPLADDVDLDKLAKLTEGFSGADLKAIVTEAGMFAIREGRDTV 305
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 397-669 7.71e-78

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: 271.01  E-value: 7.71e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  397 VRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCL 476
Cdd:TIGR01243  175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG-----AYFISINGPEIM 249

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  477 SKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDP 556
Cdd:TIGR01243  250 SKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDP 329

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  557 ALRRPGRFDREFLFNLPDQKARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGADIKALCTEAALIALRRRYPQiyass 636
Cdd:TIGR01243  330 ALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIRE----- 403

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 2462574449  637 HKLQLDVSSI---VL-----SAQDFYHAMQNIVPASQRAVM 669
Cdd:TIGR01243  404 GKINFEAEEIpaeVLkelkvTMKDFMEALKMVEPSAIREVL 444
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 370-632 4.63e-70

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 238.96  E-value: 4.63e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  370 LASGILRERVKVGASLA---------DV-----DP----MNIDKS--VRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKF 429
Cdd:PRK03992    81 VSPFIDREKLKPGARVAlnqqslaivEVlpsekDPrvqaMEVIESpnVTYEDIGGLEEQIREVREAVELPLKKPELFEEV 160

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  430 KIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkvAFFMR-KGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEID 508
Cdd:PRK03992   161 GIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATFIRvVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEID 234

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  509 GLApvrSSRQDQIHS---SIVST---LLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHIL 582
Cdd:PRK03992   235 AIA---AKRTDSGTSgdrEVQRTlmqLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEIL 311

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 2462574449  583 QIHTRDWNPKlSDAFLGELAEKCVGYCGADIKALCTEAALIALRRRYPQI 632
Cdd:PRK03992   312 KIHTRKMNLA-DDVDLEELAELTEGASGADLKAICTEAGMFAIRDDRTEV 360
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 438-572 7.30e-47

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 163.53  E-value: 7.30e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  438 LFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSR 517
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKEL-----GAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSG 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  518 QDQIHSSIVSTLLALMDGLDNR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFNL 572
Cdd:pfam00004   77 GDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 960-1044 6.77e-46

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: 160.22  E-value: 6.77e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  960 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 1039
Cdd:cd05528      1 LRELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80


                   ....*
gi 2462574449 1040 DKDPG 1044
Cdd:cd05528     81 DRDPA 85
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 433-574 9.90e-19

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: 83.96  E-value: 9.90e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449   433 PPRGCLFYGPPGTGKTLVARALANECSQGDKKVAFF------------MRKGADCLSKWVGESERQLRLLFDQAYLMRPS 500
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIdgedileevldqLLLIIVGGKKASGSGELRLRLALALARKLKPD 80

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462574449   501 IIFFDEIDGLAPVRSSRQDQihssiVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPgRFDREFLFNLPD 574
Cdd:smart00382   81 VLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
BROMO smart00297
bromo domain;
960-1039 4.77e-18

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 80.40  E-value: 4.77e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449   960 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 1039
Cdd:smart00297    5 QKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNG 84
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 982-1039 2.32e-16

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 75.04  E-value: 2.32e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574449  982 IFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 1039
Cdd:pfam00439   16 PFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNG 73
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 595-635 1.52e-10

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


Pssm-ID: 465537 [Multi-domain]  Cd Length: 45  Bit Score: 57.16  E-value: 1.52e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2462574449  595 DAFLGELAEKCVGYCGADIKALCTEAALIALRRRYPQIYAS 635
Cdd:pfam17862    1 DVDLEELAERTEGFSGADLEALCREAALAALRRGLEAVTQE 41
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 852-1038 9.69e-09

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 58.66  E-value: 9.69e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  852 LTLLQDIPSFS--PIFLLSTSETMYSELPEEVKcIFRIQYEEV-LYIQRPIEEDRRKFF-QELILNQASMAPPRRKHAAL 927
Cdd:COG5076     42 EEGSKNLFQKQlkRMPKEYITSIVDDREPGSMA-NVNDDLENVgGITYSPFEKNRPESLrFDEIVFLAIESVTPESGLGS 120

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  928 CAMEVLPLalPSPPRQLSESEKSRMEDQEENTLRELR-LFLRDVTKRlatdkrFNIFSKPVDIEEVSDYLEVIKEPMDLS 1006
Cdd:COG5076    121 LLMAHLKT--SVKKRKTPKIEDELLYADNKAIAKFKKqLFLRDGRFL------SSIFLGLPSKREYPDYYEIIKSPMDLL 192

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2462574449 1007 TVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:COG5076    193 TIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN 224
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 759-895 1.73e-04

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: 43.13  E-value: 1.73e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  759 YHQPTsyrPR-LLLSGERGSGQtSHLAPALLHTLeRFSVHRLDLPALYSVSAKTPEESCAQIFREARRTVPSIVYMPHI- 836
Cdd:cd19507     26 YGLPT---PKgLLLVGIQGTGK-SLTAKAIAGVW-QLPLLRLDMGRLFGGLVGESESRLRQMIQTAEAIAPCVLWIDEIe 100

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574449  837 ---------GDwwEAVSETVRATFLTLLQDipSFSPIFLLSTSETMYSeLPEEVkcIFRIQYEEVLYI 895
Cdd:cd19507    101 kgfsnadskGD--SGTSSRVLGTFLTWLQE--KKKPVFVVATANNVQS-LPPEL--LRKGRFDEIFFV 161
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 437-513 9.22e-04

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


Pssm-ID: 439516  Cd Length: 232  Bit Score: 42.07  E-value: 9.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  437 CLFYGPPGTGKTLVARALANE-CSQGdKKVAFFmrKGADCLSKWvGESERQLRL--LFDQayLMRPSIIFFDEIdGLAPV 513
Cdd:NF038214    93 VLLLGPPGTGKTHLAIALGYAaCRQG-YRVRFT--TAADLVEQL-AQARADGRLgrLLRR--LARYDLLIIDEL-GYLPF 165
 
Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 401-570 1.25e-117

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: 358.75  E-value: 1.25e-117
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  401 SIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKKVAFFMRKGADCLSKWV 480
Cdd:cd19517      1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  481 GESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRR 560
Cdd:cd19517     81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160

                          170
                   ....*....|
gi 2462574449  561 PGRFDREFLF 570
Cdd:cd19517    161 PGRFDREFYF 170
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 396-632 3.62e-92

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 297.30  E-value: 3.62e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  396 SVRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADC 475
Cdd:COG1222     74 DVTFDDIGGLDEQIEEIREAVELPLKNPELFRKYGIEPPKGVLLYGPPGTGKTLLAKAVAGEL-----GAPFIRVRGSEL 148

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  476 LSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSI 554
Cdd:COG1222    149 VSKYIGEGARNVREVFELAREKAPSIIFIDEIDAIAARRTDDGTsGEVQRTVNQLLAELDGFESRGDVLIIAATNRPDLL 228

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574449  555 DPALRRPGRFDREFLFNLPDQKARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGADIKALCTEAALIALRRRYPQI 632
Cdd:COG1222    229 DPALLRPGRFDRVIEVPLPDEEAREEILKIHLRD-MPLADDVDLDKLAKLTEGFSGADLKAIVTEAGMFAIREGRDTV 305
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 401-570 1.40e-78

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: 254.14  E-value: 1.40e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  401 SIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWV 480
Cdd:cd19503      1 DIGGLDEQIASLKELIELPLKYPELFRALGLKPPRGVLLHGPPGTGKTLLARAVANEA-----GANFLSISGPSIVSKYL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  481 GESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRR 560
Cdd:cd19503     76 GESEKNLREIFEEARSHAPSIIFIDEIDALAPKREEDQREVERRVVAQLLTLMDGMSSRGKVVVIAATNRPDAIDPALRR 155

                          170
                   ....*....|
gi 2462574449  561 PGRFDREFLF 570
Cdd:cd19503    156 PGRFDREVEI 165
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 397-669 7.71e-78

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: 271.01  E-value: 7.71e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  397 VRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCL 476
Cdd:TIGR01243  175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG-----AYFISINGPEIM 249

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  477 SKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDP 556
Cdd:TIGR01243  250 SKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDP 329

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  557 ALRRPGRFDREFLFNLPDQKARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGADIKALCTEAALIALRRRYPQiyass 636
Cdd:TIGR01243  330 ALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIRE----- 403

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 2462574449  637 HKLQLDVSSI---VL-----SAQDFYHAMQNIVPASQRAVM 669
Cdd:TIGR01243  404 GKINFEAEEIpaeVLkelkvTMKDFMEALKMVEPSAIREVL 444
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 349-669 5.95e-75

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


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 262.54  E-value: 5.95e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  349 KSKSMARARnRCLP---MNFRAEDLASGILRErVKVGA-----SLADVDPMNIDK------SVRFDSIGGLSHHIHALKE 414
Cdd:TIGR01243  390 KEAAMAALR-RFIRegkINFEAEEIPAEVLKE-LKVTMkdfmeALKMVEPSAIREvlvevpNVRWSDIGGLEEVKQELRE 467

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  415 MVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGdkkvaFFMRKGADCLSKWVGESERQLRLLFDQA 494
Cdd:TIGR01243  468 AVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGAN-----FIAVRGPEILSKWVGESEKAIREIFRKA 542

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  495 YLMRPSIIFFDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLP 573
Cdd:TIGR01243  543 RQAAPAIIFFDEIDAIAPARGARFDTsVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPP 622

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  574 DQKARKHILQIHTRDWnPKLSDAFLGELAEKCVGYCGADIKALCTEAALIALRRrypqIYASSHKLQLDVSS------IV 647
Cdd:TIGR01243  623 DEEARKEIFKIHTRSM-PLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRE----SIGSPAKEKLEVGEeeflkdLK 697

                          330       340
                   ....*....|....*....|..
gi 2462574449  648 LSAQDFYHAMQNIVPASQRAVM 669
Cdd:TIGR01243  698 VEMRHFLEALKKVKPSVSKEDM 719
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 366-632 2.12e-73

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


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 248.67  E-value: 2.12e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  366 RAEDLASGILRERVKVGASLADVDPMNIDKSVRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGT 445
Cdd:COG0464    123 RESAEALALAAPLVTYEDIGGLEEELLELREAILDDLGGLEEVKEELRELVALPLKRPELREEYGLPPPRGLLLYGPPGT 202

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  446 GKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSI 525
Cdd:COG0464    203 GKTLLARALAGEL-----GLPLIEVDLSDLVSKYVGETEKNLREVFDKARGLAPCVLFIDEADALAGKRGEVGDGVGRRV 277

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  526 VSTLLALMDGLdnRGEIVVIGATNRLDSIDPALRRpgRFDREFLFNLPDQKARKHILQIHTRDwNPKLSDAFLGELAEKC 605
Cdd:COG0464    278 VNTLLTEMEEL--RSDVVVIAATNRPDLLDPALLR--RFDEIIFFPLPDAEERLEIFRIHLRK-RPLDEDVDLEELAEAT 352

                          250       260
                   ....*....|....*....|....*..
gi 2462574449  606 VGYCGADIKALCTEAALIALRRRYPQI 632
Cdd:COG0464    353 EGLSGADIRNVVRRAALQALRLGREPV 379
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 370-632 4.63e-70

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 238.96  E-value: 4.63e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  370 LASGILRERVKVGASLA---------DV-----DP----MNIDKS--VRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKF 429
Cdd:PRK03992    81 VSPFIDREKLKPGARVAlnqqslaivEVlpsekDPrvqaMEVIESpnVTYEDIGGLEEQIREVREAVELPLKKPELFEEV 160

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  430 KIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkvAFFMR-KGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEID 508
Cdd:PRK03992   161 GIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATFIRvVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEID 234

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  509 GLApvrSSRQDQIHS---SIVST---LLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHIL 582
Cdd:PRK03992   235 AIA---AKRTDSGTSgdrEVQRTlmqLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEIL 311

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 2462574449  583 QIHTRDWNPKlSDAFLGELAEKCVGYCGADIKALCTEAALIALRRRYPQI 632
Cdd:PRK03992   312 KIHTRKMNLA-DDVDLEELAELTEGASGADLKAICTEAGMFAIRDDRTEV 360
26Sp45 TIGR01242
26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an ...
 369-628 4.58e-63

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: 218.52  E-value: 4.58e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  369 DLASGILRERVKVGASLA---------DVDPMNID-----------KSVRFDSIGGLSHHIHALKEMVVFPLLYPEIFEK 428
Cdd:TIGR01242   71 NVSAFIDRKSLKPGARVAlnqqtltivDVLPTSKDplvkgmeveerPNVSYEDIGGLEEQIREIREAVELPLKHPELFEE 150

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  429 FKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkvAFFMR-KGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEI 507
Cdd:TIGR01242  151 VGIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATFIRvVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEI 224

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  508 DGLAPVR---SSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQI 584
Cdd:TIGR01242  225 DAIAAKRtdsGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKI 304

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....
gi 2462574449  585 HTRDWNPKlSDAFLGELAEKCVGYCGADIKALCTEAALIALRRR 628
Cdd:TIGR01242  305 HTRKMKLA-EDVDLEAIAKMTEGASGADLKAICTEAGMFAIREE 347
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 402-567 1.26e-61

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: 206.90  E-value: 1.26e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  402 IGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKWVG 481
Cdd:cd19519      2 IGGCRKQLAQIREMVELPLRHPELFKAIGIKPPRGILLYGPPGTGKTLIARAVANETG-----AFFFLINGPEIMSKLAG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  482 ESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRP 561
Cdd:cd19519     77 ESESNLRKAFEEAEKNAPAIIFIDEIDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRF 156


                   ....*.
gi 2462574449  562 GRFDRE 567
Cdd:cd19519    157 GRFDRE 162
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 411-566 1.09e-60

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: 204.05  E-value: 1.09e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  411 ALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLL 490
Cdd:cd19511      4 ELKEAVEWPLKHPDAFKRLGIRPPKGVLLYGPPGCGKTLLAKALASEA-----GLNFISVKGPELFSKYVGESERAVREI 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462574449  491 FDQAYLMRPSIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 566
Cdd:cd19511     79 FQKARQAAPCIIFFDEIDSLAPRRGQSDSsGVTDRVVSQLLTELDGIESLKGVVVIAATNRPDMIDPALLRPGRLDK 155
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 381-632 1.65e-60

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 213.86  E-value: 1.65e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  381 VGASLADVDP----MNIDKSV--RFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARAL 454
Cdd:PTZ00361   158 VGILLDEVDPlvsvMKVDKAPleSYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAV 237

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  455 ANECSqgdkkvAFFMR-KGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLAL- 532
Cdd:PTZ00361   238 ANETS------ATFLRvVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELl 311

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  533 --MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDWNPKlSDAFLGELAEKCVGYCG 610
Cdd:PTZ00361   312 nqLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLA-EDVDLEEFIMAKDELSG 390

                          250       260
                   ....*....|....*....|..
gi 2462574449  611 ADIKALCTEAALIALRRRYPQI 632
Cdd:PTZ00361   391 ADIKAICTEAGLLALRERRMKV 412
FtsH_fam TIGR01241
ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct ...
 394-632 4.54e-56

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: 202.52  E-value: 4.54e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  394 DKSVRFDSIGGLSHHIHALKEMVVFpLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALAnecsqGDKKVAFFMRKGA 473
Cdd:TIGR01241   49 KPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVA-----GEAGVPFFSISGS 122

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  474 DCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGlapVRSSRQDQI---HSSIVSTL---LALMDGLDNRGEIVVIGA 547
Cdd:TIGR01241  123 DFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDA---VGRQRGAGLgggNDEREQTLnqlLVEMDGFGTNTGVIVIAA 199

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  548 TNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRdwNPKLS-DAFLGELAEKCVGYCGADIKALCTEAALIALR 626
Cdd:TIGR01241  200 TNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAK--NKKLApDVDLKAVARRTPGFSGADLANLLNEAALLAAR 277


                   ....*.
gi 2462574449  627 RRYPQI 632
Cdd:TIGR01241  278 KNKTEI 283
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 412-566 1.29e-54

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: 186.93  E-value: 1.29e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  412 LKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGdkkvaFFMRKGADCLSKWVGESERQLRLLF 491
Cdd:cd19529      5 LKEAVEWPLLKPEVFKRLGIRPPKGILLYGPPGTGKTLLAKAVATESNAN-----FISVKGPELLSKWVGESEKAIREIF 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  492 DQAYLMRPSIIFFDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 566
Cdd:cd19529     80 RKARQVAPCVIFFDEIDSIAPRRGTTGDSgVTERVVNQLLTELDGLEEMNGVVVIAATNRPDIIDPALLRAGRFDR 155
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 399-566 7.74e-52

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


Pssm-ID: 410910 [Multi-domain]  Cd Length: 171  Bit Score: 179.46  E-value: 7.74e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  399 FDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkvAFFMR-KGADCLS 477
Cdd:cd19502      2 YEDIGGLDEQIREIREVVELPLKHPELFEELGIEPPKGVLLYGPPGTGKTLLAKAVANHTD------ATFIRvVGSELVQ 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  478 KWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLAL---MDGLDNRGEIVVIGATNRLDSI 554
Cdd:cd19502     76 KYIGEGARLVRELFEMAREKAPSIIFIDEIDAIGAKRFDSGTGGDREVQRTMLELlnqLDGFDPRGNIKVIMATNRPDIL 155

                          170
                   ....*....|..
gi 2462574449  555 DPALRRPGRFDR 566
Cdd:cd19502    156 DPALLRPGRFDR 167
pup_AAA TIGR03689
proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some ...
 370-668 5.56e-51

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


Pssm-ID: 200312 [Multi-domain]  Cd Length: 512  Bit Score: 188.38  E-value: 5.56e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  370 LASGILRERVKVGASLAdVDPMN------IDKS------------VRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKI 431
Cdd:TIGR03689  135 LAGALADEGLRPGDTLL-VDPRAgyafeaIPRTevedlvleevpdVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGL 213

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  432 QPPRGCLFYGPPGTGKTLVARALANECSQ-----GDKKVAFFMRKGADCLSKWVGESERQLRLLFDQAYLM----RPSII 502
Cdd:TIGR03689  214 KPPKGVLLYGPPGCGKTLIAKAVANSLAArigaeGGGKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKasegRPVIV 293

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  503 FFDEIDGLAPVRSS-RQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHI 581
Cdd:TIGR03689  294 FFDEMDSLFRTRGSgVSSDVETTVVPQLLAEIDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADI 373

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  582 LQIHTRDWNPklsdaFLGELAEKcVGYCGADIKALcteaaliaLRRRYPQIYASS---HKLQL---DVSSIVLSAQDFYH 655
Cdd:TIGR03689  374 FAKYLTDDLP-----LPEDLAAH-DGDREATAAAL--------IQRVVDALYARSeanRYVEVtyaNGSTEVLYFADFVS 439

                          330
                   ....*....|....*.
gi 2462574449  656 -AM-QNIVP-ASQRAV 668
Cdd:TIGR03689  440 gAMlANIVDrAKKRAI 455
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 412-566 3.56e-50

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: 174.24  E-value: 3.56e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  412 LKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLLF 491
Cdd:cd19528      5 LQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC-----QANFISVKGPELLTMWFGESEANVRDIF 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574449  492 DQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSS---IVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 566
Cdd:cd19528     80 DKARAAAPCVLFFDELDSIAKARGGNIGDAGGAadrVINQILTEMDGMNTKKNVFIIGATNRPDIIDPAILRPGRLDQ 157
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 401-567 4.40e-50

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


Pssm-ID: 410926 [Multi-domain]  Cd Length: 169  Bit Score: 174.52  E-value: 4.40e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  401 SIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWV 480
Cdd:cd19518      1 DIGGMDSTLKELCELLIHPILPPEYFQHLGVEPPRGVLLHGPPGCGKTMLANAIAGEL-----KVPFLKISATEIVSGVS 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  481 GESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL----DNRGEIVVIGATNRLDSIDP 556
Cdd:cd19518     76 GESEEKIRELFDQAISNAPCIVFIDEIDAITPKRESAQREMERRIVSQLLTCMDELnnekTAGGPVLVIGATNRPDSLDP 155

                          170
                   ....*....|.
gi 2462574449  557 ALRRPGRFDRE 567
Cdd:cd19518    156 ALRRAGRFDRE 166
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 372-629 5.14e-49

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


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 179.57  E-value: 5.14e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  372 SGILRERVKVGASLA---------DVDPMNIDKSVR-----------FDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKI 431
Cdd:PTZ00454    97 STLNRELLKPNASVAlhrhshavvDILPPEADSSIQllqmsekpdvtYSDIGGLDIQKQEIREAVELPLTCPELYEQIGI 176

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  432 QPPRGCLFYGPPGTGKTLVARALANEcsqgdKKVAFFMRKGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLA 511
Cdd:PTZ00454   177 DPPRGVLLYGPPGTGKTMLAKAVAHH-----TTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIA 251

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  512 PVRSSRQ---DQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRD 588
Cdd:PTZ00454   252 TKRFDAQtgaDREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSK 331

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|...
gi 2462574449  589 WNpkLSDAF-LGELAEKCVGYCGADIKALCTEAALIALRR-RY 629
Cdd:PTZ00454   332 MN--LSEEVdLEDFVSRPEKISAADIAAICQEAGMQAVRKnRY 372
ftsH CHL00176
cell division protein; Validated
 366-632 2.50e-48

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 183.33  E-value: 2.50e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  366 RAEDLASGILRERVKVGASLADVDpMNIDKSVRFDSIGGlshhIHALK---EMVVFPLLYPEIFEKFKIQPPRGCLFYGP 442
Cdd:CHL00176   150 RSSNFKGGPGQNLMNFGKSKARFQ-MEADTGITFRDIAG----IEEAKeefEEVVSFLKKPERFTAVGAKIPKGVLLVGP 224

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  443 PGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSR----Q 518
Cdd:CHL00176   225 PGTGKTLLAKAIAGEAE-----VPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGigggN 299

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  519 DQiHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRdwNPKL-SDAF 597
Cdd:CHL00176   300 DE-REQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHAR--NKKLsPDVS 376

                          250       260       270
                   ....*....|....*....|....*....|....*
gi 2462574449  598 LGELAEKCVGYCGADIKALCTEAALIALRRRYPQI 632
Cdd:CHL00176   377 LELIARRTPGFSGADLANLLNEAAILTARRKKATI 411
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
424-626 3.26e-47

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 169.29  E-value: 3.26e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  424 EIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLLFDQAYLmRPSIIF 503
Cdd:COG1223     25 ENLRKFGLWPPRKILFYGPPGTGKTMLAEALAGEL-----KLPLLTVRLDSLIGSYLGETARNLRKLFDFARR-APCVIF 98

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  504 FDEIDGLAPVRSSRQD--QIHsSIVSTLLALMDGLdnRGEIVVIGATNRLDSIDPALRRpgRFDREFLFNLPDQKARKHI 581
Cdd:COG1223     99 FDEFDAIAKDRGDQNDvgEVK-RVVNALLQELDGL--PSGSVVIAATNHPELLDSALWR--RFDEVIEFPLPDKEERKEI 173

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 2462574449  582 LQIHTRDWNPKLSDAfLGELAEKCVGYCGADIKALCTEAALIALR 626
Cdd:COG1223    174 LELNLKKFPLPFELD-LKKLAKKLEGLSGADIEKVLKTALKKAIL 217
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 412-570 5.17e-47

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: 165.15  E-value: 5.17e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  412 LKEMVVFPLLYPEiFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLLF 491
Cdd:cd19481      5 LREAVEAPRRGSR-LRRYGLGLPKGILLYGPPGTGKTLLAKALAGEL-----GLPLIVVKLSSLLSKYVGESEKNLRKIF 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  492 DQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSS-IVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 570
Cdd:cd19481     79 ERARRLAPCILFIDEIDAIGRKRDSSGESGELRrVLNQLLTELDGVNSRSKVLVIAATNRPDLLDPALLRPGRFDEVIEF 158
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 438-572 7.30e-47

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 163.53  E-value: 7.30e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  438 LFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSR 517
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKEL-----GAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSG 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  518 QDQIHSSIVSTLLALMDGLDNR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFNL 572
Cdd:pfam00004   77 GDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 405-566 1.52e-46

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


Pssm-ID: 410938 [Multi-domain]  Cd Length: 161  Bit Score: 164.20  E-value: 1.52e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  405 LSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESE 484
Cdd:cd19530      1 LDHVREELTMSILRPIKRPDIYKALGIDLPTGVLLYGPPGCGKTLLAKAVANES-----GANFISVKGPELLNKYVGESE 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  485 RQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRF 564
Cdd:cd19530     76 RAVRQVFQRARASAPCVIFFDEVDALVPKRGDGGSWASERVVNQLLTEMDGLEERSNVFVIAATNRPDIIDPAMLRPGRL 155


                   ..
gi 2462574449  565 DR 566
Cdd:cd19530    156 DK 157
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
390-628 1.86e-46

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


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 176.38  E-value: 1.86e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  390 PMNIDKS-----------VRFDSIGGLSHHIHALKEMVVFpLLYPEIFEKF--KIqpPRGCLFYGPPGTGKTLVARALAN 456
Cdd:COG0465    121 AMSFGKSkaklydedkpkVTFDDVAGVDEAKEELQEIVDF-LKDPEKFTRLgaKI--PKGVLLVGPPGTGKTLLAKAVAG 197

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  457 ECsqgdkKVAFF---------MRKGadclskwVGESeRqLRLLFDQAYLMRPSIIFFDEIDGLAPVRSS--------RqD 519
Cdd:COG0465    198 EA-----GVPFFsisgsdfveMFVG-------VGAS-R-VRDLFEQAKKNAPCIIFIDEIDAVGRQRGAglggghdeR-E 262

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  520 QihssivsTL---LALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRdwNPKLS-D 595
Cdd:COG0465    263 Q-------TLnqlLVEMDGFEGNEGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDVKGREAILKVHAR--KKPLApD 333

                          250       260       270
                   ....*....|....*....|....*....|...
gi 2462574449  596 AFLGELAEKCVGYCGADIKALCTEAALIALRRR 628
Cdd:COG0465    334 VDLEVIARRTPGFSGADLANLVNEAALLAARRN 366
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 960-1044 6.77e-46

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: 160.22  E-value: 6.77e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  960 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 1039
Cdd:cd05528      1 LRELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80


                   ....*
gi 2462574449 1040 DKDPG 1044
Cdd:cd05528     81 DRDPA 85
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 402-569 1.07e-44

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: 158.67  E-value: 1.07e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  402 IGGLSHHIHALKEMVVFPLLYPEIFeKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKWVG 481
Cdd:cd19509      1 IAGLDDAKEALKEAVILPSLRPDLF-PGLRGPPRGILLYGPPGTGKTLLARAVASESG-----STFFSISASSLVSKWVG 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  482 ESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGE--IVVIGATNRLDSIDPALR 559
Cdd:cd19509     75 ESEKIVRALFALARELQPSIIFIDEIDSLLSERGSGEHEASRRVKTEFLVQMDGVLNKPEdrVLVLGATNRPWELDEAFL 154

                          170
                   ....*....|
gi 2462574449  560 RpgRFDREFL 569
Cdd:cd19509    155 R--RFEKRIY 162
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 397-567 2.04e-44

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: 158.16  E-value: 2.04e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  397 VRFDSIGGLSHHIHALKEMVVFpLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCL 476
Cdd:cd19501      1 VTFKDVAGCEEAKEELKEVVEF-LKNPEKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA-----GVPFFSISGSDFV 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  477 SKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTL---LALMDGLDNRGEIVVIGATNRLDS 553
Cdd:cd19501     75 EMFVGVGASRVRDLFEQAKKNAPCIVFIDEIDAVGRKRGAGLGGGHDEREQTLnqlLVEMDGFESNTGVIVIAATNRPDV 154

                          170
                   ....*....|....
gi 2462574449  554 IDPALRRPGRFDRE 567
Cdd:cd19501    155 LDPALLRPGRFDRQ 168
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
399-626 2.94e-41

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 162.13  E-value: 2.94e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  399 FDSIGGLSHHIHALKEMVVFpLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALAnecsqGDKKVAFFMRKGADCLSK 478
Cdd:PRK10733   151 FADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIA-----GEAKVPFFTISGSDFVEM 224

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  479 WVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTL---LALMDGLDNRGEIVVIGATNRLDSID 555
Cdd:PRK10733   225 FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLnqmLVEMDGFEGNEGIIVIAATNRPDVLD 304

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462574449  556 PALRRPGRFDREFLFNLPDQKARKHILQIHTRDWnPKLSDAFLGELAEKCVGYCGADIKALCTEAALIALR 626
Cdd:PRK10733   305 PALLRPGRFDRQVVVGLPDVRGREQILKVHMRRV-PLAPDIDAAIIARGTPGFSGADLANLVNEAALFAAR 374
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 414-566 3.98e-41

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: 148.43  E-value: 3.98e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  414 EMVVFPLLYPEIFEKfKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKWVGESERQLRLLFDQ 493
Cdd:cd19527      7 DTIQLPLEHPELFSS-GLRKRSGILLYGPPGTGKTLLAKAIATECS-----LNFLSVKGPELINMYIGESEANVREVFQK 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  494 AYLMRPSIIFFDEIDGLAPVRSSRQDQ--IHSSIVSTLLALMDGLDNRGE-IVVIGATNRLDSIDPALRRPGRFDR 566
Cdd:cd19527     81 ARDAKPCVIFFDELDSLAPSRGNSGDSggVMDRVVSQLLAELDGMSSSGQdVFVIGATNRPDLLDPALLRPGRFDK 156
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 411-566 3.68e-40

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


Pssm-ID: 410934 [Multi-domain]  Cd Length: 158  Bit Score: 145.65  E-value: 3.68e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  411 ALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKWVGESERQLRLL 490
Cdd:cd19526      4 ALEETIEWPSKYPKIFASSPLRLRSGILLYGPPGCGKTLLASAIASECG-----LNFISVKGPELLNKYIGASEQNVRDL 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  491 FDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 566
Cdd:cd19526     79 FSRAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDK 154
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
 384-560 2.51e-37

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


Pssm-ID: 410933 [Multi-domain]  Cd Length: 186  Bit Score: 138.58  E-value: 2.51e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  384 SLADVDPMNIDKSVRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKiQPPRGCLFYGPPGTGKTLVARALANECsqgdk 463
Cdd:cd19525      6 ELIMSEIMDHGPPINWADIAGLEFAKKTIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQS----- 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  464 KVAFFMRKGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGE-- 541
Cdd:cd19525     80 GATFFSISASSLTSKWVGEGEKMVRALFSVARCKQPAVIFIDEIDSLLSQRGEGEHESSRRIKTEFLVQLDGATTSSEdr 159

                          170
                   ....*....|....*....
gi 2462574449  542 IVVIGATNRLDSIDPALRR 560
Cdd:cd19525    160 ILVVGATNRPQEIDEAARR 178
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 401-564 2.80e-37

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: 137.56  E-value: 2.80e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  401 SIGGLSHHIHALKEMVVFPLLYPEIFEKFKI-QPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKW 479
Cdd:cd19520      1 DIGGLDEVITELKELVILPLQRPELFDNSRLlQPPKGVLLYGPPGCGKTMLAKATAKEAG-----ARFINLQVSSLTDKW 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  480 VGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRG--EIVVIGATNRLDSIDPA 557
Cdd:cd19520     76 YGESQKLVAAVFSLASKLQPSIIFIDEIDSFLRQRSSTDHEATAMMKAEFMSLWDGLSTDGncRVIVMGATNRPQDLDEA 155


                   ....*....
gi 2462574449  558 LRR--PGRF 564
Cdd:cd19520    156 ILRrmPKRF 164
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 396-566 2.22e-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: 132.29  E-value: 2.22e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  396 SVRFDSIGGLSHHIHALKEMVVFPLLYPEIFeKFKIQPPRGCLFYGPPGTGKTLVARALANECSQgdkkvAFFMRKGADC 475
Cdd:cd19521      3 NVKWEDVAGLEGAKEALKEAVILPVKFPHLF-TGNRKPWSGILLYGPPGTGKSYLAKAVATEANS-----TFFSVSSSDL 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  476 LSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGE-IVVIGATNRLDSI 554
Cdd:cd19521     77 VSKWMGESEKLVKQLFAMARENKPSIIFIDEVDSLCGTRGEGESEASRRIKTELLVQMNGVGNDSQgVLVLGATNIPWQL 156

                          170
                   ....*....|..
gi 2462574449  555 DPALRRpgRFDR 566
Cdd:cd19521    157 DSAIRR--RFEK 166
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
 417-565 2.27e-35

first of two ATPase domains of NSF and SEC18, and similar ATPase domains; N-ethylmaleimide-sensitive factor (NSF) and Saccharomyces cerevisiae Vesicular-fusion protein Sec18, key factors for eukaryotic trafficking, are ATPases and SNARE disassembly chaperones. NSF/Sec18 activate or prime SNAREs, the terminal catalysts of membrane fusion. Sec18/NSF associates with SNARE complexes through binding Sec17/alpha-SNAP. Sec18 has an N-terminal cap domain and two nucleotide-binding domains (D1 and D2) which form the two rings of the hexameric complex. The hydrolysis of ATP by D1 generates most of the energy necessary to disassemble inactive SNARE bundles, while the D2 ring binds ATP to stabilize the homohexamer. This subfamily includes the first (D1) ATPase domain of NSF/Sec18, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410912 [Multi-domain]  Cd Length: 177  Bit Score: 132.61  E-value: 2.27e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  417 VFPllyPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKKVAffmrKGADCLSKWVGESERQLRLLF----- 491
Cdd:cd19504     21 VFP---PEIVEQLGCKHVKGILLYGPPGTGKTLMARQIGKMLNAREPKIV----NGPEILNKYVGESEANIRKLFadaee 93

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462574449  492 DQAYLMRPS---IIFFDEIDGLAPVRSSRQDQ--IHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFD 565
Cdd:cd19504     94 EQRRLGANSglhIIIFDEIDAICKQRGSMAGStgVHDTVVNQLLSKIDGVEQLNNILVIGMTNRKDLIDEALLRPGRLE 172
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 402-560 1.04e-33

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


Pssm-ID: 410930 [Multi-domain]  Cd Length: 170  Bit Score: 127.79  E-value: 1.04e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  402 IGGLSHHIHALKEMVVFPLLYPEIFEKFKiQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVG 481
Cdd:cd19522      2 IADLEEAKKLLEEAVVLPMWMPEFFKGIR-RPWKGVLMVGPPGTGKTLLAKAVATEC-----GTTFFNVSSSTLTSKYRG 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  482 ESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIV-STLLALMDGLDNRGE-------IVVIGATNRLDS 553
Cdd:cd19522     76 ESEKLVRLLFEMARFYAPTTIFIDEIDSICSRRGTSEEHEASRRVkSELLVQMDGVGGASEnddpskmVMVLAATNFPWD 155


                   ....*..
gi 2462574449  554 IDPALRR 560
Cdd:cd19522    156 IDEALRR 162
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 402-560 2.48e-32

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


Pssm-ID: 410932 [Multi-domain]  Cd Length: 164  Bit Score: 123.42  E-value: 2.48e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  402 IGGLSHHIHALKEMVVFPLLYPEIFEKFKiQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVG 481
Cdd:cd19524      2 IAGQDLAKQALQEMVILPSLRPELFTGLR-APARGLLLFGPPGNGKTMLAKAVAAES-----NATFFNISAASLTSKYVG 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  482 ESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGE--IVVIGATNRLDSIDPA-L 558
Cdd:cd19524     76 EGEKLVRALFAVARELQPSIIFIDEVDSLLSERSEGEHEASRRLKTEFLIEFDGVQSNGDdrVLVMGATNRPQELDDAvL 155


                   ..
gi 2462574449  559 RR 560
Cdd:cd19524    156 RR 157
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 430-572 1.57e-26

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: 106.46  E-value: 1.57e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  430 KIQPPRGCLFYGPPGTGKTLVARALANECSqgDKKVAFFMRKGADCLSKWVGESERQ---LRLLFDQAYLMRPSIIFFDE 506
Cdd:cd00009     15 ELPPPKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDLLEGLVVAELFGhflVRLLFELAEKAKPGVLFIDE 92

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  507 IDGLAPvrssrqdQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNL 572
Cdd:cd00009     93 IDSLSR-------GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151
RecA-like_fidgetin cd19523
ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. ...
 402-569 6.33e-26

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: 104.97  E-value: 6.33e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  402 IGGLSHHIHALKEMVVFPLLYPEIFEKFkIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKWVG 481
Cdd:cd19523      2 IAGLGALKAAIKEEVLWPLLRPDAFSGL-LRLPRSILLFGPRGTGKTLLGRCLASQLG-----ATFLRLRGSTLVAKWAG 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  482 ESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIhSSIVSTLLALMDGLDNRGE--IVVIGATNRLDSIDPALR 559
Cdd:cd19523     76 EGEKILQASFLAARCRQPSVLFISDLDALLSSQDDEASPV-GRLQVELLAQLDGVLGSGEdgVLVVCTTSKPEEIDESLR 154

                          170
                   ....*....|
gi 2462574449  560 RpgRFDREFL 569
Cdd:cd19523    155 R--YFSKRLL 162
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 960-1043 1.04e-21

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: 90.89  E-value: 1.04e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  960 LRELRLFLRDVTKRLATDkRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 1039
Cdd:cd04369      1 LKKKLRSLLDALKKLKRD-LSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNG 79


                   ....
gi 2462574449 1040 DKDP 1043
Cdd:cd04369     80 PGSP 83
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 963-1038 9.47e-20

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: 85.14  E-value: 9.47e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  963 LRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:cd05512      2 LEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN 77
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 983-1043 1.35e-19

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


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 84.91  E-value: 1.35e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462574449  983 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDP 1043
Cdd:cd05509     22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTE 82
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 433-574 9.90e-19

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: 83.96  E-value: 9.90e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449   433 PPRGCLFYGPPGTGKTLVARALANECSQGDKKVAFF------------MRKGADCLSKWVGESERQLRLLFDQAYLMRPS 500
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIdgedileevldqLLLIIVGGKKASGSGELRLRLALALARKLKPD 80

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462574449   501 IIFFDEIDGLAPVRSSRQDQihssiVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPgRFDREFLFNLPD 574
Cdd:smart00382   81 VLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 966-1043 2.75e-18

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: 81.17  E-value: 2.75e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  966 FLRDVTKRLATDKRFNI---FSKPVDIE--EVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPD 1040
Cdd:cd05498      4 FCSGILKELFSKKHKAYawpFYKPVDPEalGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPP 83


                   ...
gi 2462574449 1041 KDP 1043
Cdd:cd05498     84 DHP 86
BROMO smart00297
bromo domain;
960-1039 4.77e-18

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 80.40  E-value: 4.77e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449   960 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 1039
Cdd:smart00297    5 QKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNG 84
ycf46 CHL00195
Ycf46; Provisional
 434-665 6.93e-18

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 88.15  E-value: 6.93e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  434 PRGCLFYGPPGTGKTLVARALANECSQGDKKVAFfmrkgADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPV 513
Cdd:CHL00195   259 PRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDV-----GKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSN 333

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  514 RSSRQDQIHSSIV-STLLALMDglDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDWNPK 592
Cdd:CHL00195   334 SESKGDSGTTNRVlATFITWLS--EKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPK 411

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  593 LSDAF-LGELAEKCVGYCGADIKALCTEAALIAL--RRRYpqiyasshklqldvssivlSAQDFYHAMQNIVPASQ 665
Cdd:CHL00195   412 SWKKYdIKKLSKLSNKFSGAEIEQSIIEAMYIAFyeKREF-------------------TTDDILLALKQFIPLAQ 468
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 427-568 2.04e-16

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: 77.79  E-value: 2.04e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  427 EKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKKV---AFFmrkgadclSKWVGESERQLRLLFDQAYLMRPSIIF 503
Cdd:cd19507     24 SAYGLPTPKGLLLVGIQGTGKSLTAKAIAGVWQLPLLRLdmgRLF--------GGLVGESESRLRQMIQTAEAIAPCVLW 95

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  504 FDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDglDNRGEIVVIGATNRLDSIDPALRRPGRFDREF 568
Cdd:cd19507     96 IDEIEKGFSNADSKGDSgTSSRVLGTFLTWLQ--EKKKPVFVVATANNVQSLPPELLRKGRFDEIF 159
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 982-1039 2.32e-16

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 75.04  E-value: 2.32e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574449  982 IFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 1039
Cdd:pfam00439   16 PFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNG 73
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 983-1038 2.76e-15

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


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 72.68  E-value: 2.76e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  983 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:cd05511     21 FHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYN 76
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 972-1043 1.02e-14

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: 70.82  E-value: 1.02e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462574449  972 KRLATDKRFNIFSKPVDIE--EVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDP 1043
Cdd:cd05506     10 RKLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGND 83
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 952-1042 8.39e-14

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


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 68.62  E-value: 8.39e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  952 MEDQEENTLRELRLFLRDVTKrlatdkrfniFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLIC 1031
Cdd:cd05510      8 FYESLDKVLNELKTYTEHSTP----------FLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIW 77

                           90
                   ....*....|.
gi 2462574449 1032 SNALEYNPDKD 1042
Cdd:cd05510     78 KNCLLYNSDPS 88
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 962-1043 6.87e-13

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: 65.77  E-value: 6.87e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  962 ELRlFLRDVTKRLATDKRFNI---FSKPVDieEVSD----YLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNA 1034
Cdd:cd05499      1 ELK-FCEEVLKELMKPKHSAYnwpFLDPVD--PVALnipnYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNC 77


                   ....*....
gi 2462574449 1035 LEYNPDKDP 1043
Cdd:cd05499     78 YTFNPEGTD 86
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 983-1041 2.13e-12

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: 64.79  E-value: 2.13e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462574449  983 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDK 1041
Cdd:cd05496     26 FRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNK 84
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 435-566 1.18e-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: 63.91  E-value: 1.18e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  435 RGCLFYGPPGTGKTLVARALANECsqgDKKVaffmrkgadC---LSKwVGESERQLRLLFDQAylMRPSIIFFDEID--- 508
Cdd:cd19510     24 RGYLLYGPPGTGKSSFIAALAGEL---DYDI---------CdlnLSE-VVLTDDRLNHLLNTA--PKQSIILLEDIDaaf 88

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462574449  509 --GLAPVRSSRQDQIHSSI-VSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 566
Cdd:cd19510     89 esREHNKKNPSAYGGLSRVtFSGLLNALDGVASSEERIVFMTTNHIERLDPALIRPGRVDM 149
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 983-1042 1.71e-11

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


Pssm-ID: 99936  Cd Length: 115  Bit Score: 62.03  E-value: 1.71e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  983 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKD 1042
Cdd:cd05504     33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHT 92
T7SS_EccA TIGR03922
type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the ...
 438-570 2.41e-11

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


Pssm-ID: 188437 [Multi-domain]  Cd Length: 557  Bit Score: 67.56  E-value: 2.41e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  438 LFYGPPGTGKTLVARALANE-CSQG---DKKVAFFMRkgADCLSKWVGESERQLRLLFDQAYlmrPSIIFFDEIDGLAPV 513
Cdd:TIGR03922  316 LFAGPPGTGKTTIARVVAKIyCGLGvlrKPLVREVSR--ADLIGQYIGESEAKTNEIIDSAL---GGVLFLDEAYTLVET 390

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462574449  514 RSSRQDQIHSSIVSTLLALMDglDNRGEIVVIGA--TNRLD---SIDPALRRpgRFDREFLF 570
Cdd:TIGR03922  391 GYGQKDPFGLEAIDTLLARME--NDRDRLVVIGAgyRKDLDkflEVNEGLRS--RFTRVIEF 448
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 983-1038 6.73e-11

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


Pssm-ID: 99945  Cd Length: 98  Bit Score: 59.73  E-value: 6.73e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  983 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:cd05513     22 FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYN 77
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 983-1038 8.53e-11

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: 59.47  E-value: 8.53e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  983 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:cd05505     21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYY 76
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 595-635 1.52e-10

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


Pssm-ID: 465537 [Multi-domain]  Cd Length: 45  Bit Score: 57.16  E-value: 1.52e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2462574449  595 DAFLGELAEKCVGYCGADIKALCTEAALIALRRRYPQIYAS 635
Cdd:pfam17862    1 DVDLEELAERTEGFSGADLEALCREAALAALRRGLEAVTQE 41
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 962-1039 2.65e-10

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: 58.61  E-value: 2.65e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  962 ELRLFLRDVTKRLATDKRFNI-FSKPVD--IEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:cd05495      3 ELRQALMPTLEKLYKQDPESLpFRQPVDpkLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYN 82


                   .
gi 2462574449 1039 P 1039
Cdd:cd05495     83 R 83
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 971-1038 2.75e-10

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: 58.48  E-value: 2.75e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  971 TKRLaTDKRFniFSKPVDIEE--VSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:cd05500     16 LKRL-KDARP--FLVPVDPVKlnIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFN 82
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
 438-558 4.97e-10

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


Pssm-ID: 410916 [Multi-domain]  Cd Length: 199  Bit Score: 60.15  E-value: 4.97e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  438 LFYGPPGTGKTLVARALANECSqgdKKVAFFMRKG-------ADCLSKWVGESERQLRLLFDQAYLM---RPSIIF--FD 505
Cdd:cd19508     56 LLHGPPGTGKTSLCKALAQKLS---IRLSSRYRYGqlieinsHSLFSKWFSESGKLVTKMFQKIQELiddKDALVFvlID 132

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462574449  506 EIDGLAPVRSSRQDQIHSS----IVSTLLALMDGLDNRGEIVVIGATNRLDSIDPAL 558
Cdd:cd19508    133 EVESLAAARSASSSGTEPSdairVVNAVLTQIDRIKRYHNNVILLTSNLLEKIDVAF 189
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 983-1043 2.11e-09

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


Pssm-ID: 99935  Cd Length: 97  Bit Score: 55.46  E-value: 2.11e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462574449  983 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDP 1043
Cdd:cd05503     21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSE 81
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 852-1038 9.69e-09

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 58.66  E-value: 9.69e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  852 LTLLQDIPSFS--PIFLLSTSETMYSELPEEVKcIFRIQYEEV-LYIQRPIEEDRRKFF-QELILNQASMAPPRRKHAAL 927
Cdd:COG5076     42 EEGSKNLFQKQlkRMPKEYITSIVDDREPGSMA-NVNDDLENVgGITYSPFEKNRPESLrFDEIVFLAIESVTPESGLGS 120

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  928 CAMEVLPLalPSPPRQLSESEKSRMEDQEENTLRELR-LFLRDVTKRlatdkrFNIFSKPVDIEEVSDYLEVIKEPMDLS 1006
Cdd:COG5076    121 LLMAHLKT--SVKKRKTPKIEDELLYADNKAIAKFKKqLFLRDGRFL------SSIFLGLPSKREYPDYYEIIKSPMDLL 192

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2462574449 1007 TVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:COG5076    193 TIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN 224
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 962-1042 1.47e-08

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


Pssm-ID: 99929  Cd Length: 107  Bit Score: 53.58  E-value: 1.47e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  962 ELRLFLRDVTKRLATDKRFNIFSKPVDIE--EVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 1039
Cdd:cd05497      5 QLQYLLKVVLKALWKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNK 84


                   ...
gi 2462574449 1040 DKD 1042
Cdd:cd05497     85 PGD 87
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 970-1042 2.09e-08

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


Pssm-ID: 99939  Cd Length: 104  Bit Score: 53.14  E-value: 2.09e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462574449  970 VTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN-PDKD 1042
Cdd:cd05507     11 VYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNsSDHD 84
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 960-1040 2.13e-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: 2.13e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  960 LRELRLFLRDVT----KRLATdkrfnIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNAL 1035
Cdd:cd05515      5 LWELYNAVKNYTdgrgRRLSL-----IFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNAC 79


                   ....*.
gi 2462574449 1036 EYN-PD 1040
Cdd:cd05515     80 KYNePD 85
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 983-1041 3.00e-08

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


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 52.68  E-value: 3.00e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462574449  983 FSKPVDiEEVSDYLEVIKEPMDLSTVITKIDKHN---YLTAKDFLKDIDLICSNALEYNPDK 1041
Cdd:cd05502     25 FHEPVS-PSVPNYYKIIKTPMDLSLIRKKLQPKSpqhYSSPEEFVADVRLMFKNCYKFNEED 85
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 438-580 6.36e-08

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


Pssm-ID: 400187 [Multi-domain]  Cd Length: 168  Bit Score: 53.35  E-value: 6.36e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  438 LFYGPPGTGKTLVARALANEcsQGDKKVAF-------FMRKGAdcLSKWVGESERQLR-----LLFDQAYLMRPSIIFFD 505
Cdd:pfam07724    7 LFLGPTGVGKTELAKALAEL--LFGDERALiridmseYMEEHS--VSRLIGAPPGYVGyeeggQLTEAVRRKPYSIVLID 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  506 EIdglapvrssrqDQIHSSIVSTLLALMDG---LDNRGE------IVVIGATNrLDSIDP--ALRRPGRFDREFLFNLPD 574
Cdd:pfam07724   83 EI-----------EKAHPGVQNDLLQILEGgtlTDKQGRtvdfknTLFIMTGN-FGSEKIsdASRLGDSPDYELLKEEVM 150


                   ....*.
gi 2462574449  575 QKARKH 580
Cdd:pfam07724  151 DLLKKG 156
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 435-565 2.51e-07

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


Pssm-ID: 410920 [Multi-domain]  Cd Length: 150  Bit Score: 51.37  E-value: 2.51e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  435 RGCLFYGPPGTGKTLVARALANEC-------SQGDkkVAFFMRKGADCLSK---WVGESERQLrllfdqaylmrpsIIFF 504
Cdd:cd19512     23 RNILFYGPPGTGKTLFAKKLALHSgmdyaimTGGD--VAPMGREGVTAIHKvfdWANTSRRGL-------------LLFV 87

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462574449  505 DEIDGLAPVRSSrqDQIHSSIVSTLLALM--DGLDNRgEIVVIGATNRLDSIDPALRrpGRFD 565
Cdd:cd19512     88 DEADAFLRKRST--EKISEDLRAALNAFLyrTGEQSN-KFMLVLASNQPEQFDWAIN--DRID 145
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 983-1038 3.03e-07

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: 49.69  E-value: 3.03e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462574449  983 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:cd05508     23 FLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYN 78
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 994-1038 4.90e-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: 48.97  E-value: 4.90e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2462574449  994 DYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:cd05517     38 DYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN 82
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 991-1038 6.36e-07

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: 48.96  E-value: 6.36e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2462574449  991 EVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:cd05516     36 ELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFN 83
RecA-like_Ycf2 cd19505
ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; ...
 433-566 9.46e-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: 49.68  E-value: 9.46e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  433 PPRGCLFYGPPGTGKTLVARALA------------NECSqgDKKVAFFMRKGADCLSKWvGESERQLRLLFDQAYLMRPS 500
Cdd:cd19505     11 PSKGILLIGSIETGRSYLIKSLAansyvplirislNKLL--YNKPDFGNDDWIDGMLIL-KESLHRLNLQFELAKAMSPC 87

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462574449  501 IIFFDEIDGLApVRSSRQDQIHSSivSTLLALM-------DGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 566
Cdd:cd19505     88 IIWIPNIHELN-VNRSTQNLEEDP--KLLLGLLlnylsrdFEKSSTRNILVIASTHIPQKVDPALIAPNRLDT 157
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 437-559 3.30e-06

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 50.85  E-value: 3.30e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  437 CLFYGPPGTGKTLVARALANECsqgdkKVAFFMrkgadcLSKwVGESERQLRLLFDQAYLMRPS----IIFFDEIDGLAp 512
Cdd:PRK13342    39 MILWGPPGTGKTTLARIIAGAT-----DAPFEA------LSA-VTSGVKDLREVIEEARQRRSAgrrtILFIDEIHRFN- 105

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2462574449  513 vrSSRQDqihssivsTLLALMDgldnRGEIVVIGAT--NRLDSIDPALR 559
Cdd:PRK13342   106 --KAQQD--------ALLPHVE----DGTITLIGATteNPSFEVNPALL 140
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 961-1038 3.45e-06

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


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 46.67  E-value: 3.45e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462574449  961 RELRLFLRDVTKRLATDKRF-NIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:cd05518      4 RMLALFLYVLEYREGSGRRLcDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 982-1039 5.51e-06

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: 46.56  E-value: 5.51e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462574449  982 IFSKPVDI-EEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 1039
Cdd:cd05529     47 YFEYPVDLrAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNE 105
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 952-1038 6.38e-06

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


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 45.69  E-value: 6.38e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  952 MEDQEENTLRELRLFlRDVTKRLatdkRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLIC 1031
Cdd:cd05522      2 YEARIKNILKGLRKE-RDENGRL----LTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMF 76


                   ....*..
gi 2462574449 1032 SNALEYN 1038
Cdd:cd05522     77 ENAKLYN 83
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 994-1039 1.08e-05

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


Pssm-ID: 99951  Cd Length: 103  Bit Score: 45.02  E-value: 1.08e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2462574449  994 DYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 1039
Cdd:cd05520     38 DYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNV 83
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 994-1046 4.66e-05

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


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 43.86  E-value: 4.66e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2462574449  994 DYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNpDKDPGEH 1046
Cdd:cd05524     40 EYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYY-KPDSPEH 91
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
431-513 7.84e-05

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


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 45.54  E-value: 7.84e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  431 IQPPRGCLFYGPPGTGKTLVARALANECSQGDKKVAFFmrkgadCLSKWVGE-----SERQLRLLFDQayLMRPSIIFFD 505
Cdd:COG1484     96 IERGENLILLGPPGTGKTHLAIALGHEACRAGYRVRFT------TAPDLVNElkearADGRLERLLKR--LAKVDLLILD 167


                   ....*...
gi 2462574449  506 EIdGLAPV 513
Cdd:COG1484    168 EL-GYLPL 174
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 438-548 8.55e-05

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 46.20  E-value: 8.55e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  438 LFYGPPGTGKTLVARALANECsqgdkKVAFFMrkgadcLSKwVGESERQLRLLFDQAYLMR----PSIIFFDEIDglapv 513
Cdd:COG2256     53 ILWGPPGTGKTTLARLIANAT-----DAEFVA------LSA-VTSGVKDIREVIEEARERRaygrRTILFVDEIH----- 115

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 2462574449  514 R--SSRQDqihssivsTLLALMDgldnRGEIVVIGAT 548
Cdd:COG2256    116 RfnKAQQD--------ALLPHVE----DGTITLIGAT 140
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 984-1045 1.60e-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: 42.03  E-value: 1.60e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462574449  984 SKPVDIEevsDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGE 1045
Cdd:cd05501     25 SKPYYIR---DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDDDFGQ 83
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 759-895 1.73e-04

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: 43.13  E-value: 1.73e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  759 YHQPTsyrPR-LLLSGERGSGQtSHLAPALLHTLeRFSVHRLDLPALYSVSAKTPEESCAQIFREARRTVPSIVYMPHI- 836
Cdd:cd19507     26 YGLPT---PKgLLLVGIQGTGK-SLTAKAIAGVW-QLPLLRLDMGRLFGGLVGESESRLRQMIQTAEAIAPCVLWIDEIe 100

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574449  837 ---------GDwwEAVSETVRATFLTLLQDipSFSPIFLLSTSETMYSeLPEEVkcIFRIQYEEVLYI 895
Cdd:cd19507    101 kgfsnadskGD--SGTSSRVLGTFLTWLQE--KKKPVFVVATANNVQS-LPPEL--LRKGRFDEIFFV 161
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
434-572 3.17e-04

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 43.37  E-value: 3.17e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  434 PRGC--LFYGPPGTGKTLVARALANE-CSQGDkKVAFFMrkgadclskwVGESERQLR-----LLFD-QAYLMRPSIIFF 504
Cdd:COG0467     18 PRGSstLLSGPPGTGKTTLALQFLAEgLRRGE-KGLYVS----------FEESPEQLLrraesLGLDlEEYIESGLLRII 86

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462574449  505 DeidglapVRSSRQDQIHSSIVSTLLALMDGLDNRgeIVVIgatnrlDSIDP---ALRRPGRFdREFLFNL 572
Cdd:COG0467     87 D-------LSPEELGLDLEELLARLREAVEEFGAK--RVVI------DSLSGlllALPDPERL-REFLHRL 141
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 437-513 9.22e-04

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


Pssm-ID: 439516  Cd Length: 232  Bit Score: 42.07  E-value: 9.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  437 CLFYGPPGTGKTLVARALANE-CSQGdKKVAFFmrKGADCLSKWvGESERQLRL--LFDQayLMRPSIIFFDEIdGLAPV 513
Cdd:NF038214    93 VLLLGPPGTGKTHLAIALGYAaCRQG-YRVRFT--TAADLVEQL-AQARADGRLgrLLRR--LARYDLLIIDEL-GYLPF 165
PRK04195 PRK04195
replication factor C large subunit; Provisional
 430-510 1.23e-03

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 42.60  E-value: 1.23e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  430 KIQPPRGCLFYGPPGTGKTLVARALAN-------ECSQGDKkvaffmrKGADCLSKWVGESERQlRLLFDQAYlmrpSII 502
Cdd:PRK04195    35 KGKPKKALLLYGPPGVGKTSLAHALANdygweviELNASDQ-------RTADVIERVAGEAATS-GSLFGARR----KLI 102


                   ....*...
gi 2462574449  503 FFDEIDGL 510
Cdd:PRK04195   103 LLDEVDGI 110
PRK08116 PRK08116
hypothetical protein; Validated
 422-467 1.37e-03

hypothetical protein; Validated


Pssm-ID: 236153 [Multi-domain]  Cd Length: 268  Bit Score: 41.93  E-value: 1.37e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2462574449  422 YPEIFEKFKIQPpRGCLFYGPPGTGKTLVARALANECSQGDKKVAF 467
Cdd:PRK08116   103 YVKKFEEMKKEN-VGLLLWGSVGTGKTYLAACIANELIEKGVPVIF 147
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
432-559 1.75e-03

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


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 42.14  E-value: 1.75e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  432 QPPRGCLFYGPPGTGKTLVARA----LANECSQGDKKVAF-------------FMRKGADCLSKWVGESERQLRllFDQA 494
Cdd:COG1474     49 ERPSNVLIYGPTGTGKTAVAKYvleeLEEEAEERGVDVRVvyvncrqastryrVLSRILEELGSGEDIPSTGLS--TDEL 126

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462574449  495 YLM---------RPSIIFFDEIDGLapvrssrQDQIHSSIVSTLLALMDGLDNRGeIVVIGATNRL---DSIDPALR 559
Cdd:COG1474    127 FDRlyealderdGVLVVVLDEIDYL-------VDDEGDDLLYQLLRANEELEGAR-VGVIGISNDLeflENLDPRVK 195
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 438-554 2.62e-03

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: 39.85  E-value: 2.62e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  438 LFYGPPGTGKTLVARALANECSQGDKK-VAF----FMRKGADCLSK-----WVGESERQlrLLFDQAYLMRPSIIFFDEI 507
Cdd:cd19499     45 LFLGPTGVGKTELAKALAELLFGDEDNlIRIdmseYMEKHSVSRLIgappgYVGYTEGG--QLTEAVRRKPYSVVLLDEI 122

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462574449  508 dglapvrssrqDQIHSSIVSTLLALMD-G--LDNRGEIVVIGAT--------------NRLDSI 554
Cdd:cd19499    123 -----------EKAHPDVQNLLLQVLDdGrlTDSHGRTVDFKNTiiimtsnhfrpeflNRIDEI 175
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 434-582 3.74e-03

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


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 39.41  E-value: 3.74e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  434 PRGCLFYGPPGTGKTLVARALANecSQGDKKVAFFMRKGADCLSK---WVGESERQLRLLFDQAYLMRPSIIFFDEIDGL 510
Cdd:pfam13191   24 PPSVLLTGEAGTGKTTLLRELLR--ALERDGGYFLRGKCDENLPYsplLEALTREGLLRQLLDELESSLLEAWRAALLEA 101

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462574449  511 APVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIgATNRLDSIDPAlrrpgrfDREFLFNLPDQKARKHIL 582
Cdd:pfam13191  102 LAPVPELPGDLAERLLDLLLRLLDLLARGERPLVL-VLDDLQWADEA-------SLQLLAALLRLLESLPLL 165
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 746-870 3.97e-03

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: 39.19  E-value: 3.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  746 AIHKPYLHFTMSPYHQPtsYRPRLLLSGERGSGQTsHLAPALLHTLeRFSVHRLDLPALYSVSAKTPEESCAQIFREARR 825
Cdd:cd19481      8 AVEAPRRGSRLRRYGLG--LPKGILLYGPPGTGKT-LLAKALAGEL-GLPLIVVKLSSLLSKYVGESEKNLRKIFERARR 83

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462574449  826 TVPSIV-------------YMPHIGDWWEAVSEtvratFLTLLQDIPSFSPIFLLSTS 870
Cdd:cd19481     84 LAPCILfideidaigrkrdSSGESGELRRVLNQ-----LLTELDGVNSRSKVLVIAAT 136
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 994-1038 4.77e-03

Bromodomain, repeat I 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: 99952  Cd Length: 106  Bit Score: 37.69  E-value: 4.77e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2462574449  994 DYLEVIKEPMDLSTVITKIDkhNYLTAKDFLKDIDLICSNALEYN 1038
Cdd:cd05521     39 DYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYN 81
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
437-457 6.03e-03

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 40.11  E-value: 6.03e-03
                           10        20
                   ....*....|....*....|.
gi 2462574449  437 CLFYGPPGTGKTLVARALANE 457
Cdd:PRK00080    54 VLLYGPPGLGKTTLANIIANE 74
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 757-855 6.38e-03

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: 38.81  E-value: 6.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  757 SPYHQPTSYR------PR-LLLSGERGSGQTsHLAPALLHTLERFsVHRLDLPALYSVSAKTPEESCAQIFREARRTVPS 829
Cdd:cd19503     18 LPLKYPELFRalglkpPRgVLLHGPPGTGKT-LLARAVANEAGAN-FLSISGPSIVSKYLGESEKNLREIFEEARSHAPS 95

                           90       100       110
                   ....*....|....*....|....*....|...
gi 2462574449  830 IVYMPHI-------GDWWEAVSETVRATFLTLL 855
Cdd:cd19503     96 IIFIDEIdalapkrEEDQREVERRVVAQLLTLM 128
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
438-462 6.84e-03

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 39.79  E-value: 6.84e-03
                           10        20
                   ....*....|....*....|....*...
gi 2462574449  438 LFYGPPGTGKTLVARALA---NeCSQGD 462
Cdd:COG2812     36 LFTGPRGVGKTTLARILAkalN-CENGP 62
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
 438-588 7.94e-03

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


Pssm-ID: 410905 [Multi-domain]  Cd Length: 251  Bit Score: 39.12  E-value: 7.94e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  438 LFYGPPGTGKTLVARALANECsqgdkKVAFFMrkgADCLS----KWVGESERQ--LRLL----FDQAYLMRpSIIFFDEI 507
Cdd:cd19497     54 LLIGPTGSGKTLLAQTLAKIL-----DVPFAI---ADATTlteaGYVGEDVENilLKLLqaadYDVERAQR-GIVYIDEI 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  508 DGLApvRSSRqdqiHSSI---VS------TLLALMDGldnrgeIVVigatnrldsidpalrrpgrfdreflfNLPDQKAR 578
Cdd:cd19497    125 DKIA--RKSE----NPSItrdVSgegvqqALLKILEG------TVA--------------------------NVPPQGGR 166

                          170
                   ....*....|....
gi 2462574449  579 KH----ILQIHTRD 588
Cdd:cd19497    167 KHpqqeFIQVDTTN 180
PRK13341 PRK13341
AAA family ATPase;
438-456 8.22e-03

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 40.04  E-value: 8.22e-03
                           10
                   ....*....|....*....
gi 2462574449  438 LFYGPPGTGKTLVARALAN 456
Cdd:PRK13341    56 ILYGPPGVGKTTLARIIAN 74
clpC CHL00095
Clp protease ATP binding subunit
 441-585 8.39e-03

Clp protease ATP binding subunit


Pssm-ID: 214361 [Multi-domain]  Cd Length: 821  Bit Score: 40.04  E-value: 8.39e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  441 GPPGTGKTLVARALANECSQGDKKvAFFMRKGADCL--------SKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAP 512
Cdd:CHL00095   207 GEPGVGKTAIAEGLAQRIVNRDVP-DILEDKLVITLdiglllagTKYRGEFEERLKRIFDEIQENNNIILVIDEVHTLIG 285

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462574449  513 VRSSRQDQIHSSIVSTLLAlmdgldnRGEIVVIGATNrLD------SIDPALRRpgRFDR------------EFLFNLPD 574
Cdd:CHL00095   286 AGAAEGAIDAANILKPALA-------RGELQCIGATT-LDeyrkhiEKDPALER--RFQPvyvgepsveetiEILFGLRS 355

                          170
                   ....*....|.
gi 2462574449  575 QKARKHILQIH 585
Cdd:CHL00095   356 RYEKHHNLSIS 366
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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