Citrus Sinensis ID: 010992

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490------
Protein Sequence
MDQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIVTDPIPL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEEEEEcccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEccHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEHEEHHHccccEEccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mdqeqpqqpqqtqtptpsttttttantasstvttsqitapssqppqqqqqtpptpstpssttiptstpttntpnpnpspspspappsrptsltpppprptsfsrpwqppqqhfshfsslpssssatpstsasppipspprggiaigvpaprptalspqpsppfsssfgqpfgglgrsgvnvpdsvrppaiqgmgvmgslgsssqmrpagisvqhhqprpvqqsslrpppsspssqspgtqnfqgqglmrvsqvgspgssspntsqsvqsfnqpwlssgsqgkpplappstyrpqmntpsmqqrshipqqhsplstnlqqqhlssvqpqqskpshqlpdhygqqfssprvpqssphqqqitrppgsatqkpsslalvqpnavqtgnqskiagtesdefgnrilTKRSIQELVnqidpserldpdvEDILVDIAEDFVESITMFGCslakhrksdtlEAKDILVHLERnwnmtlpgfsgdeiktfrkpvrivtdpipl
Flexible Loop (DISEMBL)
mdqeqpqqpqqtqtptpsttttttantassTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVqtgnqskiagtesdefgnrILTKRSIQELvnqidpserldpDVEDILVDIAEDFVESITMFGCSlakhrksdTLEAKDILVHLErnwnmtlpgfsgdeiktfrkpvrivtdpipl
Low Complexity Region (SEG)
MDQEqpqqpqqtqtptpsttttttantasstvttsqitapssqppqqqqqtpptpstpssttiptstpttntpnpnpspspspappsrptsltpppprptsFSRPWQPPQQHFSHFsslpssssatpstsasppipsppRGGIAIGVPAPRPTALspqpsppfsssfgqpfggLGRSGVNVPDSVRPPAIQgmgvmgslgsssqmRPAGISVQHHqprpvqqsslrpppsspssqspGTQNFQGQGLMRvsqvgspgssspntsqsvqsFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLqqqhlssvqpqqsKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIVTDPIPL
Disordered region (IsUnstruct)
*************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************LV**********PDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIV******
Disordered Region (DISOPRED)
***********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************QELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRI*******
Disordered Region (DISEMBL)
****************************************************************************************************************************************SPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMGSL******************************************FQGQGLMRV************************************PPSTYRPQM*****************************************************************************LALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIVTDPIPL
Disordered Region (DISPRO)
***************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIVTD****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIVTDPIPL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	496	2.2.26 [Sep-21-2011]
Q8VE65	161	Transcription initiation	yes	no	0.179	0.552	0.528	6e-27
Q16514	161	Transcription initiation	yes	no	0.179	0.552	0.528	8e-27
Q3T174	161	Transcription initiation	yes	no	0.179	0.552	0.528	8e-27
Q03761	539	Transcription initiation	yes	no	0.173	0.159	0.527	1e-26
Q555L9	627	Transcription initiation	yes	no	0.175	0.138	0.556	3e-25
O13722	450	Transcription initiation	yes	no	0.177	0.195	0.573	2e-23
Q91858	164	Transcription initiation	N/A	no	0.193	0.585	0.479	1e-20
P49905	196	Transcription initiation	yes	no	0.173	0.438	0.418	4e-17

>sp|Q8VE65|TAF12_MOUSE Transcription initiation factor TFIID subunit 12 OS=Mus musculus GN=Taf12 PE=1 SV=1

 Score =  122 bits (306), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 47/89 (52%), Positives = 70/89 (78%)

Query: 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAK 458
           N++LTK+ +Q+LV ++DP+E+LD DVE++L+ IA+DF+ES+    C LA+HRKS TLE K
Sbjct: 55  NQVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVK 114

Query: 459 DILVHLERNWNMTLPGFSGDEIKTFRKPV 487
           D+ +HLER WNM +PGF  +EI+ ++K  
Sbjct: 115 DVQLHLERQWNMWIPGFGSEEIRPYKKAC 143

TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex and TBP-free TAFII complex (TFTC). TAFs components-TIIFD are essential for mediating regulation of RNA polymerase transcription.
Mus musculus (taxid: 10090)

>sp|Q16514|TAF12_HUMAN Transcription initiation factor TFIID subunit 12 OS=Homo sapiens GN=TAF12 PE=1 SV=1

 Score =  122 bits (305), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 47/89 (52%), Positives = 70/89 (78%)

Query: 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAK 458
           N++LTK+ +Q+LV ++DP+E+LD DVE++L+ IA+DF+ES+    C LA+HRKS TLE K
Sbjct: 55  NQVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVK 114

Query: 459 DILVHLERNWNMTLPGFSGDEIKTFRKPV 487
           D+ +HLER WNM +PGF  +EI+ ++K  
Sbjct: 115 DVQLHLERQWNMWIPGFGSEEIRPYKKAC 143

TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex and TBP-free TAFII complex (TFTC). TAFs components-TIIFD are essential for mediating regulation of RNA polymerase transcription.

Homo sapiens (taxid: 9606)

>sp|Q3T174|TAF12_BOVIN Transcription initiation factor TFIID subunit 12 OS=Bos taurus GN=TAF12 PE=2 SV=1

 Score =  122 bits (305), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 47/89 (52%), Positives = 70/89 (78%)

Query: 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAK 458
           N++LTK+ +Q+LV ++DP+E+LD DVE++L+ IA+DF+ES+    C LA+HRKS TLE K
Sbjct: 55  NQVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVK 114

Query: 459 DILVHLERNWNMTLPGFSGDEIKTFRKPV 487
           D+ +HLER WNM +PGF  +EI+ ++K  
Sbjct: 115 DVQLHLERQWNMWIPGFGSEEIRPYKKAC 143

TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex and TBP-free TAFII complex (TFTC). TAFs components-TIIFD are essential for mediating regulation of RNA polymerase transcription.

Bos taurus (taxid: 9913)

>sp|Q03761|TAF12_YEAST Transcription initiation factor TFIID subunit 12 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TAF12 PE=1 SV=1

 Score =  121 bits (304), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 48/91 (52%), Positives = 69/91 (75%), Gaps = 5/91 (5%)

Query: 400 RILTKRSIQELVNQI-----DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDT 454
           R+++KR ++ELV  +     D    +D DVE++L+D+A+DFV ++T F C LAKHRKSD 
Sbjct: 413 RVMSKRKLRELVKTVGIDEGDGETVIDGDVEELLLDLADDFVTNVTAFSCRLAKHRKSDN 472

Query: 455 LEAKDILVHLERNWNMTLPGFSGDEIKTFRK 485
           LEA+DI +HLERNWN+ +PG+S DEI++ RK
Sbjct: 473 LEARDIQLHLERNWNIRIPGYSADEIRSTRK 503

Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q555L9|TAF12_DICDI Transcription initiation factor TFIID subunit 12 OS=Dictyostelium discoideum GN=TAF12 PE=3 SV=2

 Score =  117 bits (292), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 49/88 (55%), Positives = 63/88 (71%), Gaps = 1/88 (1%)

Query: 400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKD 459
            +L KR + EL+ QI P+E++D D EDIL  +A+DFVES   F C+LAKHR S TLE KD
Sbjct: 440 EVLGKRKLIELLQQISPNEKMDEDAEDILSVLADDFVESTVAFACTLAKHRNSTTLEVKD 499

Query: 460 ILVHLERNWNMTLPGFSGDE-IKTFRKP 486
           +  HLE+NWN+ +PGF   E  KTF+KP
Sbjct: 500 LQCHLEKNWNIRVPGFGNVEQYKTFKKP 527

Makes part of is a multimeric protein complex TFIID that plays a central role in mediating promoter responses to various activators and repressors.

Dictyostelium discoideum (taxid: 44689)

>sp|O13722|TAF12_SCHPO Transcription initiation factor TFIID subunit 12 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=taf12 PE=1 SV=1

 Score =  110 bits (276), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 51/89 (57%), Positives = 75/89 (84%), Gaps = 1/89 (1%)

Query: 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEA 457
           GNR+L+KR + +L+ QID  E+++P+VE++L++IA++FVES+T F C LAKHRKSDTL+ 
Sbjct: 339 GNRLLSKRKLHDLLQQIDSEEKIEPEVEELLLEIADEFVESVTNFACRLAKHRKSDTLDV 398

Query: 458 KDILVHLERNWNMTLPGFSGDEI-KTFRK 485
           +D+ +HLERNWN+ LPGF+ D+I K+ RK
Sbjct: 399 RDVQLHLERNWNIRLPGFASDDIVKSARK 427

Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation), facilitation of DNA opening and initiation of transcription. SAGA is involved in RNA polymerase II-dependent transcriptional regulation. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction and promoter selectivity, interaction with transcription activators, and chromatin modification through histone acetylation (gcn5) and deubiquitination (ubp8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q91858|TAF12_XENLA Transcription initiation factor TFIID subunit 12 OS=Xenopus laevis GN=taf12 PE=2 SV=1

 Score =  102 bits (253), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 46/96 (47%), Positives = 72/96 (75%)

Query: 390 AGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKH 449
            G  +    N++L+K+ + +LV ++DP+E+LD DVE++L+ IA+DF+ES+    C LA+H
Sbjct: 49  GGGRASPEANQVLSKKKLHDLVREVDPNEQLDEDVEEMLLQIADDFIESVVSAACQLARH 108

Query: 450 RKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRK 485
           RKS+TLE KD+ +HLER WNM +PGF  +EI+ ++K
Sbjct: 109 RKSNTLEVKDVQLHLERQWNMWIPGFGSEEIRPYKK 144

Interacts directly with TBP; additional interactions between TAFII20 and TAFII28 or TAFII30 were detected.

Xenopus laevis (taxid: 8355)

>sp|P49905|TAF12_DROME Transcription initiation factor TFIID subunit 12 OS=Drosophila melanogaster GN=Taf12 PE=1 SV=1

 Score = 89.7 bits (221), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 36/86 (41%), Positives = 59/86 (68%)

Query: 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460
           +LTK  + ELV ++D + +LD DVE++L+ I +DFVE       + AKHRKS+ +E +D+
Sbjct: 91  MLTKPRLTELVREVDTTTQLDEDVEELLLQIIDDFVEDTVKSTSAFAKHRKSNKIEVRDV 150

Query: 461 LVHLERNWNMTLPGFSGDEIKTFRKP 486
            +H ER +NM +PGF  DE++ +++ 
Sbjct: 151 QLHFERKYNMWIPGFGTDELRPYKRA 176


  Database: swissprot
    Posted date:  Mar 23, 2013  2:32 AM
  Number of letters in database: 191,569,459
  Number of sequences in database:  539,616
  
Lambda     K      H
   0.307    0.124    0.364 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 210,742,952
Number of Sequences: 539616
Number of extensions: 11038037
Number of successful extensions: 236076
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 2365
Number of HSP's successfully gapped in prelim test: 5328
Number of HSP's that attempted gapping in prelim test: 77947
Number of HSP's gapped (non-prelim): 61864
length of query: 496
length of database: 191,569,459
effective HSP length: 122
effective length of query: 374
effective length of database: 125,736,307
effective search space: 47025378818
effective search space used: 47025378818
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 63 (28.9 bits)

TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors.

Drosophila melanogaster (taxid: 7227)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	496
359481991	496	PREDICTED: uncharacterized protein LOC10	0.754	0.754	0.646	1e-117
297740082	372	unnamed protein product [Vitis vinifera]	0.596	0.795	0.710	1e-104
224087397	497	predicted protein [Populus trichocarpa]	0.733	0.732	0.582	9e-96
356548409	507	PREDICTED: uncharacterized protein LOC10	0.659	0.644	0.570	1e-86
449482360	511	PREDICTED: uncharacterized protein LOC10	0.669	0.649	0.602	3e-84
356537087	507	PREDICTED: uncharacterized protein LOC10	0.627	0.613	0.571	4e-84
255575631	451	protein with unknown function [Ricinus c	0.487	0.536	0.671	2e-82
297833786	541	tata-associated factor II 58 [Arabidopsi	0.762	0.698	0.541	3e-81
449451128	511	PREDICTED: uncharacterized protein LOC10	0.669	0.649	0.588	4e-81
18398741	539	transcription initiation factor TFIID su	0.762	0.701	0.529	2e-78

>gi|359481991|ref|XP_002277150.2| PREDICTED: uncharacterized protein LOC100242486 [Vitis vinifera]

 Score =  428 bits (1101), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 267/413 (64%), Positives = 300/413 (72%), Gaps = 39/413 (9%)

Query: 104 RPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPP--------RGGIAIGVPAPRPTAL 155
           RPWQ  Q HF HFSS  SSSS++ ST +     S          RGGIAIGVPA +PT  
Sbjct: 44  RPWQQ-QSHFQHFSSNLSSSSSSSSTPSLSTSTSSSAVSAPPSQRGGIAIGVPAGQPT-- 100

Query: 156 SPQPSPPFSS----SFGQPFGGLGRSGVNVPDSVRP-------PAIQG---MGVMGSLGS 201
                 PFSS    +FGQ +GGLGRS VNVP+SV         P+IQG   MG+MG+LGS
Sbjct: 101 ------PFSSLNPPTFGQQYGGLGRSAVNVPESVANTNTSQVRPSIQGSQGMGMMGTLGS 154

Query: 202 SSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSSP 261
            SQMRP GIS  HHQ RPVQ SSLRP  S+ ++QSP TQNFQG GL+R S VGSPG+ SP
Sbjct: 155 GSQMRPGGISA-HHQQRPVQ-SSLRPQ-STVNNQSPATQNFQGHGLLRASSVGSPGAPSP 211

Query: 262 NTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHS-PL-STNLQQ 319
           NTSQS+Q  NQPWLSSGSQGKPPL  PS +RPQM   S+ QRSHIPQQH  PL + + QQ
Sbjct: 212 NTSQSMQPHNQPWLSSGSQGKPPLPSPS-FRPQMTAQSLPQRSHIPQQHHHPLPTASQQQ 270

Query: 320 QHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPN 379
           Q  ++ QPQQ   SHQ  +HYGQQF   RVPQS PH QQI R  GS  QKPSSLA+VQP+
Sbjct: 271 QMSTAQQPQQPLLSHQQQEHYGQQFPPSRVPQSLPHPQQIGRVQGSGNQKPSSLAIVQPS 330

Query: 380 AVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESI 439
             Q G  S+ A  E+ E GNRIL+KRSI ELVNQIDPSE+LDP+VEDILVDIAEDFVESI
Sbjct: 331 TPQLGPHSRTASAEASESGNRILSKRSIHELVNQIDPSEKLDPEVEDILVDIAEDFVESI 390

Query: 440 TMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIVTD 492
           T FGCSLAKHRKS TLEAKDIL+HLERNWNMTLPGF GDEIKTF+KP   V+D
Sbjct: 391 TTFGCSLAKHRKSPTLEAKDILLHLERNWNMTLPGFGGDEIKTFKKP--FVSD 441

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297740082|emb|CBI30264.3| unnamed protein product [Vitis vinifera]

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 216/304 (71%), Positives = 241/304 (79%), Gaps = 8/304 (2%)

Query: 191 QGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRV 250
           QGMG+MG+LGS SQMRP GIS  HHQ RPVQ SSLRP  S+ ++QSP TQNFQG GL+R 
Sbjct: 20  QGMGMMGTLGSGSQMRPGGISA-HHQQRPVQ-SSLRPQ-STVNNQSPATQNFQGHGLLRA 76

Query: 251 SQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQH 310
           S VGSPG+ SPNTSQS+Q  NQPWLSSGSQGKPPL  PS +RPQM   S+ QRSHIPQQH
Sbjct: 77  SSVGSPGAPSPNTSQSMQPHNQPWLSSGSQGKPPLPSPS-FRPQMTAQSLPQRSHIPQQH 135

Query: 311 S-PL-STNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQ 368
             PL + + QQQ  ++ QPQQ   SHQ  +HYGQQF   RVPQS PH QQI R  GS  Q
Sbjct: 136 HHPLPTASQQQQMSTAQQPQQPLLSHQQQEHYGQQFPPSRVPQSLPHPQQIGRVQGSGNQ 195

Query: 369 KPSSLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDIL 428
           KPSSLA+VQP+  Q G  S+ A  E+ E GNRIL+KRSI ELVNQIDPSE+LDP+VEDIL
Sbjct: 196 KPSSLAIVQPSTPQLGPHSRTASAEASESGNRILSKRSIHELVNQIDPSEKLDPEVEDIL 255

Query: 429 VDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVR 488
           VDIAEDFVESIT FGCSLAKHRKS TLEAKDIL+HLERNWNMTLPGF GDEIKTF+KP  
Sbjct: 256 VDIAEDFVESITTFGCSLAKHRKSPTLEAKDILLHLERNWNMTLPGFGGDEIKTFKKP-- 313

Query: 489 IVTD 492
            V+D
Sbjct: 314 FVSD 317

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224087397|ref|XP_002308150.1| predicted protein [Populus trichocarpa] gi|222854126|gb|EEE91673.1| predicted protein [Populus trichocarpa]

 Score =  357 bits (915), Expect = 9e-96,   Method: Compositional matrix adjust.
 Identities = 229/393 (58%), Positives = 271/393 (68%), Gaps = 29/393 (7%)

Query: 98  RPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSP 157
           RP +  RPWQ P  H S F S+ S      S+S +P        G+A+GVPAP P + S 
Sbjct: 76  RPQTVHRPWQHPHPH-SQFPSVSSGPPIPSSSSTTPS--ISSPRGVALGVPAPSPASFS- 131

Query: 158 QPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGM--GVMGSLGSSSQMRPAGISVQHH 215
                  SSFG  F GL R+ VNVP+SV   +   +  GVM S+ S+SQMRP       H
Sbjct: 132 -------SSFGHQFVGLNRAPVNVPESVANTSNSQVRQGVMASMASNSQMRP-------H 177

Query: 216 QPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWL 275
           Q RPVQ SSLRPP SSP+     TQNF G   +R + VG+ GS  PNTSQS+QS NQ WL
Sbjct: 178 QQRPVQ-SSLRPPTSSPN-----TQNFPGHVFIRSTPVGTAGSPVPNTSQSLQSPNQLWL 231

Query: 276 SSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIP-QQHSPLSTNLQQQHLSSVQPQQSKPSH 334
           SS SQGKPPL  PS YRPQMN+PS+QQRSHIP Q HSP +T+ QQQH+S  QPQQ   SH
Sbjct: 232 SSASQGKPPLPSPS-YRPQMNSPSLQQRSHIPPQHHSPPTTS-QQQHMSPAQPQQPLQSH 289

Query: 335 QLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVQTGNQSKIAGTES 394
           Q P+HYGQQF   RV QS    QQ++R  GS   KPSSLA+  PN VQ   Q+ IA  ES
Sbjct: 290 QQPEHYGQQFPPSRVQQSLSPLQQVSRVQGSVNHKPSSLAMSHPNTVQPLPQNSIANAES 349

Query: 395 DEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDT 454
           DE GNRIL+KRSI ELV+QIDPSE+ +P+V +IL DIA++F+ S+T FGCSLAKHRKSDT
Sbjct: 350 DESGNRILSKRSIHELVSQIDPSEKFNPEVVEILADIADEFLVSVTTFGCSLAKHRKSDT 409

Query: 455 LEAKDILVHLERNWNMTLPGFSGDEIKTFRKPV 487
           LEAKDIL+HL+RNWNMTLPGF GDEIK++RK V
Sbjct: 410 LEAKDILLHLDRNWNMTLPGFCGDEIKSYRKQV 442

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356548409|ref|XP_003542594.1| PREDICTED: uncharacterized protein LOC100787779 [Glycine max]

 Score =  327 bits (837), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 203/356 (57%), Positives = 248/356 (69%), Gaps = 29/356 (8%)

Query: 140 RGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDS--------VRPPAIQ 191
           RGG+AIGVPA   +   P      SSSFGQ FGGLGR+ VNV +S         R P +Q
Sbjct: 118 RGGMAIGVPAHHQSPSPPF-----SSSFGQHFGGLGRTAVNVAESTSNSSTSQARTP-VQ 171

Query: 192 GMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVS 251
           GMG++GS     QMRP+GI    HQ R VQ SSLRPP S+P++Q  G+Q+FQG GLMR S
Sbjct: 172 GMGMLGS-----QMRPSGIGS--HQQRSVQ-SSLRPPTSAPNNQPAGSQSFQGHGLMRPS 223

Query: 252 QVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHS 311
            VGS  + SP++SQS+QS NQPWLSSGSQGKPPL P + YR Q+N  SMQQRSHIP    
Sbjct: 224 SVGSTATPSPSSSQSMQSLNQPWLSSGSQGKPPL-PSAAYRQQLNPQSMQQRSHIPPMQQ 282

Query: 312 PLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPS 371
              T+ QQQ    +   QS+      +H+GQQ    R P   PHQ Q+TR  G   QKPS
Sbjct: 283 STPTSSQQQQQQPLLSNQSQ------EHFGQQVPPSRAPLHMPHQPQVTRLQGPGNQKPS 336

Query: 372 SLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDI 431
           SL   Q +A Q G QS++  +++DE  N IL+KRSI ELVNQ+DP E+L+P+V DILVDI
Sbjct: 337 SLVAAQSSAAQPGTQSRLTNSDTDESSNSILSKRSIHELVNQVDPLEKLEPEVADILVDI 396

Query: 432 AEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPV 487
           AE+F+ESIT  GCSLAKHRKS TLE+KDIL+HLE+NWNMTLPGF GDEIK++R+P+
Sbjct: 397 AENFLESITRSGCSLAKHRKSTTLESKDILLHLEKNWNMTLPGFGGDEIKSYRRPI 452

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449482360|ref|XP_004156257.1| PREDICTED: uncharacterized protein LOC101226357 [Cucumis sativus]

 Score =  318 bits (816), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 215/357 (60%), Positives = 248/357 (69%), Gaps = 25/357 (7%)

Query: 140 RGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDS--------VRPPAIQ 191
           R G+AIGVPA +PT  SPQP+P FS+S+GQ FGGLGR GV++ D         VRPP +Q
Sbjct: 126 RSGVAIGVPAHQPTP-SPQPAP-FSASYGQHFGGLGRGGVSISDGASNSNPSQVRPP-MQ 182

Query: 192 GMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVS 251
           GM  +G LGSS         + H   RPVQ SSLRPP S+P+S S   QNFQG GL+RV 
Sbjct: 183 GMQGLGMLGSSGSSS----QMLH---RPVQ-SSLRPP-STPNSAS---QNFQGHGLLRVP 230

Query: 252 QVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHS 311
              SP SS PNTSQ +Q  NQPWL S SQGKPPL  PS YRPQ N+P+MQQRSHIPQQ +
Sbjct: 231 STSSPSSSLPNTSQGMQPTNQPWLPSSSQGKPPLPTPS-YRPQANSPAMQQRSHIPQQQN 289

Query: 312 -PLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKP 370
            PL+   QQQ +SS   QQ   SHQ  +H+ QQF   R  Q  PHQQQ  R  G A  K 
Sbjct: 290 HPLTPVSQQQQISSAPQQQPAQSHQPQEHFAQQFQQSRSSQGLPHQQQAARAQGPANPKA 349

Query: 371 SSLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVD 430
           S LA  Q N  Q    S+    E +E  +RIL+KRSI +LVNQIDPSERLDP+VEDILVD
Sbjct: 350 SPLAPPQTNNAQALTPSRAITAEVEEPCSRILSKRSIGKLVNQIDPSERLDPEVEDILVD 409

Query: 431 IAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPV 487
           +AE+FVESIT FGCSLAKHRKS TLEAKDIL+HLE+NWN+TLPGF  DEIK FRKP+
Sbjct: 410 LAEEFVESITTFGCSLAKHRKSTTLEAKDILLHLEKNWNLTLPGFGSDEIKIFRKPL 466

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356537087|ref|XP_003537062.1| PREDICTED: uncharacterized protein LOC100781682 [Glycine max]

 Score =  318 bits (815), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 204/357 (57%), Positives = 246/357 (68%), Gaps = 46/357 (12%)

Query: 143 IAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDS--------VRPPAIQGMG 194
           +AIGVPA   +      SPPFSSSFGQ FGGLGR+GVNV +S        VR P +QG G
Sbjct: 128 MAIGVPAHHQSP-----SPPFSSSFGQHFGGLGRTGVNVAESTSNSSTSQVRTP-VQGTG 181

Query: 195 VMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPP-SSPSSQSPGTQNFQGQGLMRVSQV 253
           ++GS     QMRP+GI    HQ RPVQ SSLRPPP S+P++Q  G+Q+FQG GLMR S V
Sbjct: 182 MLGS-----QMRPSGIGA--HQQRPVQ-SSLRPPPPSAPNNQPAGSQSFQGHGLMRSSSV 233

Query: 254 GSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPL 313
           GSP + SP++S S+QS NQPWLSSG QGKPPL P + YR Q+N  SMQQR HIP Q    
Sbjct: 234 GSPATPSPSSSLSMQSLNQPWLSSGPQGKPPL-PSAAYRQQLNPQSMQQRPHIPLQ---- 288

Query: 314 STNLQQQHLSSVQPQQSKP----SHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQK 369
                         QQS P    ++Q  +H+GQQ   PR P   PHQ QI R  G   QK
Sbjct: 289 --------------QQSTPTPLLANQSQEHFGQQVLPPRAPLHVPHQPQIMRVHGPGNQK 334

Query: 370 PSSLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILV 429
           PSSL   Q +A Q G +S++  T++DE  N IL+KRSI ELVNQ+DP E+L+P+V DILV
Sbjct: 335 PSSLVAAQSSAAQPGTRSRLTNTDTDESSNSILSKRSIHELVNQVDPLEKLEPEVADILV 394

Query: 430 DIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKP 486
           DIAE+F+ESIT  GCSLAKHRKS TLEAKDIL+HLE+NWNMTL GF GD+IK++R+P
Sbjct: 395 DIAENFLESITRSGCSLAKHRKSTTLEAKDILLHLEKNWNMTLLGFGGDDIKSYRRP 451

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255575631|ref|XP_002528715.1| protein with unknown function [Ricinus communis] gi|223531809|gb|EEF33627.1| protein with unknown function [Ricinus communis]

 Score =  313 bits (801), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 172/256 (67%), Positives = 195/256 (76%), Gaps = 14/256 (5%)

Query: 241 NFQGQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPS- 299
           NFQGQG +R S VGS GS +PNTSQ++QS NQPWLSSGSQGKPPL  PS YRPQ+N+PS 
Sbjct: 147 NFQGQGYIRPSLVGS-GSPAPNTSQNLQSPNQPWLSSGSQGKPPLPSPS-YRPQINSPSS 204

Query: 300 MQQRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQI 359
           +QQRSHIPQQH  L TN QQQH+S  QP QS  SH   +H GQQF   R P+S   Q  +
Sbjct: 205 LQQRSHIPQQHQSLPTNSQQQHMSPSQPHQSLTSHPPSEHLGQQFPPTRGPRSITQQLAL 264

Query: 360 TRPPGSATQKPSSLALVQP--------NAVQTGNQSKIAGTESDEFGNRILTKRSIQELV 411
              P    QKPSSLA+V P        N VQ G  ++ A  ESDE GNRIL+KR+I ELV
Sbjct: 265 QSLPN---QKPSSLAVVHPSPVANTVSNTVQPGTLNRTAIPESDESGNRILSKRNIHELV 321

Query: 412 NQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMT 471
            QIDPSE+LDP+VEDIL DIA++FVESIT FGCSLAKHRKSDTLEAKDIL+HLERNWNMT
Sbjct: 322 TQIDPSEKLDPEVEDILADIADEFVESITTFGCSLAKHRKSDTLEAKDILLHLERNWNMT 381

Query: 472 LPGFSGDEIKTFRKPV 487
           L GFSGDEIKT+RKP+
Sbjct: 382 LTGFSGDEIKTYRKPL 397

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297833786|ref|XP_002884775.1| tata-associated factor II 58 [Arabidopsis lyrata subsp. lyrata] gi|297330615|gb|EFH61034.1| tata-associated factor II 58 [Arabidopsis lyrata subsp. lyrata]

 Score =  308 bits (790), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 226/417 (54%), Positives = 268/417 (64%), Gaps = 39/417 (9%)

Query: 92  LTPPPPRPTSFSRPWQPPQQH--FSHFSSLPSSSSATPSTSASPP----IPSPPRGGIAI 145
           L  PPP+  ++SRPWQ   QH  ++HFSS  S   ++ S  AS      I    RGG+AI
Sbjct: 89  LVRPPPQ--AYSRPWQ---QHSSYTHFSSASSPLLSSSSAPASSSSSLPITGQQRGGMAI 143

Query: 146 GVPAPRPTALSP---QPSP-PFSSSFGQPFGGLGRSGVNVPDS--------VRP-PAIQG 192
           GVPA    + SP   Q +P  F  SFGQ +GGLGR  V + ++        VR     QG
Sbjct: 144 GVPASPIPSPSPTPSQHTPSAFPGSFGQQYGGLGRGTVGMSEATSNSSAPQVRMMQGTQG 203

Query: 193 MGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQ 252
           +G+MG+LGS SQMRP+G++   HQ RP Q SSLRP  SSPS+QSP  QNFQG  LMR S 
Sbjct: 204 IGMMGTLGSGSQMRPSGMA--QHQQRPTQ-SSLRPA-SSPSTQSPVAQNFQGHSLMRPSP 259

Query: 253 VGSPGSSSPNTSQ-SVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHS 311
           +GSP   S   SQ S+Q+ NQPWLSS  QGKPPL PPS YRPQ+N+PSMQQR HIPQQH 
Sbjct: 260 IGSPSVQSTGASQQSLQAINQPWLSSTPQGKPPLPPPS-YRPQVNSPSMQQRPHIPQQH- 317

Query: 312 PLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPS 371
            LST+      +S   Q        P    QQ  SP+ P   PHQ   TR  G   QK +
Sbjct: 318 -LSTSA----ATSQPQQLQSQQQHQPQEQLQQLRSPQQPLPHPHQP--TRVQGLVNQKVT 370

Query: 372 SLAL-VQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVD 430
           S  +  QP   Q GN +K    E++   +RIL KRSI EL+ QIDPSE+LDP+VEDIL D
Sbjct: 371 SPVMPSQPPVAQPGNHAKTVSAENETSDDRILGKRSIHELLQQIDPSEKLDPEVEDILAD 430

Query: 431 IAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPV 487
           IAEDFVESIT FGCSLAKHRKSDTLEAKDIL+H+ERNWN+  PGFS DE KTFRKP+
Sbjct: 431 IAEDFVESITTFGCSLAKHRKSDTLEAKDILLHVERNWNIRPPGFSSDEFKTFRKPL 487

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449451128|ref|XP_004143314.1| PREDICTED: uncharacterized protein LOC101211513 [Cucumis sativus]

 Score =  308 bits (789), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 210/357 (58%), Positives = 244/357 (68%), Gaps = 25/357 (7%)

Query: 140 RGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDS--------VRPPAIQ 191
           R G+AIGVPA +PT  SPQP+P FS+S+GQ FGGLGR GV++ D         VRPP +Q
Sbjct: 126 RSGVAIGVPAHQPTP-SPQPAP-FSASYGQHFGGLGRGGVSISDGASNSNPSQVRPP-MQ 182

Query: 192 GMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVS 251
           GM  +G LGSS         + H   RPVQ SSLRPP S+P+S S   QNFQG GL+RV 
Sbjct: 183 GMQGLGMLGSSGSSS----QMLH---RPVQ-SSLRPP-STPNSAS---QNFQGHGLLRVP 230

Query: 252 QVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHS 311
              SP SS PNTSQ +Q  NQPWL S SQGKPPL  PS YRPQ N+P+MQQRSHIPQQ +
Sbjct: 231 STSSPSSSLPNTSQGMQPTNQPWLPSSSQGKPPLPTPS-YRPQANSPAMQQRSHIPQQQN 289

Query: 312 -PLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKP 370
            PL+   QQQ +SS   QQ   SHQ  +H+ QQF   R  Q  PHQQQ  R  G A  K 
Sbjct: 290 HPLTPVSQQQQISSAPQQQPAQSHQPQEHFAQQFQQSRSSQGLPHQQQAARAQGPANPKA 349

Query: 371 SSLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVD 430
           S LA  Q N  Q    S+    E +E  +RIL+KRSI +LVNQIDPSERLDP+VEDILVD
Sbjct: 350 SPLAPPQTNNAQALTPSRAITAEMEEPCSRILSKRSIGKLVNQIDPSERLDPEVEDILVD 409

Query: 431 IAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPV 487
           +A+ +   IT FGCSLAKHRKS TLEAKDIL+HLE+NWN+TLPGF  DEIK FRKP+
Sbjct: 410 LADTYFVQITTFGCSLAKHRKSTTLEAKDILLHLEKNWNLTLPGFGSDEIKIFRKPL 466

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18398741|ref|NP_566367.1| transcription initiation factor TFIID subunit D10 [Arabidopsis thaliana] gi|6143870|gb|AAF04417.1|AC010927_10 unknown protein [Arabidopsis thaliana] gi|13492646|gb|AAK28289.1|AF344878_1 putative TBP-associated 58 kDa subunit protein [Arabidopsis thaliana] gi|39545904|gb|AAR28015.1| TAF12 [Arabidopsis thaliana] gi|62320727|dbj|BAD95394.1| hypothetical protein [Arabidopsis thaliana] gi|332641335|gb|AEE74856.1| transcription initiation factor TFIID subunit D10 [Arabidopsis thaliana]

 Score =  299 bits (765), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 221/417 (52%), Positives = 265/417 (63%), Gaps = 39/417 (9%)

Query: 92  LTPPPPRPTSFSRPWQPPQQH--FSHFSSLPSSSSATPSTSASPP----IPSPPRGGIAI 145
           L  PPP+  ++SRPWQ   QH  ++HFSS  S   ++ S  AS      I    RGG+AI
Sbjct: 87  LVRPPPQ--AYSRPWQ---QHSSYTHFSSASSPLLSSSSAPASSSSSLPISGQQRGGMAI 141

Query: 146 GVPAPRPTALSPQPSP----PFSSSFGQPFGGLGRSGVNVPDS--------VRP-PAIQG 192
           GVPA    + SP PS      F  SFGQ +GGLGR  V + ++        VR     QG
Sbjct: 142 GVPASPIPSPSPTPSQHSPSAFPGSFGQQYGGLGRGTVGMSEATSNTSSPQVRMMQGTQG 201

Query: 193 MGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQ 252
           +G+MG+LGS SQ+RP+G++   HQ RP Q SSLRP  SS S+QSP  QNFQG  LMR S 
Sbjct: 202 IGMMGTLGSGSQIRPSGMT--QHQQRPTQ-SSLRPA-SSTSTQSPVAQNFQGHSLMRPSP 257

Query: 253 VGSPGSSSPNTSQ-SVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHS 311
           + SP   S   SQ S+Q+ NQPWLSS  QGKPPL PPS YRPQ+N+PSMQQR HIPQQH 
Sbjct: 258 ISSPNVQSTGASQQSLQAINQPWLSSTPQGKPPLPPPS-YRPQVNSPSMQQRPHIPQQH- 315

Query: 312 PLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPS 371
            +ST+      +    QQ       P    QQ  SP+ P + PHQ   TR  G   QK +
Sbjct: 316 -ISTSA----ATPQPQQQQSQQQHQPQEQLQQLRSPQQPLAHPHQP--TRVQGLVNQKVT 368

Query: 372 SLAL-VQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVD 430
           S  +  QP   Q GN +K    E++   +RIL KRSI EL+ QIDPSE+LDP+VEDIL D
Sbjct: 369 SPVMPSQPPVAQPGNHAKTVSAETEPSDDRILGKRSIHELLQQIDPSEKLDPEVEDILSD 428

Query: 431 IAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPV 487
           IAEDFVESIT FGCSLAKHRKSD LEAKDIL+H+ERNWN+  PGFS DE KTFRKP+
Sbjct: 429 IAEDFVESITTFGCSLAKHRKSDILEAKDILLHVERNWNIRPPGFSSDEFKTFRKPL 485

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	496
TAIR|locus:2100053	539	TAF12 "TBP-associated factor 1	0.754	0.693	0.413	4.1e-65
TAIR|locus:2018861	683	EER4 "ENHANCED ETHYLENE RESPON	0.409	0.297	0.383	3.4e-29
POMBASE|SPAC15A10.02	450	taf12 "transcription factor TF	0.381	0.42	0.359	1.3e-27
UNIPROTKB|Q5ZKX3	161	TAF12 "Uncharacterized protein	0.247	0.763	0.464	7.3e-27
UNIPROTKB|G3MXQ4	161	G3MXQ4 "Uncharacterized protei	0.233	0.720	0.480	4e-26
MGI|MGI:1913714	161	Taf12 "TAF12 RNA polymerase II	0.235	0.726	0.458	5.2e-26
RGD|1592841	161	Taf12 "TAF12 RNA polymerase II	0.241	0.745	0.445	5.2e-26
UNIPROTKB|Q3T174	161	TAF12 "Transcription initiatio	0.233	0.720	0.472	6.6e-26
ZFIN|ZDB-GENE-031030-5	162	taf12 "TAF12 RNA polymerase II	0.237	0.728	0.475	6.6e-26
UNIPROTKB|E2QVZ3	161	TAF12 "Uncharacterized protein	0.247	0.763	0.44	8.4e-26

TAIR|locus:2100053 TAF12 "TBP-associated factor 12" [Arabidopsis thaliana (taxid:3702)]

 Score = 663 (238.4 bits), Expect = 4.1e-65, P = 4.1e-65
 Identities = 170/411 (41%), Positives = 201/411 (48%)

Query:   102 FSRPWQPPQQHFSHFXXXXXXXXXXXXXXXXXXXXX----XXRGGIAIGVPA-----PRP 152
             +SRPWQ     ++HF                           RGG+AIGVPA     P P
Sbjct:    95 YSRPWQQ-HSSYTHFSSASSPLLSSSSAPASSSSSLPISGQQRGGMAIGVPASPIPSPSP 153

Query:   153 TALXXXXXXXXXXXXXXXXXXLGRSGVNVPDSVR---PPAI------QXXXXXXXXXXXX 203
             T                    LGR  V + ++      P +      Q            
Sbjct:   154 TP-SQHSPSAFPGSFGQQYGGLGRGTVGMSEATSNTSSPQVRMMQGTQGIGMMGTLGSGS 212

Query:   204 XXRPAGISVQHHXXXXXXXXXXXXXXXXXXXXXXGTQNFQGQGLMRXXXXXX-XXXXXXX 262
               RP+G++ QH                         QNFQG  LMR              
Sbjct:   213 QIRPSGMT-QHQQRPTQSSLRPASSTSTQSPVA---QNFQGHSLMRPSPISSPNVQSTGA 268

Query:   263 XXXXXXXFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLXXXXX 322
                     NQPWLSS  QGKPPL PPS YRPQ+N+PSMQQR HIPQQH  +ST+      
Sbjct:   269 SQQSLQAINQPWLSSTPQGKPPLPPPS-YRPQVNSPSMQQRPHIPQQH--ISTS---AAT 322

Query:   323 XXXXXXXXKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALV-QPNAV 381
                     +  HQ P    QQ  SP+ P + PHQ   TR  G   QK +S  +  QP   
Sbjct:   323 PQPQQQQSQQQHQ-PQEQLQQLRSPQQPLAHPHQP--TRVQGLVNQKVTSPVMPSQPPVA 379

Query:   382 QTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITM 441
             Q GN +K    E++   +RIL KRSI EL+ QIDPSE+LDP+VEDIL DIAEDFVESIT 
Sbjct:   380 QPGNHAKTVSAETEPSDDRILGKRSIHELLQQIDPSEKLDPEVEDILSDIAEDFVESITT 439

Query:   442 FGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIVTD 492
             FGCSLAKHRKSD LEAKDIL+H+ERNWN+  PGFS DE KTFRKP  + TD
Sbjct:   440 FGCSLAKHRKSDILEAKDILLHVERNWNIRPPGFSSDEFKTFRKP--LTTD 488

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

TAIR|locus:2018861 EER4 "ENHANCED ETHYLENE RESPONSE 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 332 (121.9 bits), Expect = 3.4e-29, P = 3.4e-29
 Identities = 81/211 (38%), Positives = 115/211 (54%)

Query:   275 LSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHI---PQQHSPLS-TNLXXXXXXXXXXXXX 330
             L    Q +  L+ P  ++  M+  + QQ S I    QQ S L  + +             
Sbjct:   397 LQQQQQQQQQLSSPQLHQSSMSL-NQQQISQIIQQQQQQSQLGQSQMNQSHSQQQLQQMQ 455

Query:   331 KPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVQTGNQSKIA 390
             +   Q P    QQ    +       QQ   R    A QK  SL   QP A Q+G  +   
Sbjct:   456 QQLQQQPQQQMQQQQQQQQQMQINQQQPSPRMLSHAGQKSVSLTGSQPEATQSGTTTP-G 514

Query:   391 GTESD--EFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAK 448
             G+ S   E  N++L KR IQ+LV+Q+D   +LDPDVED+L+++A+DF++S+T F CSLAK
Sbjct:   515 GSSSQGTEATNQLLGKRKIQDLVSQVDVHAKLDPDVEDLLLEVADDFIDSVTSFACSLAK 574

Query:   449 HRKSDTLEAKDILVHLERNWNMTLPGFSGDE 479
             HRKS  LE KDIL+HLE+N ++T+PGFS ++
Sbjct:   575 HRKSSVLEPKDILLHLEKNLHLTIPGFSSED 605

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0005669 "transcription factor TFIID complex" evidence=IEA;ISS

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA;ISS

GO:0009736 "cytokinin mediated signaling pathway" evidence=IMP

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=IMP

GO:0010104 "regulation of ethylene mediated signaling pathway" evidence=IMP

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

POMBASE|SPAC15A10.02 taf12 "transcription factor TFIID complex subunit A/ SAGA complex subunit Taf12" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 309 (113.8 bits), Expect = 1.3e-27, P = 1.3e-27
 Identities = 74/206 (35%), Positives = 116/206 (56%)

Query:   286 APPSTYRPQMN----TPSMQQRSHIPQQHSPLSTNLXXXXXXXXXXXXXK-PSHQLPDHY 340
             AP     P+ +    TP     +++  + + L+T+              + PS+   +H 
Sbjct:   233 APQQRINPETSSVPETPVGVSAANVSNESTELATSATQQSGLANNVEKSQTPSYMSANHL 292

Query:   341 GQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVQTGNQSKIAGTESDEFGNR 400
              +  S   +P S P   + T   G A+    S+ L  P        S+    E D  GNR
Sbjct:   293 PKVDSKSPIPFSVP-PSRATLTGGYAS---GSIGLSTPGL------SRAPHYELDN-GNR 341

Query:   401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460
             +L+KR + +L+ QID  E+++P+VE++L++IA++FVES+T F C LAKHRKSDTL+ +D+
Sbjct:   342 LLSKRKLHDLLQQIDSEEKIEPEVEELLLEIADEFVESVTNFACRLAKHRKSDTLDVRDV 401

Query:   461 LVHLERNWNMTLPGFSGDEI-KTFRK 485
              +HLERNWN+ LPGF+ D+I K+ RK
Sbjct:   402 QLHLERNWNIRLPGFASDDIVKSARK 427

GO:0000124 "SAGA complex" evidence=IDA

GO:0000790 "nuclear chromatin" evidence=IC

GO:0000991 "core RNA polymerase II binding transcription factor activity" evidence=ISO

GO:0005634 "nucleus" evidence=IDA

GO:0005669 "transcription factor TFIID complex" evidence=ISO

GO:0006338 "chromatin remodeling" evidence=IC

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISO

GO:0016573 "histone acetylation" evidence=ISO

GO:0046982 "protein heterodimerization activity" evidence=IEA

UNIPROTKB|Q5ZKX3 TAF12 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 58/125 (46%), Positives = 86/125 (68%)

Query:   361 RPPGSATQKPSSLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERL 420
             +P  ++T   SS+A     A   G  S   G  S E  N++LTK+ +Q+LV ++DP+E+L
Sbjct:    19 KPEPASTPPQSSMANSTAVAKMPGTPSG-GGRLSPE-SNQVLTKKKLQDLVREVDPNEQL 76

Query:   421 DPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEI 480
             D DVE++L+ IA+DF+ES+    C LA+HRKS+TLE KD+ +HLER WNM +PGF  +EI
Sbjct:    77 DEDVEEMLLQIADDFIESVVTAACQLARHRKSNTLEVKDVQLHLERQWNMWIPGFGSEEI 136

Query:   481 KTFRK 485
             + ++K
Sbjct:   137 RPYKK 141

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0000125 "PCAF complex" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0030914 "STAGA complex" evidence=IEA

GO:0033276 "transcription factor TFTC complex" evidence=IEA

GO:0043966 "histone H3 acetylation" evidence=IEA

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

UNIPROTKB|G3MXQ4 G3MXQ4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 61/127 (48%), Positives = 87/127 (68%)

Query:   360 TRPPGSATQKPSSLALVQ-PNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSE 418
             T P GS     SS A+V+ P    TG      G  S E  N++LTK+ +Q+LV ++DP+E
Sbjct:    25 TPPQGSMA---SSTAVVKIPGTPGTG------GRLSPE-SNQVLTKKKLQDLVREVDPNE 74

Query:   419 RLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGD 478
             +LD DVE++L+ IA+DF+ES+    C LA+HRKS TLE K++ +HLER WNM +PGFS +
Sbjct:    75 QLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKNVQLHLERQWNMWIPGFSSE 134

Query:   479 EIKTFRK 485
             EI+ ++K
Sbjct:   135 EIRPYKK 141

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

MGI|MGI:1913714 Taf12 "TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Mus musculus (taxid:10090)]

 Score = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 60/131 (45%), Positives = 88/131 (67%)

Query:   361 RPPGSATQKPSSLALVQPNAVQTGNQSKIAGTE------SDEFGNRILTKRSIQELVNQI 414
             +P  ++T    S+A    N+   G   KIAGT       S E  N++LTK+ +Q+LV ++
Sbjct:    19 KPEPASTPPQGSMA----NSTTVG---KIAGTPGTGGRLSPE-NNQVLTKKKLQDLVREV 70

Query:   415 DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPG 474
             DP+E+LD DVE++L+ IA+DF+ES+    C LA+HRKS TLE KD+ +HLER WNM +PG
Sbjct:    71 DPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQWNMWIPG 130

Query:   475 FSGDEIKTFRK 485
             F  +EI+ ++K
Sbjct:   131 FGSEEIRPYKK 141

GO:0000125 "PCAF complex" evidence=ISO

GO:0003677 "DNA binding" evidence=ISO;IDA

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005669 "transcription factor TFIID complex" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=ISO

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISO

GO:0008134 "transcription factor binding" evidence=ISO

GO:0030914 "STAGA complex" evidence=ISO;IDA

GO:0033276 "transcription factor TFTC complex" evidence=ISO

GO:0043966 "histone H3 acetylation" evidence=ISO

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=ISO

RGD|1592841 Taf12 "TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Rattus norvegicus (taxid:10116)]

 Score = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 57/128 (44%), Positives = 85/128 (66%)

Query:   361 RPPGSATQKPSSLALVQPNAVQTGNQSKIAGTE---SDEFGNRILTKRSIQELVNQIDPS 417
             +P  ++T    S+A    N+   G      GT    S E  N++LTK+ +Q+LV ++DP+
Sbjct:    19 KPEPASTPPQGSMA----NSTTVGKMPGTPGTGGRLSPE-NNQVLTKKKLQDLVREVDPN 73

Query:   418 ERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSG 477
             E+LD DVE++L+ IA+DF+ES+    C LA+HRKS TLE KD+ +HLER WNM +PGF  
Sbjct:    74 EQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQWNMWIPGFGS 133

Query:   478 DEIKTFRK 485
             +EI+ ++K
Sbjct:   134 EEIRPYKK 141

GO:0000125 "PCAF complex" evidence=ISO

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=ISO

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=ISO

GO:0005669 "transcription factor TFIID complex" evidence=ISO

GO:0006352 "DNA-dependent transcription, initiation" evidence=ISO

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISO

GO:0008134 "transcription factor binding" evidence=ISO

GO:0008150 "biological_process" evidence=ND

GO:0030914 "STAGA complex" evidence=ISO

GO:0033276 "transcription factor TFTC complex" evidence=ISO

GO:0043966 "histone H3 acetylation" evidence=ISO

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=ISO

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISO

GO:0004402 "histone acetyltransferase activity" evidence=ISO

UNIPROTKB|Q3T174 TAF12 "Transcription initiation factor TFIID subunit 12" [Bos taurus (taxid:9913)]

 Score = 293 (108.2 bits), Expect = 6.6e-26, P = 6.6e-26
 Identities = 60/127 (47%), Positives = 86/127 (67%)

Query:   360 TRPPGSATQKPSSLALVQ-PNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSE 418
             T P GS     +S A+V+ P    TG      G  S E  N++LTK+ +Q+LV ++DP+E
Sbjct:    25 TPPQGSMA---NSTAVVKIPGTPGTG------GRLSPE-NNQVLTKKKLQDLVREVDPNE 74

Query:   419 RLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGD 478
             +LD DVE++L+ IA+DF+ES+    C LA+HRKS TLE KD+ +HLER WNM +PGF  +
Sbjct:    75 QLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQWNMWIPGFGSE 134

Query:   479 EIKTFRK 485
             EI+ ++K
Sbjct:   135 EIRPYKK 141

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

ZFIN|ZDB-GENE-031030-5 taf12 "TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Danio rerio (taxid:7955)]

 Score = 293 (108.2 bits), Expect = 6.6e-26, P = 6.6e-26
 Identities = 59/124 (47%), Positives = 86/124 (69%)

Query:   362 PPGSATQKPSSLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLD 421
             PP S++   S++A   P  +  G     AG  S E G ++L+K+ +Q+LV +IDP+E+LD
Sbjct:    25 PPLSSSMANSTVA---PGKLP-GTPGP-AGRLSPE-GPQVLSKKKLQDLVREIDPNEQLD 78

Query:   422 PDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIK 481
              DVE++L+ IA+DF+ES+    C LA+HRKS TLE KD+ +HLER WNM +PGF  DEI+
Sbjct:    79 EDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQWNMWIPGFGSDEIR 138

Query:   482 TFRK 485
              ++K
Sbjct:   139 PYKK 142

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

UNIPROTKB|E2QVZ3 TAF12 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 292 (107.8 bits), Expect = 8.4e-26, P = 8.4e-26
 Identities = 55/125 (44%), Positives = 83/125 (66%)

Query:   361 RPPGSATQKPSSLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERL 420
             +P  ++T    S+A      V+        G  S E  N++LTK+ +Q+LV ++DP+E+L
Sbjct:    19 KPEPASTPPQGSMAN-STTVVKIPGTPGTGGRLSPE-NNQVLTKKKLQDLVREVDPNEQL 76

Query:   421 DPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEI 480
             D DVE++L+ IA+DF+ES+    C LA+HRKS TLE KD+ +HLER WNM +PGF  +EI
Sbjct:    77 DEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQWNMWIPGFGSEEI 136

Query:   481 KTFRK 485
             + ++K
Sbjct:   137 RPYKK 141

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00021654001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (351 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00032691001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (676 aa)					•	•	•		0.640
	GSVIVG00034077001	SubName- Full=Chromosome chr9 scaffold_7, whole genome shotgun sequence; (177 aa)					•	•			0.574
	GSVIVG00014940001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (712 aa)					•	•	•	•	0.551
	GSVIVG00018562001	SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (1798 aa)					•	•			0.456

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	496
cd07981	72	cd07981, TAF12, TATA Binding Protein (TBP) Associa	1e-40
pfam03847	67	pfam03847, TFIID_20kDa, Transcription initiation f	6e-40
COG5624	505	COG5624, TAF61, Transcription initiation factor TF	2e-19
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-11
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	4e-09
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-08
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-08
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	8e-08
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-07
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	3e-07
pfam04652	315	pfam04652, DUF605, Vta1 like	5e-07
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	3e-06
pfam04652	315	pfam04652, DUF605, Vta1 like	3e-06
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	4e-06
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	4e-06
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	8e-06
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	9e-06
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	1e-05
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	1e-05
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	2e-05
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	2e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	3e-05
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	3e-05
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	3e-05
COG3889	872	COG3889, COG3889, Predicted solute binding protein	3e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	5e-05
COG2036	91	COG2036, HHT1, Histones H3 and H4 [Chromatin struc	6e-05
pfam05539	408	pfam05539, Pneumo_att_G, Pneumovirinae attachment	6e-05
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	7e-05
pfam04652	315	pfam04652, DUF605, Vta1 like	1e-04
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	1e-04
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	1e-04
pfam00125	75	pfam00125, Histone, Core histone H2A/H2B/H3/H4	1e-04
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	2e-04
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	2e-04
PRK13042	291	PRK13042, PRK13042, superantigen-like protein; Rev	2e-04
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	2e-04
PRK11907	814	PRK11907, PRK11907, bifunctional 2',3'-cyclic nucl	2e-04
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	3e-04
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	3e-04
PRK13335	356	PRK13335, PRK13335, superantigen-like protein; Rev	3e-04
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	4e-04
pfam11725	1771	pfam11725, AvrE, Pathogenicity factor	4e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	5e-04
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	5e-04
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	5e-04
pfam05086	910	pfam05086, Dicty_REP, Dictyostelium (Slime Mold) R	5e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	6e-04
pfam05539	408	pfam05539, Pneumo_att_G, Pneumovirinae attachment	6e-04
PHA02638	417	PHA02638, PHA02638, CC chemokine receptor-like pro	6e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	8e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	8e-04
pfam01034	207	pfam01034, Syndecan, Syndecan domain	8e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	0.001
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	0.001
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	0.001
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	0.001
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	0.001
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	0.001
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	0.002
pfam05539	408	pfam05539, Pneumo_att_G, Pneumovirinae attachment	0.002
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	0.002
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	0.002
PLN02258	590	PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygen	0.002
pfam05109	830	pfam05109, Herpes_BLLF1, Herpes virus major outer	0.002
pfam00808	65	pfam00808, CBFD_NFYB_HMF, Histone-like transcripti	0.003
PRK12495	226	PRK12495, PRK12495, hypothetical protein; Provisio	0.003
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	0.004
pfam05086	910	pfam05086, Dicty_REP, Dictyostelium (Slime Mold) R	0.004
PRK12495	226	PRK12495, PRK12495, hypothetical protein; Provisio	0.004
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.004
PTZ00449	943	PTZ00449, PTZ00449, 104 kDa microneme/rhoptry anti	0.004
pfam04484	313	pfam04484, DUF566, Family of unknown function (DUF	0.004

>gnl|CDD|173964 cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

 Score =  140 bits (354), Expect = 1e-40
 Identities = 45/72 (62%), Positives = 61/72 (84%)

Query: 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460
           ILTKR +QEL+ +IDP E+LDPDVE++L++IA+DFV+ +    C LAKHRKSDTLE KD+
Sbjct: 1   ILTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDV 60

Query: 461 LVHLERNWNMTL 472
            +HLERNWN+++
Sbjct: 61  QLHLERNWNISI 72

The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. These TAFs, with the help of specific activators, are required only for expression of a subset of genes and are not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure. TAF12 domain interacts with TAF4 and makes a novel histone-like heterodimer that binds DNA and has a core promoter function of a subset of genes. Length = 72

>gnl|CDD|112650 pfam03847, TFIID_20kDa, Transcription initiation factor TFIID subunit A

 Score =  138 bits (349), Expect = 6e-40
 Identities = 44/67 (65%), Positives = 56/67 (83%)

Query: 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILV 462
           +KR +Q+LV QID + +LD DVED+L++IA+DFVES+T F C LAKHRKSD LE +DI +
Sbjct: 1   SKRKLQDLVQQIDSNTKLDEDVEDLLLEIADDFVESVTTFACKLAKHRKSDKLEVRDIQL 60

Query: 463 HLERNWN 469
           HLERNWN
Sbjct: 61  HLERNWN 67

Length = 67

>gnl|CDD|227911 COG5624, TAF61, Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]

 Score = 90.5 bits (224), Expect = 2e-19
 Identities = 70/275 (25%), Positives = 108/275 (39%), Gaps = 28/275 (10%)

Query: 208 AGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNF-QGQGLMRVSQVGSPGSSSPNTSQS 266
           AG     H  R  ++   R P      +   +       G+ R    G P  +       
Sbjct: 215 AGGVYGVHDGRSKRRLVDRYPQFQQGQKQVLSPQQRFLHGMERYEASGMPPPAE------ 268

Query: 267 VQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQ 326
                  W  S      P       R     PS       P+      T+L  ++  +  
Sbjct: 269 -------WAGSNGLHVLPGRREEVPRGIFRCPS-------PESSRGEPTHLDYRNGMANN 314

Query: 327 PQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVQTGNQ 386
            Q+S+        Y +           P  Q +       T+  +         + T  +
Sbjct: 315 AQRSR-FPGTCSIYPENPGKRWCSTKYP--QPLVHKGDRDTE--TGGCAAPDGGLATPGR 369

Query: 387 SKIAGTESDEFGNRILTKRSIQELVNQ-IDPSERLDPDVEDILVDIAEDFVESITMFGCS 445
            K    E D+   R+ +KR ++EL +  +D  E+++ +VE++L+  A+ FVE +T F C 
Sbjct: 370 DKGPLYERDD-LWRLDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCR 428

Query: 446 LAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEI 480
           LAKHRKSDTLE +D  +HLERNWN+  PGF  D I
Sbjct: 429 LAKHRKSDTLEVRDGQLHLERNWNIRCPGFVDDII 463

Length = 505

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 66.9 bits (163), Expect = 2e-11
 Identities = 75/398 (18%), Positives = 113/398 (28%), Gaps = 35/398 (8%)

Query: 6    PQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTP---STPSSTT 62
                  +  P  +        + S          P + PP ++ +  P P   S P    
Sbjct: 2609 RGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRAR 2668

Query: 63   IPTSTPTTNTPNPNPSPSPSPAPPSRPTSLT---PPPPRPTSFSRPWQPPQQHFSHFSSL 119
                    ++P   P    +       TSL    PPPP P                 ++ 
Sbjct: 2669 RLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAA 2728

Query: 120  PSSSSATPSTSASPPIPS----------PPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQ 169
              +S A P+  A P +P+          P R     G PAP P A      P   +    
Sbjct: 2729 RQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAV 2788

Query: 170  PFGGLGRSGVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPP 229
                  R  +  P     P    +    +L  ++   PAG             +   PP 
Sbjct: 2789 ASLSESRESLPSPWDPADPPAAVLAPAAALPPAA--SPAGPLPP--PTSAQPTAPPPPPG 2844

Query: 230  SSPSSQSPGTQNFQGQGLMRVSQVGSPGS-------------SSPNTSQSVQSFNQPWLS 276
              P S   G     G  + R     SP +             + P  S+S +SF  P   
Sbjct: 2845 PPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQ 2904

Query: 277  SGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQL 336
                 +P   PP   +PQ   P   Q    P                + +P  + P   L
Sbjct: 2905 PERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWL 2964

Query: 337  PDHYGQQFSSPR--VPQSSPHQQQITRPPGSATQKPSS 372
                  + + PR  VPQ +P ++         T    S
Sbjct: 2965 GALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSLS 3002

Length = 3151

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 59.0 bits (143), Expect = 4e-09
 Identities = 75/353 (21%), Positives = 115/353 (32%), Gaps = 18/353 (5%)

Query: 12  TQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPS---TPSSTTIPTSTP 68
              P P   T   AN + ST T S  T   + P ++   TPP PS    P  T  P S P
Sbjct: 68  PTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPP 127

Query: 69  TTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPS 128
            +  P+ +    P  +P   P +  P      +         +  +   S P  ++  PS
Sbjct: 128 PSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSSPEETARAPS 187

Query: 129 TSASPPIPSPPRGGIAIGVPAPRPT----ALSPQPSPPFSSSFGQPFGGLGRSGVNVPDS 184
           +  + P PS P    +   P         A SP P+P  S++          S       
Sbjct: 188 SPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGC 247

Query: 185 VRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPP---SSPSSQSPGTQN 241
              P  +      +  +                RP   SS   P     SPS  SPG+  
Sbjct: 248 GWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGP 307

Query: 242 FQGQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQ 301
                    S   S  SSS +TS S +S     +S G       +P     P  +  S  
Sbjct: 308 APSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRP-PPPADPSS-- 364

Query: 302 QRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSP 354
                P++    S        S+ +P + +    +     ++ ++ R P   P
Sbjct: 365 -----PRKRPRPSRAPSSPAASAGRPTRRRARAAVAGRARRRDATGRFPAGRP 412

Length = 1352

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 56.9 bits (137), Expect = 2e-08
 Identities = 64/323 (19%), Positives = 94/323 (29%), Gaps = 22/323 (6%)

Query: 6    PQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPT 65
            P  P   +    +  + T      +    +    P++  P      P TP  P+    P 
Sbjct: 2702 PPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPAR---PA 2758

Query: 66   STPTTNTPNPNPSPSPSPAPPSRPT-SLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSS 124
              PTT  P   P+P+P  AP + P   LT P     S SR   P     +   +   + +
Sbjct: 2759 RPPTTAGP---PAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPA 2815

Query: 125  ATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDS 184
            A    +ASP  P PP         + +PTA  P P P          G +   G      
Sbjct: 2816 AALPPAASPAGPLPP-------PTSAQPTA--PPPPPGPPPPSLPLGGSVAPGG---DVR 2863

Query: 185  VRPPAIQGMGVMGSLGSSSQMRPAGISVQHH-QPRPVQQSSLRPPPSSPSSQSPGTQNFQ 243
             RPP+        +       R A  +V    +   +       PP   +   P  Q   
Sbjct: 2864 RRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQP 2923

Query: 244  GQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGK--PPLAPPSTYRPQMNTPSMQ 301
                        P    P  + +         S          L P     P+   P   
Sbjct: 2924 PPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPA 2983

Query: 302  QRSHIPQQHSPLSTNLQQQHLSS 324
                 P   +P  T      +SS
Sbjct: 2984 PSREAPASSTPPLTGHSLSRVSS 3006

Length = 3151

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 56.9 bits (137), Expect = 2e-08
 Identities = 43/188 (22%), Positives = 58/188 (30%), Gaps = 11/188 (5%)

Query: 4    EQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTI 63
              P        P P++   T           S     S  P    ++ PP+ S  +    
Sbjct: 2818 LPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAA 2877

Query: 64   PTSTPTTNTPNPNPSPS------PSPAPPSRPTSLTPPPPRPTSF----SRPWQPPQQHF 113
            P   P      P  S S      P   P   P    PPPP+P        +P  PP    
Sbjct: 2878 PARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPP 2937

Query: 114  SHFSSLPSSSSATPSTSASPPIPSPPRGGIAIG-VPAPRPTALSPQPSPPFSSSFGQPFG 172
                 L  ++    +   S  +P P  G +  G V  PR     P PS    +S   P  
Sbjct: 2938 RPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLT 2997

Query: 173  GLGRSGVN 180
            G   S V+
Sbjct: 2998 GHSLSRVS 3005

Length = 3151

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 54.9 bits (132), Expect = 8e-08
 Identities = 76/417 (18%), Positives = 113/417 (27%), Gaps = 48/417 (11%)

Query: 14   TPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPS-TPSSTTIPTSTPTTNT 72
             P  S      A   S    TS+   P + P   + + P      P     P+  P    
Sbjct: 2563 APDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTH 2622

Query: 73   PNPNPSPSPSPAPPSRP---TSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATP-- 127
                P PSPSPA            PPP RP     P +  +   +      + +S+ P  
Sbjct: 2623 APDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQR 2682

Query: 128  -------------STSASPPIPSPPRGGIAIGVPAPRPTALSPQ-PSPPFSSSFGQPFGG 173
                         ++ A PP P P         P P P AL    P PP  ++  Q    
Sbjct: 2683 PRRRAARPTVGSLTSLADPPPPPPT--------PEPAPHALVSATPLPPGPAAARQASPA 2734

Query: 174  LGR--------SGVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSL 225
            L          +G   P     PA           +      AG   +  +P     S  
Sbjct: 2735 LPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSES 2794

Query: 226  RPPPSSPSSQSPGTQNFQGQG-LMRVSQVGSPGSSSPNTSQSVQS-----FNQPWLSSGS 279
            R    SP   +            +  +   +     P ++Q            P L  G 
Sbjct: 2795 RESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGG 2854

Query: 280  QGKP--PLAPPSTYRPQMNTPSMQQR---SHIPQQHSPLSTNLQQQHLSSVQPQQSKPSH 334
               P   +      R     P+   R     + +     ST          +      + 
Sbjct: 2855 SVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAP 2914

Query: 335  QLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVQTGNQSKIAG 391
              P    Q    P+ PQ  P      +PP + T  P+          Q    + + G
Sbjct: 2915 PPPQPQPQPPPPPQ-PQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPG 2970

Length = 3151

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 54.2 bits (131), Expect = 1e-07
 Identities = 57/397 (14%), Positives = 90/397 (22%), Gaps = 46/397 (11%)

Query: 9   PQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTP 68
           P        +         A++    +   AP++ P       P       +   P    
Sbjct: 394 PAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGA 453

Query: 69  TTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPS 128
            +  P   PS  P+PAP + P     P P P +   P   P          P++ +A   
Sbjct: 454 PSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAA--------PAAPAAPAG 505

Query: 129 TSASPPIPS---------PPRGGIAIGVPAPRPTALSPQ--------PSPPFSSSFGQP- 170
              +  +           P R      +  P  T L  +         +   +  F  P 
Sbjct: 506 ADDAATLRERWPEILAAVPKRSRKTWAILLPEATVLGVRGDTLVLGFSTGGLARRFASPG 565

Query: 171 ------------FGGLGRSGVNV---PDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHH 215
                        G  G   V     P               S       RPA  +    
Sbjct: 566 NAEVLVTALAEELG--GDWQVEAVVGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAA 623

Query: 216 QPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWL 275
              P    +      + +S +P       +   +   V                   P  
Sbjct: 624 PAAPAPAGA--AAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGA-APAA 680

Query: 276 SSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQ 335
              +      A P+   P    P+        Q   P +   Q    +S     +     
Sbjct: 681 PPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVP 740

Query: 336 LPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSS 372
           LP            P   P           A   P S
Sbjct: 741 LPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPS 777

Length = 824

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 52.7 bits (127), Expect = 3e-07
 Identities = 30/171 (17%), Positives = 45/171 (26%), Gaps = 3/171 (1%)

Query: 3   QEQPQQPQQT-QTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSST 61
             +P  P        P+      A   +S      + AP   P                 
Sbjct: 612 AARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPA 671

Query: 62  TIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTS--FSRPWQPPQQHFSHFSSL 119
               + P    P P P+   +PA  +       P   P +     P   P Q     S+ 
Sbjct: 672 KAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAP 731

Query: 120 PSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQP 170
             ++         P  P  P G  A   P P P   +   + P  S   + 
Sbjct: 732 SPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEE 782

Length = 824

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 51.2 bits (123), Expect = 5e-07
 Identities = 30/156 (19%), Positives = 46/156 (29%), Gaps = 22/156 (14%)

Query: 11  QTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTT 70
           + + P P          A    T S  + P            P+    SS  +P+     
Sbjct: 144 EGEDPNPGPPLDEEDEDADVATTNSDNSFPGEDA--DPASASPSDPPSSSPGVPSFPSPP 201

Query: 71  NTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTS 130
             P+     S  PAP S  +   PP P                      P++ S  P  +
Sbjct: 202 EDPSSPSDSSLPPAPSSFQSDTPPPSPES--------------------PTNPSPPPGPA 241

Query: 131 ASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSS 166
           A PP P      ++   P P   + +P P    +  
Sbjct: 242 APPPPPVQQVPPLSTAKPTPPSASATPAPIGGITLD 277

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 49.6 bits (119), Expect = 3e-06
 Identities = 33/199 (16%), Positives = 49/199 (24%), Gaps = 19/199 (9%)

Query: 39  APSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPR 98
           AP+S  P ++   P  P+ P++   P        P    +                  P 
Sbjct: 602 APASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPD 661

Query: 99  PTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQ 158
            +     W               ++       A+P  P+      A   PAP  T  + Q
Sbjct: 662 ASDGGDGWPAKAG------GAAPAAPPPAPAPAAPAAPAGAAP--AQPAPAPAATPPAGQ 713

Query: 159 PSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPR 218
              P +       G    S         PP                  PAG   Q   P 
Sbjct: 714 ADDPAAQPPQAAQGASAPSPAADDPVPLPPE-----------PDDPPDPAGAPAQPPPPP 762

Query: 219 PVQQSSLRPPPSSPSSQSP 237
               ++       PS  S 
Sbjct: 763 APAPAAAPAAAPPPSPPSE 781

Length = 824

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 48.5 bits (116), Expect = 3e-06
 Identities = 23/114 (20%), Positives = 41/114 (35%), Gaps = 2/114 (1%)

Query: 4   EQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTI 63
           E+ +      T + ++     A+ AS++ +    ++P         + P +PS  S    
Sbjct: 156 EEDEDADVATTNSDNSFPGEDADPASASPSDPPSSSPGVPSFPSPPEDPSSPSDSSLPPA 215

Query: 64  PTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPP--PRPTSFSRPWQPPQQHFSH 115
           P+S  +   P    SP+    PP       PP     P S ++P  P       
Sbjct: 216 PSSFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPLSTAKPTPPSASATPA 269

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 49.4 bits (118), Expect = 4e-06
 Identities = 54/348 (15%), Positives = 82/348 (23%), Gaps = 21/348 (6%)

Query: 25  ANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPA 84
              A           P         ++  TP+   ST  P S       +P P    SP 
Sbjct: 58  GAAACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREG--SPTPPGPSSPD 115

Query: 85  PPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIA 144
           PP        PPP P         P          P ++S   + ++   + S       
Sbjct: 116 PPPPTPPPASPPPSPAPDLSEMLRP----VGSPGPPPAASPPAAGASPAAVASDAASSRQ 171

Query: 145 IGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMGSLGSSSQ 204
             +P   P   +  PS P +                   S                S+S 
Sbjct: 172 AALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPI--------------SASA 217

Query: 205 MRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSSPNTS 264
             PA    +         SS      S                  ++       +S    
Sbjct: 218 SSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNG 277

Query: 265 QSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSS 324
            S +       SS  +  P  +P S       +      S    + S  S+       S 
Sbjct: 278 PSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSR 337

Query: 325 VQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSS 372
                  PS         +   P  P S   + + +R P S       
Sbjct: 338 GAAVSPGPSPS-RSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGR 384

Length = 1352

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 49.0 bits (117), Expect = 4e-06
 Identities = 39/191 (20%), Positives = 52/191 (27%), Gaps = 11/191 (5%)

Query: 200 GSSSQMRPAGISVQHHQPRPVQQSS--LRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPG 257
           G++ +  P        QP+P   +   L         Q         Q   +V   G P 
Sbjct: 127 GTAPKPEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPP 186

Query: 258 SSSPNTSQSVQS----FNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPL 313
             +    Q        + QP      Q +P    P    P            +PQQ  PL
Sbjct: 187 RQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLP---APSQAPAQPPLPPQLPQQPPPL 243

Query: 314 STNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRV--PQSSPHQQQITRPPGSATQKPS 371
                      + P   +P  Q       Q   P    P   P   Q    P    Q+P 
Sbjct: 244 QQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQ 303

Query: 372 SLALVQPNAVQ 382
            L LVQ    Q
Sbjct: 304 LLPLVQQPQGQ 314

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 48.3 bits (115), Expect = 8e-06
 Identities = 21/93 (22%), Positives = 31/93 (33%), Gaps = 5/93 (5%)

Query: 6   PQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPT 65
           P    Q   PT +  +      A ST   +   A        ++   P P  P     P 
Sbjct: 362 PVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPR----PV 417

Query: 66  STPTTNTPNPNPSPSPSPAP-PSRPTSLTPPPP 97
           + P  +TP   P  + +  P   +P    P PP
Sbjct: 418 APPVPHTPESAPKLTRAAIPVDEKPKYTPPAPP 450

Length = 585

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.9 bits (114), Expect = 9e-06
 Identities = 22/106 (20%), Positives = 30/106 (28%), Gaps = 9/106 (8%)

Query: 44  PPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFS 103
            PQ  + T   PS    T  P++ P        P   P     + P    P PPRP +  
Sbjct: 365 APQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPP----PVPPRPVAPP 420

Query: 104 RPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPA 149
            P  P          L  ++          P   P     A+    
Sbjct: 421 VPHTPESA-----PKLTRAAIPVDEKPKYTPPAPPKEEEKALIADG 461

Length = 585

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.5 bits (113), Expect = 1e-05
 Identities = 28/106 (26%), Positives = 39/106 (36%), Gaps = 8/106 (7%)

Query: 2   DQEQPQQPQQTQTPT----PSTTTTTTANTASSTVTTSQITAPSSQPPQ--QQQQTPPTP 55
           D    + P+Q   P      +    + A  AS + + S   A  S P    Q   TPPT 
Sbjct: 368 DASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTV 427

Query: 56  STPSSTTIPTSTPTT--NTPNPNPSPSPSPAPPSRPTSLTPPPPRP 99
           S      +P + P+T      P         P S+ +SL P   RP
Sbjct: 428 SVDPPAAVPVNPPSTAPQAVRPAQFKEEKKIPVSKVSSLGPSTLRP 473

Length = 614

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 47.6 bits (114), Expect = 1e-05
 Identities = 24/116 (20%), Positives = 37/116 (31%), Gaps = 7/116 (6%)

Query: 3   QEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTP--SS 60
                 PQ    P P  +    A       TTSQ+ A   Q  + Q  T    S P  +S
Sbjct: 388 TAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQQLQRAQGATKAKKSEPAAAS 447

Query: 61  TTIPTSTPTTNTPNPNPSPSPSPAPPS-----RPTSLTPPPPRPTSFSRPWQPPQQ 111
              P ++      +  P+PS     P+     R  +  P   +    + P    + 
Sbjct: 448 RARPVNSALERLASVRPAPSALEKAPAKKEAYRWKATNPVEVKKEPVATPKALKKA 503

Length = 647

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 46.7 bits (111), Expect = 2e-05
 Identities = 43/255 (16%), Positives = 59/255 (23%), Gaps = 26/255 (10%)

Query: 120 PSSSSATPSTSASPPIPSPPRGGIAIGVPA---PRPTALSPQPSPPFSSSFGQPFGGLGR 176
              S  +  TS   P  S               P P+     P P               
Sbjct: 88  GPDSDLSQKTSTFSPCQSGYEASTDPEYIPDLQPDPSLWGTAPKP-------------EP 134

Query: 177 SGVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSS--PSS 234
                P+S   P      ++      +Q++    + Q  QP         PP  +  P  
Sbjct: 135 QPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQ 194

Query: 235 QSPGTQNFQGQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQ 294
             P       Q      +   P    P  SQ+      P                    Q
Sbjct: 195 GPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQ 254

Query: 295 MNTPSM-----QQRSHIPQQHSP---LSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSS 346
           M  P       QQ+   PQ   P     T           P       QL     Q    
Sbjct: 255 MPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQ 314

Query: 347 PRVPQSSPHQQQITR 361
            R PQ      Q+++
Sbjct: 315 QRGPQFREQLVQLSQ 329

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 46.8 bits (112), Expect = 2e-05
 Identities = 21/163 (12%), Positives = 40/163 (24%), Gaps = 18/163 (11%)

Query: 6   PQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPT 65
           P  P   +   P  +    A+  ++   T+ +  P +        + P  +        T
Sbjct: 361 PAAPLP-EPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETT 419

Query: 66  S------TPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSL 119
           S                 +    PA  SR   +     R  S        ++        
Sbjct: 420 SQLLAARQQLQRAQGATKAKKSEPAAASRARPVNSALERLASVRPAPSALEK-------- 471

Query: 120 PSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPP 162
             +        A+ P+            P     AL  + +P 
Sbjct: 472 APAKKEAYRWKATNPVEVKKEPVAT---PKALKKALEHEKTPE 511

Length = 647

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 46.5 bits (111), Expect = 3e-05
 Identities = 23/131 (17%), Positives = 39/131 (29%), Gaps = 12/131 (9%)

Query: 32  VTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTS 91
           +  +      +          P  +   +   P +          P+P+ +P P   P  
Sbjct: 385 LGVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAA-------PAPAAAPQPAPAPAP 437

Query: 92  LTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPR 151
              PP    +      P        ++ PS+  A    +A  P  +P     A   PA  
Sbjct: 438 APAPPSPAGNAPAGGAPSPPP----AAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAA 493

Query: 152 PTALSPQPSPP 162
           P A    P+ P
Sbjct: 494 PAA-PAAPAAP 503

Length = 824

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 46.3 bits (110), Expect = 3e-05
 Identities = 66/359 (18%), Positives = 95/359 (26%), Gaps = 36/359 (10%)

Query: 35  SQITAPSSQPPQQQQQTPPTPST-PSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLT 93
                          Q+    ST P         P+     P P P P  AP S+P   T
Sbjct: 89  PDSDLSQKTSTFSPCQSGYEASTDPEYIPDLQPDPSLWGTAPKPEPQPPQAPESQPQPQT 148

Query: 94  P------PPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGV 147
           P               +  Q PQ        LP      P  +A P    P +       
Sbjct: 149 PAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMP--PRQAAFPQQGPPEQPPGYPQP 206

Query: 148 PAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMGSLGSSSQMRP 207
           P   P  + PQ   P  S                     P     +      G S QM P
Sbjct: 207 PQGHPEQVQPQQFLPAPSQAPAQP---------PLPPQLPQQPPPLQQPQFPGLSQQMPP 257

Query: 208 AGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSSPNTSQSV 267
                   Q +P Q  +  PP + P+      Q               P    P   Q  
Sbjct: 258 PPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRG 317

Query: 268 QSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQP 327
             F +  +    Q +  L+     R +        +     +++ L T   +  ++ +Q 
Sbjct: 318 PQFREQLVQLSQQQREALSQEEAKRAKRR-----HKIVSLSKYNGLMTPRDKDFITRIQL 372

Query: 328 QQSKPSHQL-PDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVQTGN 385
            Q         D Y Q +S             I R   S  Q  +  A  Q    Q+G+
Sbjct: 373 SQLVTEDPYNEDFYFQVYS----------AGIIQRGRQSPEQPLNQFA--QTYLEQSGH 419

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 46.3 bits (110), Expect = 3e-05
 Identities = 20/100 (20%), Positives = 29/100 (29%), Gaps = 11/100 (11%)

Query: 15  PTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPN 74
           P P     T A  +    T +  T P +          P   T         TP    P 
Sbjct: 364 PAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETA--------TPPPVPPR 415

Query: 75  P--NPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQH 112
           P   P P    + P    +  P   +P   + P  P ++ 
Sbjct: 416 PVAPPVPHTPESAPKLTRAAIPVDEKPKY-TPPAPPKEEE 454

Length = 585

>gnl|CDD|226406 COG3889, COG3889, Predicted solute binding protein [General function prediction only]

 Score = 46.4 bits (110), Expect = 3e-05
 Identities = 21/86 (24%), Positives = 33/86 (38%), Gaps = 7/86 (8%)

Query: 11  QTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTT 70
            T   T  T T     + + T TT   +A S+     +  +       + T   T T   
Sbjct: 763 GTSITTSGTFTAEVPQSPTKTETTLSYSAYSNTSILIETTSV----VITKTVTQTQTT-- 816

Query: 71  NTPNPNPSPSPSPAPPSRPTSLTPPP 96
            T +P+P+ + SP   S  T+ T  P
Sbjct: 817 -TSSPSPTQTTSPTQTSTSTTTTTSP 841

Length = 872

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 45.7 bits (109), Expect = 5e-05
 Identities = 24/162 (14%), Positives = 36/162 (22%), Gaps = 1/162 (0%)

Query: 2   DQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSST 61
               P        P  ++        A            +S             +  +  
Sbjct: 623 APAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPP 682

Query: 62  TIPTST-PTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLP 120
             P    P          P+P+PA          P  +P   ++    P         LP
Sbjct: 683 PAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLP 742

Query: 121 SSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPP 162
                 P  + +P  P PP        PA  P    P     
Sbjct: 743 PEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEE 784

Length = 824

>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and dynamics]

 Score = 41.5 bits (98), Expect = 6e-05
 Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

Query: 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDIL 461
           L K  ++ ++ +    ER+     + L +  E+++E I      LA+H K  T++A+DI 
Sbjct: 20  LPKAPVRRILRKAGA-ERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIK 78

Length = 91

>gnl|CDD|114270 pfam05539, Pneumo_att_G, Pneumovirinae attachment membrane glycoprotein G

 Score = 45.0 bits (106), Expect = 6e-05
 Identities = 36/138 (26%), Positives = 49/138 (35%), Gaps = 9/138 (6%)

Query: 3   QEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTT 62
           Q QP   Q  QT T +   ++T    +   TTS    P ++PP  Q+    +P  P STT
Sbjct: 196 QSQPA-TQGHQTATANQRLSSTEPVGTQGTTTSSNPEPQTEPPPSQRGPSGSPQHPPSTT 254

Query: 63  IP--TSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFS------RPWQPPQQHFS 114
               ++T             P+ +    P S   PPP            RP    Q   S
Sbjct: 255 SQDQSTTGDGQEHTQRRKTPPATSNRRSPHSTATPPPTTKRQETGRPTPRPTATTQSGSS 314

Query: 115 HFSSLPSSSSATPSTSAS 132
              S P    A P+T   
Sbjct: 315 PPHSSPPGVQANPTTQNL 332

Length = 408

>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 44.6 bits (106), Expect = 7e-05
 Identities = 18/92 (19%), Positives = 27/92 (29%), Gaps = 1/92 (1%)

Query: 1   MDQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSS 60
             Q  P     T  P  +       +T  +   T  +    +     QQ     PS  + 
Sbjct: 158 SGQSVPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQANV 217

Query: 61  TTIPTSTPTTNTPNPNPSPSPS-PAPPSRPTS 91
            T  T  P         +P P+  A  S P +
Sbjct: 218 DTAATPAPAAPATPDGAAPLPTDQAGVSTPAA 249

Length = 331

>gnl|CDD|218191 pfam04652, DUF605, Vta1 like

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 30/133 (22%), Positives = 47/133 (35%), Gaps = 13/133 (9%)

Query: 51  TPPTPSTP-------SSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFS 103
             P P  P       +      S  +    + +P+ +    PPS    +   P  P   S
Sbjct: 146 EDPNPGPPLDEEDEDADVATTNSDNSFPGEDADPASASPSDPPSSSPGVPSFPSPPEDPS 205

Query: 104 RPWQPPQQHF--SHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSP 161
            P          S  S  P  S  +P+  + PP P+ P       VP       + +P+P
Sbjct: 206 SPSDSSLPPAPSSFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPLS----TAKPTP 261

Query: 162 PFSSSFGQPFGGL 174
           P +S+   P GG+
Sbjct: 262 PSASATPAPIGGI 274

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Length = 315

>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 23/104 (22%), Positives = 36/104 (34%), Gaps = 4/104 (3%)

Query: 2   DQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSST 61
           DQ   +  Q +    P  T+TTT        T +      + P   Q     T   P+  
Sbjct: 148 DQSSAELSQNSGQSVPLDTSTTTDPAT----TPAPAAPVDTTPTNSQTPAVATAPAPAVD 203

Query: 62  TIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRP 105
               +    +  N + + +P+PA P+ P    P P      S P
Sbjct: 204 PQQNAVVAPSQANVDTAATPAPAAPATPDGAAPLPTDQAGVSTP 247

Length = 331

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 44.2 bits (105), Expect = 1e-04
 Identities = 15/67 (22%), Positives = 24/67 (35%)

Query: 35  SQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTP 94
           S+I   S+         P  P  P   + P +     TP+P P+ +  P P     +   
Sbjct: 366 SEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAEPTEPS 425

Query: 95  PPPRPTS 101
           P P   +
Sbjct: 426 PTPPANA 432

Length = 620

>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4

 Score = 40.2 bits (95), Expect = 1e-04
 Identities = 16/56 (28%), Positives = 24/56 (42%)

Query: 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460
           R ++EL        R+       L +  ED +E I      LA+H K  T+  +DI
Sbjct: 13  RVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKRKTITPRDI 68

Length = 75

>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 16/96 (16%), Positives = 32/96 (33%), Gaps = 5/96 (5%)

Query: 2   DQEQPQQPQQTQTPTPSTTTTTTANTASSTV-TTSQITAPSSQPPQQQQQTPPTPSTPSS 60
           +  Q      + T  P+TT    A   ++   + +   A +  P    QQ      + ++
Sbjct: 157 NSGQSVPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQAN 216

Query: 61  TTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPP 96
                 T  T  P    +P  +   P+    ++ P 
Sbjct: 217 VD----TAATPAPAAPATPDGAAPLPTDQAGVSTPA 248

Length = 331

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 21/95 (22%), Positives = 33/95 (34%), Gaps = 8/95 (8%)

Query: 68  PTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATP 127
           P        P+   +PA P        P  +  +   P   P        +  +S+ A P
Sbjct: 366 PAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAP--------AAAASAPAAP 417

Query: 128 STSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPP 162
             +A P   + P        PA  P A++  P+PP
Sbjct: 418 PAAAPPAPVAAPAAAAPAAAPAAAPAAVALAPAPP 452

Length = 618

>gnl|CDD|183854 PRK13042, PRK13042, superantigen-like protein; Reviewed

 Score = 43.1 bits (101), Expect = 2e-04
 Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 16  TPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTP---PTPSTPSSTTIPTSTPTTNT 72
           T    TTTT    ++T +++++ AP S PP  + + P   P  +TP ST +     T N 
Sbjct: 17  TTGVITTTTQAANATTPSSTKVEAPQSTPPSTKVEAPQSKPNATTPPSTKVEAPQQTPNA 76

Query: 73  PNPNPSPSPSPAPPSR---PTSLTP 94
             P+ +   +P  P+    PT + P
Sbjct: 77  TTPSSTKVETPQSPTTKQVPTEINP 101

Length = 291

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 43.7 bits (104), Expect = 2e-04
 Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 9/84 (10%)

Query: 17  PSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPN 76
            ST   T A  A++   ++   AP+++ P      PP  + P+             P   
Sbjct: 39  GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPA---------APPKPAAA 89

Query: 77  PSPSPSPAPPSRPTSLTPPPPRPT 100
            + + +PA P    +   P     
Sbjct: 90  AAAAAAPAAPPAAAAAAAPAAAAV 113

Length = 1228

>gnl|CDD|237019 PRK11907, PRK11907, bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein; Reviewed

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 19/88 (21%), Positives = 31/88 (35%), Gaps = 6/88 (6%)

Query: 8   QPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTST 67
           Q ++  T TP+T+T     T   +  T +     +          P+ S  + T+ PTS 
Sbjct: 27  QAEEIVTTTPATSTEAEQTTPVESDATEEADNTETPVAATTAAEAPSSSETAETSDPTSE 86

Query: 68  PTTNTPNPNPSPSPSPAPPSRPTSLTPP 95
            T  T       S +       T  + P
Sbjct: 87  ATDTT------TSEARTVTPAATETSKP 108

Length = 814

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.0 bits (102), Expect = 3e-04
 Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 1/79 (1%)

Query: 9   PQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTP 68
           P    +   + +       A +         PS+   +Q   TP  P   +S  IP    
Sbjct: 361 PSAFISEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAE 420

Query: 69  TTNTPNPNPSPSPSPAPPS 87
            T  P+P P  + + APPS
Sbjct: 421 PT-EPSPTPPANAANAPPS 438

Length = 620

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.3 bits (102), Expect = 3e-04
 Identities = 31/228 (13%), Positives = 61/228 (26%), Gaps = 13/228 (5%)

Query: 5   QPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIP 64
           +P Q      P  +          ++    +   AP++ P           +  +    P
Sbjct: 364 RPGQSGGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAP 423

Query: 65  TSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSS 124
                          + +  P   P     P   P + +RP     +  +  ++   + +
Sbjct: 424 ARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARA 483

Query: 125 ATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDS 184
           A  +  A      PP   +     +P P      P+   + S   P           PD 
Sbjct: 484 APAAAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDP-------ATADPDD 536

Query: 185 VRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSP 232
                        +  ++   R A  +     PRP + S+   P    
Sbjct: 537 AFETLAP------APAAAPAPRAAAATEPVVAPRPPRASASGLPDMFD 578

Length = 700

>gnl|CDD|139494 PRK13335, PRK13335, superantigen-like protein; Reviewed

 Score = 42.8 bits (100), Expect = 3e-04
 Identities = 26/97 (26%), Positives = 39/97 (40%), Gaps = 9/97 (9%)

Query: 5   QPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSST-TI 63
           Q    +Q +TP          NT     + S+I    SQP Q++Q++    +TP+     
Sbjct: 64  QAANTRQERTPKLEKA----PNTNEEKTSASKIEK-ISQPKQEEQKSLNISATPAPKQEQ 118

Query: 64  PTSTPTTNTPNPNPSPSPS---PAPPSRPTSLTPPPP 97
             +T  + TP    +  PS   P P     S TP  P
Sbjct: 119 SQTTTESTTPKTKVTTPPSTNTPQPMQSTKSDTPQSP 155

Length = 356

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.6 bits (101), Expect = 4e-04
 Identities = 15/83 (18%), Positives = 20/83 (24%), Gaps = 2/83 (2%)

Query: 27  TASSTVTTSQI--TAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPA 84
             S     S      P+  P        P+           S P      P P P+    
Sbjct: 364 FISEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAEPTE 423

Query: 85  PPSRPTSLTPPPPRPTSFSRPWQ 107
           P   P +     P   +    WQ
Sbjct: 424 PSPTPPANAANAPPSLNLEELWQ 446

Length = 620

>gnl|CDD|221188 pfam11725, AvrE, Pathogenicity factor

 Score = 43.2 bits (102), Expect = 4e-04
 Identities = 57/295 (19%), Positives = 91/295 (30%), Gaps = 21/295 (7%)

Query: 21  TTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPS 80
              + NTA+ T    + T  +  P   QQ       T  ++    S    N         
Sbjct: 2   QLISINTATKTAVQPEATPSAGAPTGLQQS--SESPTQRASHSLASEGKKNRKKMPKVFQ 59

Query: 81  PSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPR 140
            S AP        PP     + + P            +LP        T A    PS  R
Sbjct: 60  KSSAPRQ--IQAAPPQALNPTAAAPQSSRGPTLRELLALPEDD---GETQAPESSPSARR 114

Query: 141 GGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMGSLG 200
              + GV       L+ +P     +        L +S      S RPP  +  G    + 
Sbjct: 115 LTRSEGVARHEMEDLAGRPVVKPDADRQLRQDILNKSS----SSRRPPVSKEEGTSSKMP 170

Query: 201 -----SSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGS 255
                S++  +   I  +    R  Q S  R   S  +  +        Q ++  S  G 
Sbjct: 171 ATALASAALFKDDEIRQEVDAARSDQASQSRLSRSRGNPPAIPPDAAPRQPMLTRSAGGR 230

Query: 256 PGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQH 310
                 N  +++Q   Q  ++   +GK   +  +   P +NT  +QQ    P Q 
Sbjct: 231 FEGEDENLERNLQP--QSPITLDKKGKLDFSGFNP--PALNT-LLQQTLGKPGQT 280

This family is secreted by gram-negative Gammaproteobacteria such as Pseudomonas syringae of tomato and the fire blight plant pathogen Erwinia amylovora, amongst others. It is an essential pathogenicity factor of approximately 198 kDa. Its injection into the host-plant is dependent upon the bacterial type III or Hrp secretion system. The family is long and carries a number of predicted functional regions, including an ERMS or endoplasmic reticulum membrane retention signal at both the C- and the N-termini, a leucine-zipper motif from residues 539-560, and a nuclear localisation signal at 1358-1361. this conserved AvrE-family of effectors is among the few that are required for full virulence of many phytopathogenic pseudomonads, erwinias and pantoeas. Length = 1771

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 42.5 bits (100), Expect = 5e-04
 Identities = 49/244 (20%), Positives = 69/244 (28%), Gaps = 34/244 (13%)

Query: 1   MDQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSS 60
                   P  +     ++     ++ ASS     Q   P S P +    T   PS+P +
Sbjct: 140 PVGSPGPPPAASPPAAGASPAAVASDAASS----RQAALPLSSPEE----TARAPSSPPA 191

Query: 61  TTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLP 120
              P++ P         + SP P   S P S +   P P              S  SS  
Sbjct: 192 EPPPSTPP--------AAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSE 243

Query: 121 SSSSATPSTSASP-------PIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGG 173
           SS       +  P        +P+          P+ RP   S   SP   S    P   
Sbjct: 244 SSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSP 303

Query: 174 LGRSGVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPS 233
                 + P +             S  SS +   +  S      R    S    P  SPS
Sbjct: 304 GSGPAPSSPRAS-----------SSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPS 352

Query: 234 SQSP 237
              P
Sbjct: 353 PSRP 356

Length = 1352

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.3 bits (100), Expect = 5e-04
 Identities = 19/92 (20%), Positives = 30/92 (32%), Gaps = 6/92 (6%)

Query: 11  QTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTT 70
           ++Q+ + S T  T      S         P+  PP  Q      P TP       +  ++
Sbjct: 511 ESQSGSASNTAKTPPPPQKSP------PPPAPTPPLPQPTATAPPPTPPPPPPTATQASS 564

Query: 71  NTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSF 102
           N P   P+ S  P P     + +P        
Sbjct: 565 NAPAQIPADSSPPPPIPEEPTPSPTKDSSPEE 596

Length = 620

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 42.6 bits (101), Expect = 5e-04
 Identities = 19/110 (17%), Positives = 38/110 (34%), Gaps = 11/110 (10%)

Query: 40  PSSQPPQ-----QQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTP 94
           P+S  P             T +  ++     +  +     P      +PAP     +   
Sbjct: 22  PNSVDPSWREFFADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPA 81

Query: 95  PPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIA 144
            PP+P + +     P       +   ++++A P+ +A     +P RG  A
Sbjct: 82  APPKPAAAAAAAAAP------AAPPAAAAAAAPAAAAVEDEVTPLRGAAA 125

Length = 1228

>gnl|CDD|218421 pfam05086, Dicty_REP, Dictyostelium (Slime Mold) REP protein

 Score = 42.5 bits (100), Expect = 5e-04
 Identities = 18/96 (18%), Positives = 28/96 (29%), Gaps = 10/96 (10%)

Query: 8   QPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTST 67
           QP +    T +TTTTTT  T        +          Q  +     + P        +
Sbjct: 247 QPSKRPNNTTTTTTTTTTTTFQPRTRKRKSIDDHKLSLNQAPEKFKNNTKPDDDPQSDFS 306

Query: 68  PTT--------NTPNPNPSPSPSPAPPSRPTSLTPP 95
                      +    N S S S    +   S++P 
Sbjct: 307 DKGSRKSGSLKDVRIDNISCSVSHNGVN--ISISPT 340

This family consists of REP proteins from Dictyostelium (Slime molds). REP protein is likely involved in transcription regulation and control of DNA replication, specifically amplification of plasmid at low copy numbers. The formation of homomultimers may be required for their regulatory activity. Length = 910

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.1 bits (99), Expect = 6e-04
 Identities = 18/94 (19%), Positives = 29/94 (30%), Gaps = 4/94 (4%)

Query: 22  TTTANTASSTVTTSQITAPS-SQP---PQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNP 77
           T   + AS      Q   P  +QP   PQ       +PS   S+     +   +   P  
Sbjct: 363 TQKGDDASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAG 422

Query: 78  SPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQ 111
           +P      P     + PP   P +        ++
Sbjct: 423 TPPTVSVDPPAAVPVNPPSTAPQAVRPAQFKEEK 456

Length = 614

>gnl|CDD|114270 pfam05539, Pneumo_att_G, Pneumovirinae attachment membrane glycoprotein G

 Score = 41.6 bits (97), Expect = 6e-04
 Identities = 32/134 (23%), Positives = 46/134 (34%), Gaps = 2/134 (1%)

Query: 6   PQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPT 65
           P Q      P      T TAN   S+ T    T  ++     + QT P PS    +  P 
Sbjct: 190 PSQVTPQSQPATQGHQTATANQRLSS-TEPVGTQGTTTSSNPEPQTEPPPSQRGPSGSPQ 248

Query: 66  STPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSA 125
             P+T + + + +         R T       R    +    P  +        P  ++ 
Sbjct: 249 HPPSTTSQDQSTTGDGQEHTQRRKTPPATSNRRSPHSTATPPPTTKRQETGRPTPRPTAT 308

Query: 126 TPSTSASPPIPSPP 139
           T S S SPP  SPP
Sbjct: 309 TQSGS-SPPHSSPP 321

Length = 408

>gnl|CDD|165021 PHA02638, PHA02638, CC chemokine receptor-like protein; Provisional

 Score = 41.9 bits (98), Expect = 6e-04
 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 23 TTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTT-IPTSTPTTNTPNPNPSPSP 81
           ++ T SS + +S   +P++    +           + T  IPT  PT+ +P+PN + S 
Sbjct: 3  NSSTTLSSIILSSSTLSPTTFFTIETSMDESKSIISTFTEIIPTEIPTSESPSPNSNSSS 62

Query: 82 SPAPPSRPTS 91
          S +  S   +
Sbjct: 63 SSSSSSSSIT 72

Length = 417

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 41.8 bits (98), Expect = 8e-04
 Identities = 75/371 (20%), Positives = 100/371 (26%), Gaps = 60/371 (16%)

Query: 45   PQQQQQTPPTPSTPSSTTIPTSTPTTNTP------------------NPNPSPSPSPAPP 86
                   PP PS  +   +P                              P P P  APP
Sbjct: 2502 GPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTWIRGLEELASDDAGDPPPPLPPAAPP 2561

Query: 87   SRPTSLTPPP---PRPTS------FSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPS 137
            + P    PPP   PRP+         RP  PPQ                P    +PP P 
Sbjct: 2562 AAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGP----APPSPL 2617

Query: 138  PPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMG 197
            PP         AP P   SP P+        +P      +          PA     V  
Sbjct: 2618 PP------DTHAPDPPPPSPSPAA------NEPDPHPPPTVPPPERPRDDPA--PGRVSR 2663

Query: 198  SLGSSSQMRPAGISVQHHQPRPVQ--------QSSLRPPPSSPSSQSPGTQNFQGQGLMR 249
               +    R A  S    +PR            S   PPP  P+ +           L  
Sbjct: 2664 PRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPP 2723

Query: 250  VSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTP-----SMQQRS 304
                    S +   + +  +      + G   +P   PP+T  P    P     +   R 
Sbjct: 2724 GPAAARQASPALPAAPAPPAVPAGPATPGGPARPA-RPPTTAGPPAPAPPAAPAAGPPRR 2782

Query: 305  HIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPG 364
                  + LS + +        P     +   P       +SP  P   P   Q T PP 
Sbjct: 2783 LTRPAVASLSESRESLPSPW-DPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPP 2841

Query: 365  SATQKPSSLAL 375
                 P SL L
Sbjct: 2842 PPGPPPPSLPL 2852

Length = 3151

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.7 bits (98), Expect = 8e-04
 Identities = 16/102 (15%), Positives = 28/102 (27%), Gaps = 4/102 (3%)

Query: 7   QQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQ--TPPTPSTPSSTTIP 64
           Q  Q+    +             +    +   + ++       Q      PS P S T P
Sbjct: 361 QLTQKGDDASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQP 420

Query: 65  -TSTPTTNTPNPNPSP-SPSPAPPSRPTSLTPPPPRPTSFSR 104
             + PT +   P   P +P    P           +    S+
Sbjct: 421 AGTPPTVSVDPPAAVPVNPPSTAPQAVRPAQFKEEKKIPVSK 462

Length = 614

>gnl|CDD|216257 pfam01034, Syndecan, Syndecan domain

 Score = 40.5 bits (95), Expect = 8e-04
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 2   DQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSST 61
           D E  +    + TP   TTT+++ +  ++T +TS  T+P+            T ++PS T
Sbjct: 64  DDEDSEPVTTSATPPKLTTTSSSPSNDTTTASTSTKTSPTVSTTV------TTTTSPSET 117

Query: 62  TIPTSTPTTNTPNPNPSPSPSPAPPSRP 89
               +T T +T  P    S +   PS+ 
Sbjct: 118 DTEEATTTVSTETPTEGGSSAATDPSKN 145

Syndecans are transmembrane heparin sulfate proteoglycans which are implicated in the binding of extracellular matrix components and growth factors. Length = 207

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.1 bits (97), Expect = 0.001
 Identities = 32/203 (15%), Positives = 53/203 (26%), Gaps = 12/203 (5%)

Query: 64  PTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSS 123
           P          P P+ S  P   +RP +  P  P   +   P           ++     
Sbjct: 590 PAPGAAGGEGPPAPASSGPPEEAARPAA--PAAPAAPAAPAPAGAAAAPAEASAAPAPGV 647

Query: 124 SATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPD 183
           +A         +P    GG      A      +P P+P   ++   P G         P 
Sbjct: 648 AAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPA-PAAPAAPAGAAPAQPAPAPA 706

Query: 184 SVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQ 243
           +  P                  +P   +     P P     +  PP       P     Q
Sbjct: 707 ATPPAG---------QADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQ 757

Query: 244 GQGLMRVSQVGSPGSSSPNTSQS 266
                  +   +P ++ P +  S
Sbjct: 758 PPPPPAPAPAAAPAAAPPPSPPS 780

Length = 824

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 22/114 (19%), Positives = 36/114 (31%), Gaps = 12/114 (10%)

Query: 47  QQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPW 106
           Q+         P     P  T     P P+ + + SP+P    +S    P  P S ++P 
Sbjct: 364 QKGDDASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQ--SSAAAQPSAPQSATQPA 421

Query: 107 QPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPS 160
             P       S  P ++      S +P    P +          +   +S   S
Sbjct: 422 GTPPT----VSVDPPAAVPVNPPSTAPQAVRPAQ------FKEEKKIPVSKVSS 465

Length = 614

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.5 bits (98), Expect = 0.001
 Identities = 21/79 (26%), Positives = 25/79 (31%)

Query: 27  TASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPP 86
           +AS+T  T      S  PP      P   +T    T P   PT    + N          
Sbjct: 516 SASNTAKTPPPPQKSPPPPAPTPPLPQPTATAPPPTPPPPPPTATQASSNAPAQIPADSS 575

Query: 87  SRPTSLTPPPPRPTSFSRP 105
             P     P P PT  S P
Sbjct: 576 PPPPIPEEPTPSPTKDSSP 594

Length = 620

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.1 bits (97), Expect = 0.001
 Identities = 20/78 (25%), Positives = 25/78 (32%)

Query: 35  SQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTP 94
           S   +  +        TP    +P    I  S P T      PSP P+ A P  P    P
Sbjct: 362 SAFISEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAEP 421

Query: 95  PPPRPTSFSRPWQPPQQH 112
             P PT  +     P   
Sbjct: 422 TEPSPTPPANAANAPPSL 439

Length = 620

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 19/126 (15%), Positives = 41/126 (32%), Gaps = 1/126 (0%)

Query: 17  PSTTTTTTANTASSTVTTSQITAPS-SQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNP 75
           P+      A     T    +  AP+ +   Q      P  +  ++ + P + P    P P
Sbjct: 366 PAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAP 425

Query: 76  NPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPI 135
             +P+ +    +   +       P   ++            +  P+ +SA P+ +A+P  
Sbjct: 426 VAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAA 485

Query: 136 PSPPRG 141
                 
Sbjct: 486 ARLTPT 491

Length = 618

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.4 bits (97), Expect = 0.001
 Identities = 22/170 (12%), Positives = 45/170 (26%), Gaps = 5/170 (2%)

Query: 3   QEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTT 62
               +       P         A  AS+    + +T  +      +       +   +  
Sbjct: 371 GVPARVAGAVPAPGA---RAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPP 427

Query: 63  IPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSS 122
              + P T     + +   +P P       +         ++P        +  S  P  
Sbjct: 428 AAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPD 487

Query: 123 SSATPSTSASPPIPSPPRGGIAIGVPA--PRPTALSPQPSPPFSSSFGQP 170
           ++  P+  A+ P  + P        PA   R  A +    P   +    P
Sbjct: 488 AAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTP 537

Length = 830

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 40.6 bits (96), Expect = 0.002
 Identities = 23/128 (17%), Positives = 35/128 (27%), Gaps = 25/128 (19%)

Query: 39  APSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPR 98
           AP  +P    Q   P  S  ++   PT+          P P P+ AP   P    P    
Sbjct: 363 APLPEPEVPPQSAAPAASAQATAA-PTAAVAPPQAPAVPPP-PASAPQQAPAVPLPETTS 420

Query: 99  PTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQ 158
               +R              L  +  AT +  + P   S             RP   + +
Sbjct: 421 QLLAARQ------------QLQRAQGATKAKKSEPAAAS-----------RARPVNSALE 457

Query: 159 PSPPFSSS 166
                  +
Sbjct: 458 RLASVRPA 465

Length = 647

>gnl|CDD|114270 pfam05539, Pneumo_att_G, Pneumovirinae attachment membrane glycoprotein G

 Score = 40.4 bits (94), Expect = 0.002
 Identities = 47/152 (30%), Positives = 61/152 (40%), Gaps = 3/152 (1%)

Query: 18  STTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNP 77
           +T+ TT+  T  S  T      P SQP  Q  QT       SST    +  TT + NP P
Sbjct: 173 TTSKTTSWPTEVSHPTYPSQVTPQSQPATQGHQTATANQRLSSTEPVGTQGTTTSSNPEP 232

Query: 78  SPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPS 137
              P P+      S   PP   +         Q+H     + P++S+     S + P P+
Sbjct: 233 QTEPPPSQRGPSGSPQHPPSTTSQDQSTTGDGQEHTQRRKTPPATSNRRSPHSTATPPPT 292

Query: 138 PPRGGIAIGVPAPRPTA-LSPQPSPPFSSSFG 168
             R     G P PRPTA      SPP SS  G
Sbjct: 293 TKR--QETGRPTPRPTATTQSGSSPPHSSPPG 322

Length = 408

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 21/143 (14%), Positives = 36/143 (25%), Gaps = 15/143 (10%)

Query: 34  TSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSR--PTS 91
            +   A    P + +   P       +   P            P+  P+ APP+     +
Sbjct: 371 EAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPA 430

Query: 92  LTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPR 151
              P   P +                     + A P T A P   +P          A  
Sbjct: 431 AAAPAAAPAAAPAAVALAP---------APPAQAAPETVAIPVRVAPEPA----VASAAP 477

Query: 152 PTALSPQPSPPFSSSFGQPFGGL 174
             A +P  +    +  G  +   
Sbjct: 478 APAAAPAAARLTPTEEGDVWHAT 500

Length = 618

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 40.3 bits (95), Expect = 0.002
 Identities = 10/78 (12%), Positives = 21/78 (26%), Gaps = 6/78 (7%)

Query: 24  TANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSP 83
            +  A +    +   A S+       + P  P+         + P      P P+ + + 
Sbjct: 39  GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAP------PKPAAAAAA 92

Query: 84  APPSRPTSLTPPPPRPTS 101
           A              P +
Sbjct: 93  AAAPAAPPAAAAAAAPAA 110

Length = 1228

>gnl|CDD|215145 PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 8/74 (10%)

Query: 45  PQQQQQTPPTPSTPSSTTIPTST-PTTNTPNPN-------PSPSPSPAPPSRPTSLTPPP 96
            + Q     + S+ S ++ P+ST P      P+       PS  P P   S        P
Sbjct: 8   SRSQSHASSSSSSSSQSSPPSSTSPRPRRRKPSASSLLHTPSILPLPKLSSPSPPSVTLP 67

Query: 97  PRPTSFSRPWQPPQ 110
           P  T+ +    P Q
Sbjct: 68  PAATTQTPQLNPLQ 81

Length = 590

>gnl|CDD|218439 pfam05109, Herpes_BLLF1, Herpes virus major outer envelope glycoprotein (BLLF1)

 Score = 40.5 bits (94), Expect = 0.002
 Identities = 62/322 (19%), Positives = 109/322 (33%), Gaps = 28/322 (8%)

Query: 9   PQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTP 68
           P+ T   + +T+ T  A + +  VTT   T+P++      Q+T  TP+  S T I     
Sbjct: 483 PEDTSPTSRTTSATPNATSPTPAVTTPNATSPTT------QKTSDTPNATSPTPIVIGVT 536

Query: 69  TTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPS 128
           TT T  P  + S   A   + T  +P     T+       P    S  +S  ++      
Sbjct: 537 TTATSPPTGTTSVPNATSPQVTEESPVN--NTNTPVVTSAP----SVLTSAVTTGQHGTG 590

Query: 129 TSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPP 188
           +S +   P  P            P + S   +P  +S+   P GG   +    P      
Sbjct: 591 SSPTSQQPGIPS------SSHSTPRSNSTSTTPLLTSA--HPTGGENITEET-PSVPSTT 641

Query: 189 AIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLM 248
            +  +      G++SQ+   G S     P  V  +   P P++ S  +P  Q      + 
Sbjct: 642 HVSTLSPGPGPGTTSQVSGPGNSSTSRYPGEVHVTEGMPNPNATSPSAPSGQKTAVPTVT 701

Query: 249 RVSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQ-------GKPPLAPPSTYRPQMNTPSMQ 301
                 +  +   + S  + S +        +          P +  S  RP+    S  
Sbjct: 702 STGGKANSTTKETSGSTLMASTSPHTNEGAFRTTPYNATTYLPPSTSSKLRPRWTFTSPP 761

Query: 302 QRSHIPQQHSPLSTNLQQQHLS 323
             +       P + +    +LS
Sbjct: 762 VTTKQATVPVPPTQHPDHSNLS 783

This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. Length = 830

>gnl|CDD|201453 pfam00808, CBFD_NFYB_HMF, Histone-like transcription factor (CBF/NF-Y) and archaeal histone

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 11/55 (20%), Positives = 27/55 (49%)

Query: 407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDIL 461
           ++ ++     + R+  D ++++ +  E+F+E I      + K  K  T+ A+ I 
Sbjct: 8   VKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIK 62

This family includes archaebacterial histones and histone like transcription factors from eukaryotes. Length = 65

>gnl|CDD|183558 PRK12495, PRK12495, hypothetical protein; Provisional

 Score = 38.7 bits (90), Expect = 0.003
 Identities = 16/87 (18%), Positives = 27/87 (31%), Gaps = 3/87 (3%)

Query: 9   PQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTP 68
           P     P         +    ++ T++   A +  P     +  PTP   +    P +  
Sbjct: 96  PDDDAQPAAEAEAADQSAPPEASSTSATDEAATDPPATAAARDGPTPDPTAQ---PATPD 152

Query: 69  TTNTPNPNPSPSPSPAPPSRPTSLTPP 95
              +P   P  S  P  PS P +    
Sbjct: 153 ERRSPRQRPPVSGEPPTPSTPDAHVAG 179

Length = 226

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 39.4 bits (92), Expect = 0.004
 Identities = 19/111 (17%), Positives = 22/111 (19%)

Query: 5   QPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIP 64
                   Q P P                      P   P   QQQ  P           
Sbjct: 221 PAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQN 280

Query: 65  TSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSH 115
             TP    P    +P P P  P     +  P  +        Q  Q     
Sbjct: 281 QPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQFREQLVQLSQQQ 331

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|218421 pfam05086, Dicty_REP, Dictyostelium (Slime Mold) REP protein

 Score = 39.4 bits (92), Expect = 0.004
 Identities = 13/63 (20%), Positives = 21/63 (33%)

Query: 2   DQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSST 61
           +  Q    Q ++ P  +TTTTTT  T +    T +  +         Q      +     
Sbjct: 239 ENIQRINSQPSKRPNNTTTTTTTTTTTTFQPRTRKRKSIDDHKLSLNQAPEKFKNNTKPD 298

Query: 62  TIP 64
             P
Sbjct: 299 DDP 301

This family consists of REP proteins from Dictyostelium (Slime molds). REP protein is likely involved in transcription regulation and control of DNA replication, specifically amplification of plasmid at low copy numbers. The formation of homomultimers may be required for their regulatory activity. Length = 910

>gnl|CDD|183558 PRK12495, PRK12495, hypothetical protein; Provisional

 Score = 38.3 bits (89), Expect = 0.004
 Identities = 20/92 (21%), Positives = 28/92 (30%), Gaps = 1/92 (1%)

Query: 20  TTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSP 79
             T  ++  S           +      Q   P   ST ++    T  P T      P+P
Sbjct: 83  EATAPSDAGSQASPDDDAQPAAEAEAADQSAPPEASSTSATDEAATDPPATAAARDGPTP 142

Query: 80  SPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQ 111
            P+ A P+ P     P  RP     P  P   
Sbjct: 143 DPT-AQPATPDERRSPRQRPPVSGEPPTPSTP 173

Length = 226

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 39.0 bits (91), Expect = 0.004
 Identities = 32/143 (22%), Positives = 37/143 (25%), Gaps = 13/143 (9%)

Query: 2   DQEQPQQPQQTQTPTPST----TTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPS- 56
           D      P   Q P P      T    A  A      +  T   +  P      P  P+ 
Sbjct: 50  DPSPQAPPPVAQLPQPLPQPPPTQALQALPAGDQQQHNTPTGSPAANPPATFALPAGPAG 109

Query: 57  ----TPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQH 112
               T      P   P   T NP  SP   PA       L      P S     Q P Q 
Sbjct: 110 PTIQTEPGQLYPVQVPVMVTQNPANSPLDQPAQQRALQQLQQRYGAPASG----QLPSQQ 165

Query: 113 FSHFSSLPSSSSATPSTSASPPI 135
            S   +  S     P+    P  
Sbjct: 166 QSAQKNDESQLQQQPNGETPPQQ 188

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|185628 PTZ00449, PTZ00449, 104 kDa microneme/rhoptry antigen; Provisional

 Score = 39.7 bits (92), Expect = 0.004
 Identities = 39/167 (23%), Positives = 58/167 (34%), Gaps = 9/167 (5%)

Query: 2   DQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSST 61
           D E+P++P++ ++    T   +        +  S     S + P++    PP P  PSS 
Sbjct: 590 DPEEPKKPKRPRSAQRPTRPKSPKLPELLDIPKSPKRPESPKSPKR----PPPPQRPSSP 645

Query: 62  TIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSS-LP 120
             P       +P P  SP P P  P              + S+  +        F S L 
Sbjct: 646 ERPEGPKIIKSPKPPKSPKP-PFDPKFKEKFYDDYLDAAAKSKETKTTVVLDESFESILK 704

Query: 121 SSSSATPSTSASPPIPSP---PRGGIAIGVPAPRPTALSPQPSPPFS 164
            +   TP T  + P P P   PR       P   P A  P     F+
Sbjct: 705 ETLPETPGTPFTTPRPLPPKLPRDEEFPFEPIGDPDAEQPDDIEFFT 751

Length = 943

>gnl|CDD|218107 pfam04484, DUF566, Family of unknown function (DUF566)

 Score = 38.8 bits (90), Expect = 0.004
 Identities = 21/120 (17%), Positives = 36/120 (30%), Gaps = 2/120 (1%)

Query: 53  PTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSR--PWQPPQ 110
            + S  +S+   +S    ++   + S S  P   + P S     P   + S        Q
Sbjct: 8   GSTSGDASSPRSSSRRRLSSSFLSTSASSRPRRLNAPASPPSSSPARNTSSSSSFGLSKQ 67

Query: 111 QHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQP 170
           +  S      SS   +PS  +     S                + S + +    SS   P
Sbjct: 68  RPSSLSRGRLSSRFVSPSRGSPSAAASLNGSLATASTSGSSSPSRSRRTTSSDLSSGNGP 127

Family of related proteins that is plant specific. Length = 313

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	496
KOG1142	258	consensus Transcription initiation factor TFIID, s	100.0
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	99.96
COG5624	505	TAF61 Transcription initiation factor TFIID, subun	99.94
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	99.93
PLN00035	103	histone H4; Provisional	98.85
cd00076	85	H4 Histone H4, one of the four histones, along wit	98.8
PTZ00015	102	histone H4; Provisional	98.78
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	98.59
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	98.4
smart00803	65	TAF TATA box binding protein associated factor. TA	98.35
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	98.27
smart00417	74	H4 Histone H4.	98.23
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	98.15
KOG3467	103	consensus Histone H4 [Chromatin structure and dyna	98.14
smart00428	105	H3 Histone H3.	98.1
PLN00161	135	histone H3; Provisional	97.86
PLN00121	136	histone H3; Provisional	97.72
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	97.71
smart00576	77	BTP Bromodomain transcription factors and PHD doma	97.68
PTZ00018	136	histone H3; Provisional	97.63
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	97.56
PLN00160	97	histone H3; Provisional	97.54
PF02269	93	TFIID-18kDa: Transcription initiation factor IID,	97.42
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	97.25
smart00427	89	H2B Histone H2B.	97.19
PF02969	66	TAF: TATA box binding protein associated factor (T	97.06
KOG0869	168	consensus CCAAT-binding factor, subunit A (HAP3) [	96.85
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	96.83
PLN00158	116	histone H2B; Provisional	96.82
PTZ00463	117	histone H2B; Provisional	96.74
KOG3334	148	consensus Transcription initiation factor TFIID, s	96.55
cd07978	92	TAF13 The TATA Binding Protein (TBP) Associated Fa	96.55
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	96.53
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	96.26
KOG0871	156	consensus Class 2 transcription repressor NC2, bet	96.05
KOG1744	127	consensus Histone H2B [Chromatin structure and dyn	95.85
KOG2549	576	consensus Transcription initiation factor TFIID, s	95.74
KOG3423	176	consensus Transcription initiation factor TFIID, s	95.67
PF09415	72	CENP-X: CENP-S associating Centromere protein X; I	95.67
PF04719	90	TAFII28: hTAFII28-like protein conserved region; I	95.16
PF15511	414	CENP-T: Centromere kinetochore component CENP-T; P	94.68
KOG0870	172	consensus DNA polymerase epsilon, subunit D [Trans	94.67
PF03540	51	TFIID_30kDa: Transcription initiation factor TFIID	94.1
PF05236	264	TAF4: Transcription initiation factor TFIID compon	94.04
KOG1745	137	consensus Histones H3 and H4 [Chromatin structure	93.9
cd08045	212	TAF4 TATA Binding Protein (TBP) Associated Factor	93.79
COG5094	145	TAF9 Transcription initiation factor TFIID, subuni	92.77
COG5162	197	Transcription initiation factor TFIID, subunit TAF	92.64
COG5248	126	TAF19 Transcription initiation factor TFIID, subun	91.99
COG5150	148	Class 2 transcription repressor NC2, beta subunit	91.82
KOG3901	109	consensus Transcription initiation factor IID subu	91.13
smart00350	509	MCM minichromosome maintenance proteins.	88.86
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	88.84
PRK00411	394	cdc6 cell division control protein 6; Reviewed	88.67
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	88.32
smart00414	106	H2A Histone 2A.	88.24
COG5095	450	TAF6 Transcription initiation factor TFIID, subuni	87.56
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	86.24
COG5208	286	HAP5 CCAAT-binding factor, subunit C [Transcriptio	86.24
KOG3219	195	consensus Transcription initiation factor TFIID, s	85.47
KOG4336	323	consensus TBP-associated transcription factor Prod	84.88
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	84.14
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	83.48
PTZ00017	134	histone H2A; Provisional	81.22
PTZ00171	148	acyl carrier protein; Provisional	80.21

>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=100.00  E-value=3.3e-47  Score=366.62  Aligned_cols=215  Identities=35%  Similarity=0.479  Sum_probs=164.9

Q ss_pred             cccCccccccCCCCCCCCCCCCCCCCCCCCcchhccccCcccCCCCcchhhhhhcccccCCCCCCCCCCccccccccCC-
Q 010992          268 QSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSS-  346 (496)
Q Consensus       268 Q~~~Q~WL~~~~q~~p~l~sp~s~r~q~~~~~~QQr~h~~qQ~~~~~t~lqqqqlsq~qqqq~~~~~qqq~h~~QQl~~-  346 (496)
                      |..+++||+.+..+.++...| ++|+|++.+.+.+|.++.+|+-+.  +..+.+.   ....+...+..++|+. ++.. 
T Consensus        25 q~~qq~~~~~~~~~~s~~~~~-s~~~q~~~~~~~~~~~~~qq~~s~--~~~~~~~---~n~~~~s~~~~~~~~~-~~~~~   97 (258)
T KOG1142|consen   25 QARQQQWLRQIQGIPSPESYP-SQRQQRFSPTCSIRENPNQQWIST--GYPQPQV---SNGGPPSQALNQQDSQ-QSAIS   97 (258)
T ss_pred             HHHHhhhhccccCCCCCCCCh-hhccccCCCcccccCCCCcccccc--ccCcccc---ccCCchHHhhhhhhHH-hhccc
Confidence            455889999999898888886 999999999999998887777533  2221111   1111111112222332 2222 


Q ss_pred             -CCCCCCCccccccCCCCCCCCCCcccccc-CCCCccccCCcccCCCCcCCCcCCccCCHHHHHHHHHhhCCCCCCCHHH
Q 010992          347 -PRVPQSSPHQQQITRPPGSATQKPSSLAL-VQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDV  424 (496)
Q Consensus       347 -~~~~~~~~~qqq~~r~~~~~~qk~~sl~~-sqp~~~~~g~~~~~~~~~~~e~~nrILtKrKLqELVrqIDPsesLDpDV  424 (496)
                       .+.++....+....++.....++...-.. ++......+++.++.....++++++||.|+||+|||++||++++||+||
T Consensus        98 ~~q~P~~~~~q~~~~~~~~~~~~~~~~P~~~~~g~~~g~~~sp~~s~s~~~~~~~~il~k~kl~dLvqqId~~~~LD~dV  177 (258)
T KOG1142|consen   98 QQQQPASSPSQGSSMSNQTSSVQKDPAPVIGSQGSVSGGGTSPAGSSSQDEPGNNPILSKRKLDDLVQQIDGTTKLDDDV  177 (258)
T ss_pred             cCCCCccCCCCCCCccccCcccccCCCCCCCCCCccCCCCCCCCcccccccCCCCccccccchhHHHHhhcCcccccHHH
Confidence             34444455556666777777776654433 2233333455556777788999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCcccccccCCcccc
Q 010992          425 EDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRI  489 (496)
Q Consensus       425 EELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~rk~~~~  489 (496)
                      ||+||||||||||+|++|||+||||||+++||+|||+|||||+|||+||||++||+|.|||++..
T Consensus       178 edlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf~sd~~~~~~k~~pT  242 (258)
T KOG1142|consen  178 EDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGFSSDEKRSKKKALPT  242 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCccccccccccccCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999864

>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []

Probab=99.96  E-value=1.6e-30  Score=208.13  Aligned_cols=68  Identities=63%  Similarity=1.135  Sum_probs=57.9

Q ss_pred             CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCc
Q 010992          403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNM  470 (496)
Q Consensus       403 tKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI  470 (496)
                      +|++|++||++|||+++||+||||+|++||||||++|+++||+||||||+++||+|||+|||||+|||
T Consensus         1 ~K~~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~~ni   68 (68)
T PF03847_consen    1 SKRKLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERNWNI   68 (68)
T ss_dssp             -HHHHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHHS--
T ss_pred             ChHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhhcCC
Confidence            69999999999999999999999999999999999999999999999999999999999999999997

; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.

>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=99.94  E-value=5.1e-29  Score=253.42  Aligned_cols=102  Identities=44%  Similarity=0.670  Sum_probs=93.9

Q ss_pred             ccCCCCcCCCcCCccCCHHHHHHHHHhh-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          387 SKIAGTESDEFGNRILTKRSIQELVNQI-DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       387 ~~~~~~~~~e~~nrILtKrKLqELVrqI-DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      .|++-++. ++..||+.|+||+||++.| |..++||.||||+||++|||||+.|.+|+|+||||||+|+||++||+||||
T Consensus       370 ~k~p~ye~-D~~~Rl~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhlE  448 (505)
T COG5624         370 DKGPLYER-DDLWRLDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHLE  448 (505)
T ss_pred             cCCCchhc-chhhhhhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeeec
Confidence            34555542 4568999999999999999 999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCccccCCCccccc-ccCCcccc
Q 010992          466 RNWNMTLPGFSGDEIK-TFRKPVRI  489 (496)
Q Consensus       466 RnWNI~IPGFssDEIr-~~rk~~~~  489 (496)
                      |+|||++|||.+|+|+ .|||....
T Consensus       449 rnwnIr~pGf~~d~I~~s~rk~~pt  473 (505)
T COG5624         449 RNWNIRCPGFVDDIIHMSYRKQKPT  473 (505)
T ss_pred             cccceecCcchHHHHHHHHHhcCCC
Confidence            9999999999999998 99998754

>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=99.93  E-value=7.8e-26  Score=180.62  Aligned_cols=72  Identities=63%  Similarity=1.080  Sum_probs=70.7

Q ss_pred             cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992          401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I  472 (496)
                      +++|++|++||++||++++||+||+++|+++|||||++|+++||+||||||++||+++||+|||||+|||+|
T Consensus         1 i~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~~~~~   72 (72)
T cd07981           1 ILTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNWNISI   72 (72)
T ss_pred             CCcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCC
Confidence            689999999999999999999999999999999999999999999999999999999999999999999986

The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind

>PLN00035 histone H4; Provisional

Probab=98.85  E-value=1.3e-08  Score=88.55  Aligned_cols=74  Identities=24%  Similarity=0.358  Sum_probs=69.1

Q ss_pred             CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCc
Q 010992          402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSG  477 (496)
Q Consensus       402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFss  477 (496)
                      |+|..|.+|++.- .-+.|.+|+.|.|.++.++|+++|+..|+.+|+|.+-.||+++||.|.|+|.+. .+.||+.
T Consensus        30 ipk~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~-~lyGf~~  103 (103)
T PLN00035         30 ITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR-TLYGFGG  103 (103)
T ss_pred             CCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCC-cCCCCCC
Confidence            8999999999986 578999999999999999999999999999999999999999999999999755 8999963

>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution

Probab=98.80  E-value=2.2e-08  Score=84.28  Aligned_cols=74  Identities=24%  Similarity=0.384  Sum_probs=69.4

Q ss_pred             ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992          400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF  475 (496)
Q Consensus       400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF  475 (496)
                      .-|+|..|.+|++.- +-..|.+|+.|.|.++.++|+++|+..|+.+|+|.+-.||+..||.+.|+|. |..+-||
T Consensus        12 ~gi~k~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~-g~~~ygf   85 (85)
T cd00076          12 KGITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQ-GRTLYGY   85 (85)
T ss_pred             ccCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHC-CCCccCC
Confidence            449999999999985 5789999999999999999999999999999999999999999999999995 8888887

>PTZ00015 histone H4; Provisional

Probab=98.78  E-value=3e-08  Score=86.14  Aligned_cols=76  Identities=24%  Similarity=0.337  Sum_probs=69.3

Q ss_pred             CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992          398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF  475 (496)
Q Consensus       398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF  475 (496)
                      .-+-|+|..|.+|++.- .-+.|.+|+.|.|.++.++|+++|+..|+.+|+|.+-.||+++||.|.|+|.+. .+-||
T Consensus        27 ~i~gI~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~-~~ygf  102 (102)
T PTZ00015         27 NIRGITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR-TLYGF  102 (102)
T ss_pred             cccCCCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC-CCCCC
Confidence            34568999999999974 778999999999999999999999999999999999999999999999999755 77777

>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]

Probab=98.59  E-value=8.6e-08  Score=81.85  Aligned_cols=71  Identities=24%  Similarity=0.386  Sum_probs=66.4

Q ss_pred             CcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          396 EFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      .+...+|++..+.+|+|++... ++..++.|.|.+.+++|+..|.+.||.+|+|.|..||+.+||++.|++.
T Consensus        14 ~~~~~~Lp~apv~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~   84 (91)
T COG2036          14 RSTDLLLPKAPVRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRL   84 (91)
T ss_pred             hhhhhhcCchHHHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHh
Confidence            3566789999999999999665 9999999999999999999999999999999999999999999999885

>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]

Probab=98.40  E-value=5e-07  Score=70.85  Aligned_cols=68  Identities=22%  Similarity=0.317  Sum_probs=61.5

Q ss_pred             CccCCHHHHHHHHHhhCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          399 NRILTKRSIQELVNQIDPS----ERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPs----esLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      ...+.|--+..|+++|..+    ..++.++.++|..++|+|+.+|++.|+.+|+|.|..+|..+||++++..
T Consensus         3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~   74 (75)
T PF00125_consen    3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI   74 (75)
T ss_dssp             SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred             ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence            3456778888888888665    7999999999999999999999999999999999999999999998864

Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....

>smart00803 TAF TATA box binding protein associated factor

Probab=98.35  E-value=2e-06  Score=68.77  Aligned_cols=64  Identities=22%  Similarity=0.308  Sum_probs=59.6

Q ss_pred             cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      +|++..|.+|++.++- ..|.+|+.+.|.+.++.|+..|+..|+++++|-|..||...||.+.|+
T Consensus         2 ~~p~~~i~ria~~~Gi-~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk   65 (65)
T smart00803        2 WLPKETIKDVAESLGI-GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR   65 (65)
T ss_pred             CCCHHHHHHHHHHCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence            5789999999999744 589999999999999999999999999999999999999999999885

TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.

>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=98.27  E-value=3.5e-06  Score=73.86  Aligned_cols=68  Identities=13%  Similarity=0.288  Sum_probs=60.3

Q ss_pred             HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcccc
Q 010992          405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLP  473 (496)
Q Consensus       405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IP  473 (496)
                      +-+..+++.. +-+.++++|...|+|++..++.+|+..|..+|||-|.++|+++||+|.++...+..|-
T Consensus         5 ~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~   72 (117)
T cd07979           5 RVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFT   72 (117)
T ss_pred             HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCC
Confidence            3466777765 5578999999999999999999999999999999999999999999999998885553

The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi

>smart00417 H4 Histone H4

Probab=98.23  E-value=3e-06  Score=70.12  Aligned_cols=64  Identities=19%  Similarity=0.299  Sum_probs=59.2

Q ss_pred             CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHH
Q 010992          398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILV  462 (496)
Q Consensus       398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQL  462 (496)
                      ..+-|+|..|.+|+++ .+-+.|..++.|.|.++.++|+++|+..|+.+|+|.+-.||++.||.|
T Consensus        10 ~i~gI~k~~IrRLaRr-~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~   73 (74)
T smart00417       10 NIQGITKPAIRRLARR-GGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY   73 (74)
T ss_pred             hhcCCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence            3456999999999997 477899999999999999999999999999999999999999999975

>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin

Probab=98.15  E-value=7.8e-06  Score=63.49  Aligned_cols=63  Identities=14%  Similarity=0.274  Sum_probs=55.6

Q ss_pred             CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992          402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL  464 (496)
Q Consensus       402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL  464 (496)
                      |.+.++..+++.......+..|+.++|.+.++.||+.++..|...|++.+..||..+||...|
T Consensus         3 lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av   65 (65)
T PF00808_consen    3 LPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV   65 (65)
T ss_dssp             S-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred             CChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence            678899999999855668999999999999999999999999999999999999999997664

The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....

>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]

Probab=98.14  E-value=8.1e-06  Score=70.85  Aligned_cols=78  Identities=24%  Similarity=0.333  Sum_probs=69.1

Q ss_pred             CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCc
Q 010992          398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSG  477 (496)
Q Consensus       398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFss  477 (496)
                      .-+-|+|-.|.+|.+.- .-..+..-..|-.-..+.+||+||+..||-.+.|-|.+||...||.+.|+|. ++.+-||++
T Consensus        26 nIqgitKpaIRRlARr~-GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~-G~~~~g~~~  103 (103)
T KOG3467|consen   26 NIQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ-GRTLYGFGG  103 (103)
T ss_pred             hccccchHHHHHHHHhc-CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHc-CceeeccCC
Confidence            34557899999999974 4567788888889999999999999999999999999999999999999996 999999974

>smart00428 H3 Histone H3

Probab=98.10  E-value=8.5e-06  Score=71.28  Aligned_cols=69  Identities=25%  Similarity=0.241  Sum_probs=63.0

Q ss_pred             CcCCccCCHHHHHHHHHhhCC------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992          396 EFGNRILTKRSIQELVNQIDP------SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL  464 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqIDP------sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL  464 (496)
                      .+.+-+|.|.-+.+||++|..      +..+.+++.++|.+.+|+|+.++.+.+..+|+|.|-.||..|||+|+.
T Consensus        24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~   98 (105)
T smart00428       24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLAR   98 (105)
T ss_pred             cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHH
Confidence            356678899999999999942      468999999999999999999999999999999999999999999986

>PLN00161 histone H3; Provisional

Probab=97.86  E-value=4.2e-05  Score=69.80  Aligned_cols=78  Identities=21%  Similarity=0.125  Sum_probs=67.5

Q ss_pred             CcCCccCCHHHHHHHHHhhC-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCc
Q 010992          396 EFGNRILTKRSIQELVNQID-----PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNM  470 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqID-----PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI  470 (496)
                      .+.+-+|.|--++.||++|-     .+..+..++.++|.|.+|+|+-++.+.+-..|.|+|--||..|||+|+. |--+.
T Consensus        50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~-rirg~  128 (135)
T PLN00161         50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLAR-RIRGP  128 (135)
T ss_pred             cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHH-Hhccc
Confidence            45677889999999999993     3478999999999999999999999999999999999999999999986 44455


Q ss_pred             cccC
Q 010992          471 TLPG  474 (496)
Q Consensus       471 ~IPG  474 (496)
                      ++.+
T Consensus       129 ~~~~  132 (135)
T PLN00161        129 IYGI  132 (135)
T ss_pred             cccc
Confidence            5543

>PLN00121 histone H3; Provisional

Probab=97.72  E-value=7.2e-05  Score=68.28  Aligned_cols=69  Identities=23%  Similarity=0.201  Sum_probs=63.8

Q ss_pred             CcCCccCCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992          396 EFGNRILTKRSIQELVNQID----PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL  464 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqID----PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL  464 (496)
                      .+.+-+|.|--+..||++|.    .+..+..++.++|.|.+|+|+-++.+.+-..|.|.|--||..|||+|+.
T Consensus        57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~  129 (136)
T PLN00121         57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR  129 (136)
T ss_pred             cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence            45678899999999999994    4579999999999999999999999999999999999999999999986

>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []

Probab=97.71  E-value=0.00011  Score=66.25  Aligned_cols=73  Identities=16%  Similarity=0.330  Sum_probs=52.5

Q ss_pred             ccCCH--HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcccc
Q 010992          400 RILTK--RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLP  473 (496)
Q Consensus       400 rILtK--rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IP  473 (496)
                      ..+.|  +.|..|++.+ +-...|+.|.-.|||+|-.|+.+|+..|-.+|+|.+..++++.||+|.++-..+..|-
T Consensus         9 ~~~PrDa~~i~~iL~~~-Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~   83 (129)
T PF02291_consen    9 KSLPRDARVIHLILKSM-GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFT   83 (129)
T ss_dssp             ----HHHHHHHHHHHHT-T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT------
T ss_pred             ccCChHHHHHHHHHHHc-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhcc
Confidence            34444  4577888887 4456899999999999999999999999999999999999999999999977776663

TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=97.68  E-value=0.00028  Score=57.26  Aligned_cols=68  Identities=12%  Similarity=0.261  Sum_probs=58.3

Q ss_pred             CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992          403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       403 tKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I  472 (496)
                      -|..+..+++.. +-+.+++++.|.|.+|+++|+..+...+-++|+|-+..++.+.||.+.|++ .|+.+
T Consensus         8 l~~~Vaqil~~~-Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~-~gi~~   75 (77)
T smart00576        8 LRIAVAQILESA-GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN-LGISV   75 (77)
T ss_pred             HHHHHHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH-hCccc
Confidence            355566666654 457899999999999999999999999999999999999999999999987 47765

subdomain of archael histone-like transcription factors

>PTZ00018 histone H3; Provisional

Probab=97.63  E-value=9.8e-05  Score=67.40  Aligned_cols=69  Identities=23%  Similarity=0.201  Sum_probs=63.9

Q ss_pred             CcCCccCCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992          396 EFGNRILTKRSIQELVNQID----PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL  464 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqID----PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL  464 (496)
                      ...+-+|.|--+..||++|.    .+..+..++.++|.|.+|+|+-++.+.+-..|.|.|--||..|||+|+.
T Consensus        57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~  129 (136)
T PTZ00018         57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR  129 (136)
T ss_pred             ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence            45678899999999999994    4679999999999999999999999999999999999999999999885

>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=97.56  E-value=0.00041  Score=69.72  Aligned_cols=75  Identities=23%  Similarity=0.287  Sum_probs=63.5

Q ss_pred             HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCccc
Q 010992          404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDE  479 (496)
Q Consensus       404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDE  479 (496)
                      ++.+.++++.+ +-+.+++|+.+.|.+.+++++..|+..|+++|||-|..+|.+.||.+.|+..=--.+-||..-+
T Consensus         2 ~~~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~eplyG~~~~~   76 (343)
T cd08050           2 QESIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVEPLYGFSSSE   76 (343)
T ss_pred             hhHHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCCcccCCCCCc
Confidence            45677777776 4568999999999999999999999999999999999999999999999885334566776543

The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as

>PLN00160 histone H3; Provisional

Probab=97.54  E-value=0.00018  Score=62.56  Aligned_cols=69  Identities=19%  Similarity=0.135  Sum_probs=62.5

Q ss_pred             CcCCccCCHHHHHHHHHhhCC-----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992          396 EFGNRILTKRSIQELVNQIDP-----SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL  464 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqIDP-----sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL  464 (496)
                      .+.+-+|.|.-++.||++|..     +..+..++.++|.+.+|+|+-.+.+.+-..|.|.|--||..||++|+.
T Consensus        16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~   89 (97)
T PLN00160         16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR   89 (97)
T ss_pred             cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence            345678899999999999942     368899999999999999999999999999999999999999999985

>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18)

Probab=97.42  E-value=0.00016  Score=61.19  Aligned_cols=61  Identities=20%  Similarity=0.405  Sum_probs=31.9

Q ss_pred             HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      |..|+--.+-...-.+|..++|-+|+-+||-+++..|+++|.+||+..|.++|+.|.|.|+
T Consensus         7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D   67 (93)
T PF02269_consen    7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKD   67 (93)
T ss_dssp             CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC----------------------
T ss_pred             HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcC
Confidence            5667776666678889999999999999999999999999999999999999999999885

Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.

>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C

Probab=97.25  E-value=0.00072  Score=56.18  Aligned_cols=61  Identities=18%  Similarity=0.282  Sum_probs=50.8

Q ss_pred             HHHHHHhh--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          407 IQELVNQI--DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       407 LqELVrqI--DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      +..+++++  +.+..+.+++...|.||+-++++++...--.+|||.|.+||+.+||.|...||
T Consensus        11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn   73 (76)
T PF15630_consen   11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRN   73 (76)
T ss_dssp             HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-
T ss_pred             HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcC
Confidence            34566666  35668999999999999999999999999999999999999999999999887

>smart00427 H2B Histone H2B

Probab=97.19  E-value=0.0016  Score=56.17  Aligned_cols=60  Identities=22%  Similarity=0.372  Sum_probs=56.4

Q ss_pred             HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      |...+++|.|+..|...+..+|--+++|+.|.|...|++||+..|..||..+||+...+-
T Consensus         7 i~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl   66 (89)
T smart00427        7 IYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRL   66 (89)
T ss_pred             HHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence            678899999999999999999999999999999999999999999999999999877654

>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex

Probab=97.06  E-value=0.0028  Score=51.62  Aligned_cols=64  Identities=17%  Similarity=0.297  Sum_probs=50.7

Q ss_pred             cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      +++++.+......++ -..|++|+..+|.+-++-.|..|+..|+++++|-|..+|...||...|+
T Consensus         3 ~~~~esvk~iAes~G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen    3 VFSQESVKDIAESLG-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR   66 (66)
T ss_dssp             ---HHHHHHHHHHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred             cCCHHHHHHHHHHcC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence            677888888888874 4679999999999999999999999999999999999999999998874

TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.

>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]

Probab=96.85  E-value=0.0034  Score=59.29  Aligned_cols=71  Identities=13%  Similarity=0.298  Sum_probs=64.3

Q ss_pred             CcCCccCCHHHHHHHHHhh-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          396 EFGNRILTKRSIQELVNQI-DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqI-DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      -+..++|.=.++-+++|++ .++.+|.+|+.|.+.|++.|||.=|+..|...|-.-|.+||...||.+.|..
T Consensus        27 reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~t   98 (168)
T KOG0869|consen   27 REQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMST   98 (168)
T ss_pred             chhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHH
Confidence            4567889989999999886 6688999999999999999999999999999999999999999999877664

>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO)

Probab=96.83  E-value=0.0088  Score=48.06  Aligned_cols=64  Identities=16%  Similarity=0.297  Sum_probs=53.2

Q ss_pred             HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992          407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I  472 (496)
                      +..+++.+ +=+...+.+.|.|.+|+.+||.++...+-++|.|.+.....+.||.+.|+. .|+.+
T Consensus        12 va~il~~~-GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~-~gi~v   75 (77)
T PF07524_consen   12 VAQILKHA-GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEE-MGISV   75 (77)
T ss_pred             HHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH-hCCCC
Confidence            33344432 346789999999999999999999999999999999999999999999976 46654

The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].

>PLN00158 histone H2B; Provisional

Probab=96.82  E-value=0.0047  Score=55.60  Aligned_cols=59  Identities=20%  Similarity=0.355  Sum_probs=56.1

Q ss_pred             HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      |...+++|.|...|...+..+|--+.+|+.|.|...|++||++.+..||..+||+-..+
T Consensus        33 I~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvr   91 (116)
T PLN00158         33 IYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVR   91 (116)
T ss_pred             HHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence            88899999999999999999999999999999999999999999999999999987654

>PTZ00463 histone H2B; Provisional

Probab=96.74  E-value=0.0058  Score=55.12  Aligned_cols=65  Identities=25%  Similarity=0.410  Sum_probs=59.1

Q ss_pred             HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992          407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF  475 (496)
Q Consensus       407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF  475 (496)
                      |...|++|.|...|...+..+|--+.+|..|.|...|++||+..+..||..+||+-.++    +.+||-
T Consensus        34 I~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvr----LlLpGE   98 (117)
T PTZ00463         34 IFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIR----LVLPGE   98 (117)
T ss_pred             HHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHh----hcccHH
Confidence            88999999999999999999999999999999999999999999999999999987754    445653

>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=96.55  E-value=0.01  Score=55.31  Aligned_cols=68  Identities=15%  Similarity=0.289  Sum_probs=61.0

Q ss_pred             HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992          406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPG  474 (496)
Q Consensus       406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPG  474 (496)
                      .|.-+++.+ +-...|+-|.-.|||+|-.++..|+..|--+++|-+..+|++.||.|.++..-|..|-+
T Consensus        18 ~i~~iL~s~-GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~   85 (148)
T KOG3334|consen   18 VIASILKSL-GIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTP   85 (148)
T ss_pred             HHHHHHHHc-CccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCC
Confidence            345666665 66789999999999999999999999999999999999999999999999988888866

>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=96.55  E-value=0.014  Score=49.94  Aligned_cols=62  Identities=16%  Similarity=0.410  Sum_probs=52.6

Q ss_pred             HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      +.|..|+--.+-...-.+|..++|-+|.-+||-+++..||.+|..|++. +.++|+.|.|.++
T Consensus         6 ~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~~r~~k-~~~eD~~FliR~D   67 (92)
T cd07978           6 KEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQRRRGK-VKVEDLIFLLRKD   67 (92)
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC-CCHHHHHHHHhcC
Confidence            4488888877666677888999999999999999999999999955555 5999999999764

The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy

>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=96.53  E-value=0.014  Score=49.44  Aligned_cols=65  Identities=17%  Similarity=0.244  Sum_probs=57.5

Q ss_pred             CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC---CCcchhhHHHHHhhh
Q 010992          402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS---DTLEAKDILVHLERN  467 (496)
Q Consensus       402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS---dTLEvKDVQLhLERn  467 (496)
                      |+|.++..|+..+.. .++.++|..+|..||..||-++++.|..+.+.++.   .-|..+.|.-.+.|.
T Consensus        17 f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl   84 (85)
T cd08048          17 FPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL   84 (85)
T ss_pred             ccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence            899999999999866 89999999999999999999999999999999887   677777776666553

The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes

>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome

Probab=96.26  E-value=0.014  Score=51.88  Aligned_cols=69  Identities=10%  Similarity=0.168  Sum_probs=63.5

Q ss_pred             CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      .+-+|.-.+++.++++-...++++.++-..|..+.|.|+.+|++.|..+|||.|...|..+||++.+..
T Consensus        17 agL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n   85 (115)
T cd00074          17 AGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN   85 (115)
T ss_pred             cCccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence            456788999999999765678999999999999999999999999999999999999999999999876

The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.

>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]

Probab=96.05  E-value=0.031  Score=52.55  Aligned_cols=74  Identities=14%  Similarity=0.338  Sum_probs=68.3

Q ss_pred             CCCcCCccCCHHHHHHHHHhhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          394 SDEFGNRILTKRSIQELVNQIDP-SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       394 ~~e~~nrILtKrKLqELVrqIDP-sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      +.++++--|.|..++.+|++|=| +..+..|+.|+|.+.+-+||.-|...|-++|-.+...||-.+-|.-.||+.
T Consensus         5 ~~~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~L   79 (156)
T KOG0871|consen    5 GKEDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENL   79 (156)
T ss_pred             ccccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHc
Confidence            34566777999999999999977 889999999999999999999999999999999999999999999999874

>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]

Probab=95.85  E-value=0.026  Score=51.55  Aligned_cols=60  Identities=17%  Similarity=0.308  Sum_probs=54.9

Q ss_pred             HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +...+++|++..-|..+...++--+.+||+|+|+..|-+||..+|..||..++|+..++-
T Consensus        43 v~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rL  102 (127)
T KOG1744|consen   43 VYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRL  102 (127)
T ss_pred             hhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHH
Confidence            334889999999999999999999999999999999999999999999999999886554

>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=95.74  E-value=0.052  Score=59.28  Aligned_cols=93  Identities=20%  Similarity=0.235  Sum_probs=78.2

Q ss_pred             CcCCccCC-HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992          396 EFGNRILT-KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPG  474 (496)
Q Consensus       396 e~~nrILt-KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPG  474 (496)
                      +..+-|+. +..++.+++.| +-+.|++|+.++|.+-.+.-|.+|+..|.+.-+|-|..+|.+.||...|.-.-=--+-|
T Consensus         5 ~~~~~v~s~~Es~k~vAEsl-Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVep~yg   83 (576)
T KOG2549|consen    5 KESPTVVSPKESVKVVAESL-GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVEPLYG   83 (576)
T ss_pred             cccccccCcHHHHHHHHHHh-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccccccC
Confidence            34455666 77777777776 66889999999999999999999999999999999999999999998776543366789


Q ss_pred             CCcccccccCCcccc
Q 010992          475 FSGDEIKTFRKPVRI  489 (496)
Q Consensus       475 FssDEIr~~rk~~~~  489 (496)
                      |++-|+-.||+....
T Consensus        84 ~~s~~~i~fr~a~~~   98 (576)
T KOG2549|consen   84 FGAQEIIPFRKASGG   98 (576)
T ss_pred             cccCceeeccccCCC
Confidence            999999999987655

>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=95.67  E-value=0.056  Score=51.67  Aligned_cols=69  Identities=23%  Similarity=0.347  Sum_probs=58.0

Q ss_pred             CHHHHHHHHHhhCC------------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC------------
Q 010992          403 TKRSIQELVNQIDP------------------SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS------------  452 (496)
Q Consensus       403 tKrKLqELVrqIDP------------------sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS------------  452 (496)
                      .-..|.||+.++|-                  -.+.|+-|..||.-.|-+||.||+..|.+.||-|..            
T Consensus        69 ~d~~l~efl~qLddYtP~IPDavt~~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kd  148 (176)
T KOG3423|consen   69 KDTHLEEFLAQLDDYTPTIPDAVTDHYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKD  148 (176)
T ss_pred             cchHHHHHHHHHhcCCCCCcHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccc
Confidence            34568889988863                  357788899999999999999999999999999984            


Q ss_pred             --CCcchhhHHHHHhhhcCccc
Q 010992          453 --DTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       453 --dTLEvKDVQLhLERnWNI~I  472 (496)
                        -||.++|+.-+|+. |||.|
T Consensus       149 kK~tLtmeDL~~AL~E-yGinv  169 (176)
T KOG3423|consen  149 KKYTLTMEDLSPALAE-YGINV  169 (176)
T ss_pred             cceeeeHHHHHHHHHH-hCccc
Confidence              27899999888875 89887

>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex

Probab=95.67  E-value=0.013  Score=48.24  Aligned_cols=60  Identities=17%  Similarity=0.216  Sum_probs=47.3

Q ss_pred             HHHHHHHHhh--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCC-cchhhHHHHH
Q 010992          405 RSIQELVNQI--DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDT-LEAKDILVHL  464 (496)
Q Consensus       405 rKLqELVrqI--DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdT-LEvKDVQLhL  464 (496)
                      +-|.+|++.-  |.+.+|.+|+-+++.++.|-||...+.+|+..|+-.+.+. ||+.|++-++
T Consensus         3 ~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~   65 (72)
T PF09415_consen    3 ELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKIL   65 (72)
T ss_dssp             HHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHC
T ss_pred             HHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence            3455666632  6778999999999999999999999999999999999999 9999986543

The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.

>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex

Probab=95.16  E-value=0.082  Score=45.55  Aligned_cols=60  Identities=20%  Similarity=0.276  Sum_probs=44.7

Q ss_pred             CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC-CcchhhHH
Q 010992          402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD-TLEAKDIL  461 (496)
Q Consensus       402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd-TLEvKDVQ  461 (496)
                      |+|..|..|++.+..+..+.+.|.-+|..||.-||-++|+.|..+.+.++.. .|..+.|.
T Consensus        24 ~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlr   84 (90)
T PF04719_consen   24 FNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLR   84 (90)
T ss_dssp             --HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHH
T ss_pred             CCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHH
Confidence            7899999999999988999999999999999999999999999999976644 34444443

The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.

>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T

Probab=94.68  E-value=0.057  Score=56.18  Aligned_cols=60  Identities=18%  Similarity=0.233  Sum_probs=43.1

Q ss_pred             ccCCHHHHHHHHHhhC-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhh
Q 010992          400 RILTKRSIQELVNQID-----PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKD  459 (496)
Q Consensus       400 rILtKrKLqELVrqID-----PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKD  459 (496)
                      --|....++.|+..+.     .+.+|.+|+.++|.++.|.|.+.+++.-+.+|||-|-+|||-.|
T Consensus       350 P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD  414 (414)
T PF15511_consen  350 PSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD  414 (414)
T ss_dssp             --S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred             CCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence            3344444444444442     46799999999999999999999999999999999999999887

>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]

Probab=94.67  E-value=0.047  Score=52.08  Aligned_cols=85  Identities=20%  Similarity=0.246  Sum_probs=68.1

Q ss_pred             ccCCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCc
Q 010992          400 RILTKRSIQELVNQIDP--SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSG  477 (496)
Q Consensus       400 rILtKrKLqELVrqIDP--sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFss  477 (496)
                      -.|.+.-|.+||+++=+  +..|..|+..+|.+-|--||..++.+|-.+||.-+..||.+.||.-.|+.-=+-.|-+-..
T Consensus         9 l~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~~plk   88 (172)
T KOG0870|consen    9 LNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFVNPLK   88 (172)
T ss_pred             hhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHhhHHH
Confidence            45788999999999954  4689999999999999999999999999999999999999999998888643333333223


Q ss_pred             ccccccC
Q 010992          478 DEIKTFR  484 (496)
Q Consensus       478 DEIr~~r  484 (496)
                      +.+--||
T Consensus        89 ~~Le~yk   95 (172)
T KOG0870|consen   89 SALEAYK   95 (172)
T ss_pred             HHHHHHH
Confidence            3444444

>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors

Probab=94.10  E-value=0.23  Score=39.33  Aligned_cols=50  Identities=16%  Similarity=0.213  Sum_probs=40.4

Q ss_pred             cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 010992          401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRK  451 (496)
Q Consensus       401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRK  451 (496)
                      +|....++-.+++. +-..-|+-+..|+.-.|.+||.||++.|++.||.|.
T Consensus         2 ~IPD~v~~~yL~~~-G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~r~   51 (51)
T PF03540_consen    2 TIPDEVTDYYLERS-GFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKIRT   51 (51)
T ss_pred             CCCHHHHHHHHHHC-CCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            34455555566654 556789999999999999999999999999999883

The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus

>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site

Probab=94.04  E-value=0.051  Score=52.75  Aligned_cols=59  Identities=20%  Similarity=0.319  Sum_probs=36.9

Q ss_pred             CcCCccCCHHHHHHHHHhhC---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCC
Q 010992          396 EFGNRILTKRSIQELVNQID---PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDT  454 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqID---PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdT  454 (496)
                      +....+|+...|...|++|.   ....+|+||.++|..-+++++.+||+.+..+|+||....
T Consensus        38 ~~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~   99 (264)
T PF05236_consen   38 EKEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSS   99 (264)
T ss_dssp             ------S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH----------
T ss_pred             cccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccc
Confidence            34556899999999999996   345699999999999999999999999999999998764

Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.

>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]

Probab=93.90  E-value=0.042  Score=50.81  Aligned_cols=69  Identities=23%  Similarity=0.218  Sum_probs=61.0

Q ss_pred             cCCccCCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          397 FGNRILTKRSIQELVNQID----PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       397 ~~nrILtKrKLqELVrqID----PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      ..+-+|.|--.+.||++|.    ++..+-.+++..|.|.+|.|+-...+.+-..|-|-|--||..|||+|++.
T Consensus        59 stdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArr  131 (137)
T KOG1745|consen   59 STDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR  131 (137)
T ss_pred             hhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhh
Confidence            4556777888899999884    45688899999999999999999999999999999999999999999764

>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=93.79  E-value=0.17  Score=47.92  Aligned_cols=59  Identities=15%  Similarity=0.224  Sum_probs=50.9

Q ss_pred             CCcCCccCCHHHHHHHHHhhCCCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992          395 DEFGNRILTKRSIQELVNQIDPSE---RLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD  453 (496)
Q Consensus       395 ~e~~nrILtKrKLqELVrqIDPse---sLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd  453 (496)
                      ......+|.+..|...|++|....   .+|+|+.++|...+++|+-+|++.+..+|+||...
T Consensus        38 ~~~~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~   99 (212)
T cd08045          38 SQKDPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDS   99 (212)
T ss_pred             ccchhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            345567899999999999996543   67999999999999999999999999999999554

The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are

>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=92.77  E-value=0.36  Score=44.86  Aligned_cols=71  Identities=18%  Similarity=0.221  Sum_probs=57.4

Q ss_pred             HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC---CCcchhhHHHHHhhhcCccccCCCc
Q 010992          406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS---DTLEAKDILVHLERNWNMTLPGFSG  477 (496)
Q Consensus       406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS---dTLEvKDVQLhLERnWNI~IPGFss  477 (496)
                      -|+=+++.+ .-+..++.|.=-||++|-.|..+|++.|.-+|||-|+   .+|.++||.|.|.-.-|..|-+--.
T Consensus        19 lihliL~Sl-gi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F~pppP   92 (145)
T COG5094          19 LIHLILRSL-GIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHFVPPPP   92 (145)
T ss_pred             HHHHHHHhc-CchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCcCCCCh
Confidence            344455544 5567888899999999999999999999999999854   4678899999999888888755443

>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=92.64  E-value=0.41  Score=46.21  Aligned_cols=47  Identities=23%  Similarity=0.422  Sum_probs=38.5

Q ss_pred             HHHHHHHHhhCC------------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 010992          405 RSIQELVNQIDP------------------SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRK  451 (496)
Q Consensus       405 rKLqELVrqIDP------------------sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRK  451 (496)
                      +.|.+|+..+|-                  -.+.|.-|..||.-+|-+||.||...|.++-|-|.
T Consensus        73 ktlee~l~~mDsy~PliPd~v~DYyl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~  137 (197)
T COG5162          73 KTLEELLQNMDSYTPLIPDSVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQ  137 (197)
T ss_pred             HHHHHHHHhcccCCCCccHHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            568899999984                  24567888899999999999999998888776664

>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]

Probab=91.99  E-value=0.71  Score=42.15  Aligned_cols=59  Identities=17%  Similarity=0.238  Sum_probs=49.0

Q ss_pred             HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      |..|+=..+-...--.|..+.|-+++-|++.++|..|..+|-.|+.  +.++|.+|+|.|.
T Consensus        15 ikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~rnK--~k~eDfkfaLr~D   73 (126)
T COG5248          15 IKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNK--TKTEDFKFALRRD   73 (126)
T ss_pred             HHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhccc--chHHHHHHHHhhC
Confidence            5566665555566667888999999999999999999999997765  5789999999874

>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]

Probab=91.82  E-value=0.76  Score=42.88  Aligned_cols=71  Identities=14%  Similarity=0.284  Sum_probs=63.8

Q ss_pred             CcCCccCCHHHHHHHHHhh-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          396 EFGNRILTKRSIQELVNQI-DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqI-DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      .+++--|.|..++.+|..| +.+..+..|+.|++.+.+=+||.-+...|-.+|...+..||..+.|--.||.
T Consensus         6 ~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALen   77 (148)
T COG5150           6 NDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALEN   77 (148)
T ss_pred             ccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHh
Confidence            4566779999999999998 5577999999999999999999999999999999999999999988777775

>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]

Probab=91.13  E-value=1.1  Score=40.49  Aligned_cols=64  Identities=16%  Similarity=0.360  Sum_probs=48.7

Q ss_pred             ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      ++++|. |.-|+=-.+-...-=+|..++|-+|+=|||.++++.|..++   +.+.|.++|++|.|.|.
T Consensus         9 ~lF~Kd-l~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRkD   72 (109)
T KOG3901|consen    9 HLFSKD-LRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRKD   72 (109)
T ss_pred             HHHHHH-HHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHhC
Confidence            344443 66666655555555667788999999999999999999888   34457899999999874

>smart00350 MCM minichromosome maintenance proteins

Probab=88.86  E-value=1.6  Score=46.25  Aligned_cols=67  Identities=21%  Similarity=0.282  Sum_probs=53.3

Q ss_pred             CccCCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHHH-------------------HHHHHHHHHHhhhhcCCCCcch
Q 010992          399 NRILTKRSIQELVNQIDP--SERLDPDVEDILVDIAEDF-------------------VESITMFGCSLAKHRKSDTLEA  457 (496)
Q Consensus       399 nrILtKrKLqELVrqIDP--sesLDpDVEELLLeIADDF-------------------VDsVvt~ACrLAKHRKSdTLEv  457 (496)
                      ..+++...|.+.+..+-.  .-.|+++++++|.+++.+.                   ++.++..|..+||.|.++.|+.
T Consensus       415 ~~~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~  494 (509)
T smart00350      415 EVPISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEE  494 (509)
T ss_pred             cccCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCH
Confidence            357887777777655533  2358999999999887663                   3788999999999999999999


Q ss_pred             hhHHHHHh
Q 010992          458 KDILVHLE  465 (496)
Q Consensus       458 KDVQLhLE  465 (496)
                      +||+.+++
T Consensus       495 ~Dv~~ai~  502 (509)
T smart00350      495 ADVEEAIR  502 (509)
T ss_pred             HHHHHHHH
Confidence            99987765

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=88.84  E-value=1.2  Score=47.60  Aligned_cols=66  Identities=18%  Similarity=0.211  Sum_probs=51.9

Q ss_pred             cCCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHH--HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          401 ILTKRSIQELVNQIDP--SERLDPDVEDILVDIAED--FVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       401 ILtKrKLqELVrqIDP--sesLDpDVEELLLeIADD--FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      -|++..|.++++.+-.  +..|++++.++|.+.+.+  .+.+++..||.+|..++...|+.+||..+|+.
T Consensus       262 pL~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~  331 (531)
T TIGR02902       262 PLLDEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAEN  331 (531)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCC
Confidence            4566777777776632  357899999988877653  35678899999999999999999999999874

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=88.67  E-value=2.1  Score=42.30  Aligned_cols=66  Identities=15%  Similarity=0.211  Sum_probs=50.7

Q ss_pred             CCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHHH------HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          402 LTKRSIQELVNQID----PSERLDPDVEDILVDIAED------FVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       402 LtKrKLqELVrqID----PsesLDpDVEELLLeIADD------FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      ++++.+.++++.--    ....+++++.+++.+++..      ++-+++..|+.+|+.|+.++|+.+||.-++++.
T Consensus       207 y~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~  282 (394)
T PRK00411        207 YTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS  282 (394)
T ss_pred             CCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            35666666655431    1346899999999998854      345788999999999999999999999888875

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=88.32  E-value=1.8  Score=40.19  Aligned_cols=67  Identities=6%  Similarity=0.050  Sum_probs=54.0

Q ss_pred             ccCCHHHHHHHHHhh----C--CCCCCCHHHHHHHHHHHHH---HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          400 RILTKRSIQELVNQI----D--PSERLDPDVEDILVDIAED---FVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       400 rILtKrKLqELVrqI----D--PsesLDpDVEELLLeIADD---FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      .-|+...+.++++..    .  ....+++++.+.|.++++-   +|+.++..+...|..++.+.|+..||...+..
T Consensus       190 ~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~  265 (269)
T TIGR03015       190 GPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAE  265 (269)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            345666777766543    2  2346999999999999997   89999999999999999999999999887765

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>smart00414 H2A Histone 2A

Probab=88.24  E-value=1.5  Score=38.70  Aligned_cols=68  Identities=10%  Similarity=0.176  Sum_probs=60.8

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +-.+.-.+++.++++-.-..+++..+--.|..+-|-++.+|++.|...||.-|...|..+||++.+..
T Consensus         7 gL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n   74 (106)
T smart00414        7 GLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN   74 (106)
T ss_pred             CccCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence            34567788999999876678999999999999999999999999999999999999999999988765

>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=87.56  E-value=2.1  Score=45.19  Aligned_cols=76  Identities=18%  Similarity=0.249  Sum_probs=63.0

Q ss_pred             ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcC-ccccCCCc
Q 010992          400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWN-MTLPGFSG  477 (496)
Q Consensus       400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWN-I~IPGFss  477 (496)
                      -|.+|+.|.++...+ +-+.||||+-.+|..=.+--|..||..|.++-.|-|.++|.+.||-..|.- .| -.+-||..
T Consensus         4 t~ws~et~KdvAesl-Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~-lNVePLyGyd~   80 (450)
T COG5095           4 TLWSKETLKDVAESL-GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRS-LNVEPLYGYDP   80 (450)
T ss_pred             eeecHHHHHHHHHHc-CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHh-cCCCcccCCCC
Confidence            356788888888765 567899999999988888899999999999999999999999999988865 35 33455554

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=86.24  E-value=2.8  Score=40.85  Aligned_cols=66  Identities=9%  Similarity=0.127  Sum_probs=49.7

Q ss_pred             CCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHH------HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          402 LTKRSIQELVNQID----PSERLDPDVEDILVDIAE------DFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       402 LtKrKLqELVrqID----PsesLDpDVEELLLeIAD------DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      +++..|.++++..-    ....+|+|+.+++.++++      ..+.+++..|+.+|..++.+.|+.+||.-.++..
T Consensus       199 ~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~  274 (365)
T TIGR02928       199 YDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKI  274 (365)
T ss_pred             CCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            46677777776442    234699999999988885      3566788899999999999999999988665543

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]

Probab=86.24  E-value=1.1  Score=45.18  Aligned_cols=65  Identities=20%  Similarity=0.314  Sum_probs=49.3

Q ss_pred             CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       403 tKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      .=.+|..++|-=|.-.-|..||--++.++.+.||+.++.+|.-.||..|..+|...||.-.+++.
T Consensus       111 PlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kS  175 (286)
T COG5208         111 PLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKS  175 (286)
T ss_pred             cHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHH
Confidence            33445555543222234555666788999999999999999999999999999999998887763

>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]

Probab=85.47  E-value=1.2  Score=43.53  Aligned_cols=67  Identities=19%  Similarity=0.259  Sum_probs=56.1

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC-CCcchhhHHHHHhh
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS-DTLEAKDILVHLER  466 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS-dTLEvKDVQLhLER  466 (496)
                      ...|.|..|..|+.+|-+.. |++.|.=++..||.-||-+||+.|..++..++. .-|-.+.|.-.+.|
T Consensus       110 rs~f~Ka~iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rr  177 (195)
T KOG3219|consen  110 RSAFPKAQIKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRR  177 (195)
T ss_pred             HhcCCHHHHHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHH
Confidence            44679999999999998777 999999999999999999999999999877764 46667777555544

>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]

Probab=84.88  E-value=2.7  Score=43.75  Aligned_cols=70  Identities=10%  Similarity=0.168  Sum_probs=56.7

Q ss_pred             HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCc
Q 010992          406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSG  477 (496)
Q Consensus       406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFss  477 (496)
                      .+..|+.+. +-+.+++.++|-|++|.+.+|+.|...+--+|.|-|.......||.|.|-+ +||.|+-+..
T Consensus        10 VV~~Ll~~~-gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~-mnI~v~sL~~   79 (323)
T KOG4336|consen   10 VVSNLLKTK-GFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIE-MNIKVSSLYA   79 (323)
T ss_pred             HHHHHHHHh-CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHH-hCCChhhhHH
Confidence            355566654 335699999999999999999999988888888888888899999999976 7998876543

>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=84.14  E-value=2.7  Score=44.63  Aligned_cols=64  Identities=20%  Similarity=0.331  Sum_probs=51.1

Q ss_pred             CHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHHH----HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          403 TKRSIQELVNQI--DPSERLDPDVEDILVDIAED----FVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       403 tKrKLqELVrqI--DPsesLDpDVEELLLeIADD----FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +++.+.++++-=  .....|++|+.|+|..|..+    |.-.+++.|...|..||..++++.||+.+++-
T Consensus       359 ~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~L  428 (454)
T KOG2680|consen  359 TEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYRL  428 (454)
T ss_pred             cHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHHH
Confidence            566666665522  23568999999999999876    77889999999999999999999999766543

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=83.48  E-value=2  Score=46.06  Aligned_cols=63  Identities=24%  Similarity=0.363  Sum_probs=49.3

Q ss_pred             CHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHHH----HHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          403 TKRSIQELVNQI--DPSERLDPDVEDILVDIAED----FVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       403 tKrKLqELVrqI--DPsesLDpDVEELLLeIADD----FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      +++.|+++++-=  .-+..||+|+-|.|.+|-.+    |.-..++-|..+||.||+.+|+++||..+.|
T Consensus       362 ~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~  430 (450)
T COG1224         362 SREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE  430 (450)
T ss_pred             CHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH
Confidence            566666666522  23457999999999998875    6777888888899999999999999976654

>PTZ00017 histone H2A; Provisional

Probab=81.22  E-value=3.7  Score=38.09  Aligned_cols=69  Identities=10%  Similarity=0.165  Sum_probs=62.0

Q ss_pred             CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      .+-.+.-.+|+.|+++-.-..+|...+--.|.-+.|-++.+|++.|...|+.-+..-|..++|++.+..
T Consensus        24 agL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n   92 (134)
T PTZ00017         24 AGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN   92 (134)
T ss_pred             CCcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence            355678889999999876778999999999999999999999999999999999999999999998854

>PTZ00171 acyl carrier protein; Provisional

Probab=80.21  E-value=0.46  Score=43.81  Aligned_cols=45  Identities=24%  Similarity=0.519  Sum_probs=34.1

Q ss_pred             HHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCcccccccC
Q 010992          440 TMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFR  484 (496)
Q Consensus       440 vt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~r  484 (496)
                      ++..+.+..--+-|.|+.-||.+.||++|||.||---.+++++++
T Consensus        90 I~~ds~~~~dLg~DSLd~veLv~~LEdeFgI~Ipded~~~i~TV~  134 (148)
T PTZ00171         90 ITPESNFVKDLGADSLDVVELLIAIEQEFNLTIPDHDAEKIKTVQ  134 (148)
T ss_pred             CCCCcchhhhcCCCHHHHHHHHHHHHHHHCCccCHHHHHHCCCHH
Confidence            444556667778999999999999999999999854444555443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	496
1h3o_B	76	Crystal Structure Of The Human Taf4-Taf12 (Tafii135		2e-19

>pdb|1H3O|B Chain B, Crystal Structure Of The Human Taf4-Taf12 (Tafii135-Tafii20) Complex Length = 76

Iteration: 1
 Score = 94.0 bits (232), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 39/69 (56%), Positives = 55/69 (79%)
Query: 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460
           +LTK+ +Q+LV ++DP+E+LD DVE+ L+ IA+DF+ES+    C LA+HRKS TLE KD+
Sbjct: 5   VLTKKKLQDLVREVDPNEQLDEDVEEXLLQIADDFIESVVTAACQLARHRKSSTLEVKDV 64
Query: 461 LVHLERNWN 469
            +HLER WN
Sbjct: 65  QLHLERQWN 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	496
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	9e-44
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	4e-11
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	1e-08
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	3e-09
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-08
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	5e-07
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	5e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	3e-07
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	4e-05
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	2e-04
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	5e-04
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	7e-07
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	8e-07
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	9e-07
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-06
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	6e-06
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	8e-06
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	6e-04
1pk8_A	422	RAT synapsin I; ATP binding, ATP grAsp, calcium (I	9e-06
1pk8_A	422	RAT synapsin I; ATP binding, ATP grAsp, calcium (I	2e-05
3nwa_A	703	GB, GB-1, GB1, envelope glycoprotein B; coiled-coi	1e-05
3nwa_A	703	GB, GB-1, GB1, envelope glycoprotein B; coiled-coi	2e-04
3nwa_A	703	GB, GB-1, GB1, envelope glycoprotein B; coiled-coi	2e-04
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	1e-05
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	1e-05
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	2e-05
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	3e-05
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	8e-04
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	8e-04
3sv0_A	483	Casein kinase I-like; typical kinase domain fold,	8e-05
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	8e-04

>1h3o_B Transcription initiation factor TFIID 20/15 kDa subunits; transcription/TBP-associated factors, TBP-associated factors; 2.3A {Homo sapiens} SCOP: a.22.1.3 Length = 76

 Score =  148 bits (374), Expect = 9e-44
 Identities = 40/75 (53%), Positives = 59/75 (78%)

Query: 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEA 457
            + +LTK+ +Q+LV ++DP+E+LD DVE++L+ IA+DF+ES+    C LA+HRKS TLE 
Sbjct: 2   SHMVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEV 61

Query: 458 KDILVHLERNWNMTL 472
           KD+ +HLER WNM +
Sbjct: 62  KDVQLHLERQWNMWI 76

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 64.7 bits (157), Expect = 4e-11
 Identities = 58/323 (17%), Positives = 93/323 (28%), Gaps = 38/323 (11%)

Query: 1    MDQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSS 60
            +D+E   +    Q  T          T  S  +       +    + +    P   + S+
Sbjct: 1445 IDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLV---NADLDVKDELMFSPLVDSGSN 1501

Query: 61   TTIPTSTPTTNTPNPNPSPSPSPAPPSRPTS--LTPPPPRPTSFSRPWQPPQQHFSHFSS 118
              +          +   + SP  A    PTS       P  +  S  + P    +S  S 
Sbjct: 1502 DAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTS- 1560

Query: 119  LPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSG 178
             PS S  +PS S + P  SP     +   P+  PT+ S  P+ P  S     +       
Sbjct: 1561 -PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS------ 1613

Query: 179  VNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPG 238
                                  +S    P   S     P     S    P S   S +  
Sbjct: 1614 ---------------------PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1652

Query: 239  TQNFQGQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTP 298
            + +         S   SP S S + +    S   P  S  S    P +P  +Y P   +P
Sbjct: 1653 SYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSP--SYSPT--SP 1708

Query: 299  SMQQRSHIPQQHSPLSTNLQQQH 321
                 S           + + ++
Sbjct: 1709 GYSPGSPAYSPKQDEQKHNENEN 1731

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 56.6 bits (136), Expect = 1e-08
 Identities = 57/279 (20%), Positives = 85/279 (30%), Gaps = 31/279 (11%)

Query: 2    DQEQPQQPQQTQTPTP---STTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTP 58
              E                S    + +N A +   T+   A   +           P++P
Sbjct: 1474 SNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSP 1533

Query: 59   S--------STTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQ 110
                     S T PT +PT        SP+ SP  P    S +P  P  +  S  + P  
Sbjct: 1534 GFGVSSPGFSPTSPTYSPT--------SPAYSPTSP----SYSPTSPSYSPTSPSYSPTS 1581

Query: 111  QHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQP 170
              +S  S   S +S  PS S + P  SP     +   P+  PT+ S  P+ P  S     
Sbjct: 1582 PSYSPTSPSYSPTS--PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1639

Query: 171  FGGLGRSGVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPS 230
            +     S      S  P +           +S    P   S     P     S    P S
Sbjct: 1640 YSPTSPSYSPTSPSYSPTSPAYS------PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1693

Query: 231  SPSSQSPGTQNFQGQGLMRVSQVGSPGSSSPNTSQSVQS 269
               S +  + +    G    S   SP       +++  S
Sbjct: 1694 PNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENS 1732

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 58.9 bits (142), Expect = 3e-09
 Identities = 57/319 (17%), Positives = 87/319 (27%), Gaps = 34/319 (10%)

Query: 7    QQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPS----TPSSTT 62
             Q         +   T   +   ++        P  + P        +P     +P    
Sbjct: 1452 DQDMLMNYSLGTAVPTLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAFSPLVQG 1511

Query: 63   IPTSTPTTNTPNPNPSPSP-----SPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFS 117
                           + SP     SP   S  +S   P    TS S            +S
Sbjct: 1512 GSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPS------------YS 1559

Query: 118  SLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRS 177
                  S +P+   S P  SP     +   P+  PT+ S  P+ P  S+    +     S
Sbjct: 1560 PSSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPS 1619

Query: 178  GVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSP 237
                  S  P             +S    P   S     P     S    P S   S + 
Sbjct: 1620 YSPTSPSYSP-------------TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1666

Query: 238  GTQNFQGQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNT 297
             + +         S   SP S S + +    S   P  S  S    P +P  +      +
Sbjct: 1667 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1726

Query: 298  PSMQQRSHIPQQHSPLSTN 316
            P+    S     +SP S +
Sbjct: 1727 PTSPSYSPTSPSYSPTSPS 1745

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 55.9 bits (134), Expect = 2e-08
 Identities = 54/296 (18%), Positives = 82/296 (27%), Gaps = 28/296 (9%)

Query: 77   PSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIP 136
                     P   + +       +  +  + P  Q  S             + S    + 
Sbjct: 1476 SQLPEGAGTPYERSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGLLGAASPYKGVQ 1535

Query: 137  SPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVM 196
            SP          +P     SP  SP  S  +      +  S    P S   P+       
Sbjct: 1536 SPGYTSPFSSAMSPGYGLTSPSYSPS-SPGYSTSPAYMPSSPSYSPTS---PSYSPTSPS 1591

Query: 197  GSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSP 256
             S  +S    P   S  +    P    +      +  S SP + ++        S   SP
Sbjct: 1592 YS-PTSPSYSPT--SPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPT-----SPSYSP 1643

Query: 257  GSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTN 316
             S S + +    S   P  S  S    P +P  +      +P+    S     +SP S +
Sbjct: 1644 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1703

Query: 317  LQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSS 372
                  S   P  S  S            SP  P  SP        P S +  P+S
Sbjct: 1704 -----YSPTSPSYSPTSPS---------YSPTSPSYSPTSPS--YSPTSPSYSPTS 1743

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 51.6 bits (123), Expect = 5e-07
 Identities = 45/161 (27%), Positives = 70/161 (43%), Gaps = 2/161 (1%)

Query: 6    PQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPT 65
            P  P  + +P    ++ + + T+ S   TS   +P+S        +    S   S T P+
Sbjct: 1560 PSSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPS 1619

Query: 66   STPTTNTPNPNPSPSPSPAPPS-RPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSS 124
             +PT+ + +P  SPS SP  PS  PTS +  P  P+             S+  + PS S 
Sbjct: 1620 YSPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1678

Query: 125  ATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSS 165
             +PS S + P  SP     +   P+  PT+ S  P+ P  S
Sbjct: 1679 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1719

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 51.6 bits (123), Expect = 5e-07
 Identities = 57/263 (21%), Positives = 81/263 (30%), Gaps = 37/263 (14%)

Query: 6    PQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPT 65
                    +P     +    +  SS ++        S  P     +      PSS +   
Sbjct: 1521 DYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSP 1580

Query: 66   STPTTNTPNPNPSP-SPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSS 124
            ++P+ +  +P+ SP SPS +P S   S T P   PTS                  PS S 
Sbjct: 1581 TSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTS------------------PSYSP 1622

Query: 125  ATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDS 184
             +PS S + P  SP     +   P+  PT  SP  SP   S           S    P S
Sbjct: 1623 TSPSYSPTSPSYSPTSPSYSPTSPSYSPT--SPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1680

Query: 185  VRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQG 244
                            +S    P   S     P     S    P S   S +  + +   
Sbjct: 1681 PSYS-----------PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1729

Query: 245  QGLMRVSQVGSPGS-----SSPN 262
                  S   SP S     +SP+
Sbjct: 1730 PSYSPTSPSYSPTSPSYSPTSPS 1752

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 56.4 bits (135), Expect = 2e-08
 Identities = 50/332 (15%), Positives = 80/332 (24%), Gaps = 114/332 (34%)

Query: 212 VQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSS-------PNTS 264
            +++  R      LR    +     P  +N    G +    +GS G +            
Sbjct: 127 AKYNVSRLQPYLKLR---QALLELRPA-KNVLIDG-V----LGS-GKTWVALDVCLSYKV 176

Query: 265 QSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSS 324
           Q    F   WL+                                 +SP +     Q L  
Sbjct: 177 QCKMDFKIFWLNLK-----------------------------NCNSPETVLEMLQKLLY 207

Query: 325 VQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVQTG 384
              Q         DH      S  +       Q   R    +    + L LV  N VQ  
Sbjct: 208 ---QIDPNWTSRSDH------SSNIKLRIHSIQAELRRLLKSKPYENCL-LVLLN-VQN- 255

Query: 385 NQSKIAGTESDEFGN--RIL-TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITM 441
             +K      + F    +IL T R  Q + + +  +      ++   + +  D  E  ++
Sbjct: 256 --AKAW----NAFNLSCKILLTTRFKQ-VTDFLSAATTTHISLDHHSMTLTPD--EVKSL 306

Query: 442 FGCSLAK--HRKSDTL--EAKDI--LV----------HLER--NWN------------MT 471
                 K    +   L  E                   L    NW              +
Sbjct: 307 L----LKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESS 362

Query: 472 LPGFSGDEIKT-------FRKPVRIVTDPIPL 496
           L      E +        F     I   P  L
Sbjct: 363 LNVLEPAEYRKMFDRLSVFPPSAHI---PTIL 391

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 51.6 bits (123), Expect = 3e-07
 Identities = 23/131 (17%), Positives = 35/131 (26%)

Query: 43  QPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSF 102
                      +    SS T PT   +   P+ +PS  P    P +  S       P + 
Sbjct: 6   HHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPING 65

Query: 103 SRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPP 162
             P            S+   ++ T   S   P  S P   ++       P  L+     P
Sbjct: 66  MGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVP 125

Query: 163 FSSSFGQPFGG 173
              S       
Sbjct: 126 AHPSGNMASFT 136

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 45.1 bits (106), Expect = 4e-05
 Identities = 21/133 (15%), Positives = 35/133 (26%), Gaps = 8/133 (6%)

Query: 35  SQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPP-------- 86
             +         Q   +  +P+   S   P+  P+      +P    SP           
Sbjct: 7   HHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGM 66

Query: 87  SRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIG 146
             P S+   P  P S S P  P     +    L S  +   S+    P            
Sbjct: 67  GPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPA 126

Query: 147 VPAPRPTALSPQP 159
            P+    + +   
Sbjct: 127 HPSGNMASFTKHI 139

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 42.4 bits (99), Expect = 2e-04
 Identities = 26/144 (18%), Positives = 41/144 (28%), Gaps = 8/144 (5%)

Query: 8   QPQQTQTPTPSTTTTTTAN-TASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTS 66
                         +T  N + +S      + APS  P        P   +P     P S
Sbjct: 3   HHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSL-----GPGIGSPGQLHSPIS 57

Query: 67  TPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSAT 126
           T ++      P P    + P  P S++ P   PT       P      +  S        
Sbjct: 58  TLSSPINGMGP-PFSVISSPMGPHSMSVPTT-PTLGFSTGSPQLSSPMNPVSSSEDIKPP 115

Query: 127 PSTSASPPIPSPPRGGIAIGVPAP 150
              +    +P+ P G +A      
Sbjct: 116 LGLNGVLKVPAHPSGNMASFTKHI 139

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 41.6 bits (97), Expect = 5e-04
 Identities = 24/140 (17%), Positives = 42/140 (30%), Gaps = 14/140 (10%)

Query: 70  TNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPST 129
            +    +   + S   P+   S+  P   P+       P Q H       P S+ ++P  
Sbjct: 11  DDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHS------PISTLSSPIN 64

Query: 130 SASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPA 189
              PP                 P ++S   +P    S G P      + V+  + ++PP 
Sbjct: 65  GMGPPFSVIS--------SPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPL 116

Query: 190 IQGMGVMGSLGSSSQMRPAG 209
                +      S  M    
Sbjct: 117 GLNGVLKVPAHPSGNMASFT 136

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 51.0 bits (121), Expect = 7e-07
 Identities = 24/166 (14%), Positives = 44/166 (26%)

Query: 207 PAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSSPNTSQS 266
           P           P+QQ +   PP  P++               V  +G     +P   Q 
Sbjct: 10  PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69

Query: 267 VQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQ 326
            Q  +Q   S        +              +Q  + + QQ  P++     Q  +++ 
Sbjct: 70  HQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMG 129

Query: 327 PQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSS 372
                 +   P     +   P    + P    +  P         S
Sbjct: 130 QNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELS 175

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 50.6 bits (120), Expect = 8e-07
 Identities = 22/202 (10%), Positives = 41/202 (20%), Gaps = 2/202 (0%)

Query: 73  PNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSAS 132
                 P          T L  P                         +  S       +
Sbjct: 4   HKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLT 63

Query: 133 PPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQG 192
           P      +               +     P +    Q    +G         +  PA   
Sbjct: 64  PAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQ 123

Query: 193 MGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQ 252
                        +   I +    P P+   +L PPP     +     +           
Sbjct: 124 PSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSN--ASPDY 181

Query: 253 VGSPGSSSPNTSQSVQSFNQPW 274
           + S  ++ P  S  ++    P+
Sbjct: 182 IRSTLNAVPKNSSLLKKSKLPF 203

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 50.6 bits (120), Expect = 9e-07
 Identities = 26/188 (13%), Positives = 55/188 (29%), Gaps = 5/188 (2%)

Query: 46  QQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRP 105
             +++  P                     P    +   +       + P    P+   + 
Sbjct: 3   HHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYG--QMGMPPQGAVPSMGQQQ 60

Query: 106 WQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSS 165
           +  P Q   H     +++S       + P+  P    +   VP    T L  Q  P  + 
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPN-AYMQPQVPVQMGTPLQQQQQPMAAP 119

Query: 166 SFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSL 225
           ++GQP   +G++    P +   P      +   +   +   P  +        P + S+ 
Sbjct: 120 AYGQPSAAMGQN--MRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNA 177

Query: 226 RPPPSSPS 233
            P     +
Sbjct: 178 SPDYIRST 185

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 49.1 bits (116), Expect = 3e-06
 Identities = 19/155 (12%), Positives = 37/155 (23%), Gaps = 5/155 (3%)

Query: 34  TSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLT 93
            +Q+    +  P QQ      P  P++  +             PS             L 
Sbjct: 11  QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLH 70

Query: 94  PPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPT 153
               + T+          H  +   +  ++   P        P   +          +P+
Sbjct: 71  QQIDQATT-----SMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPS 125

Query: 154 ALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPP 188
           A   Q   P +  +           +       PP
Sbjct: 126 AAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPP 160

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 47.9 bits (113), Expect = 6e-06
 Identities = 20/171 (11%), Positives = 36/171 (21%), Gaps = 2/171 (1%)

Query: 1   MDQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSS 60
           M   + +   Q Q        T     A          A  S            PS    
Sbjct: 1   MSHHKKRVYPQAQLQ-YGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQ 59

Query: 61  TTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLP 120
             +  +    +      + S +         + P              P Q      + P
Sbjct: 60  QFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAP 119

Query: 121 SSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPF 171
           +    + +   +    +     I +    P P      P PP      +  
Sbjct: 120 AYGQPSAAMGQNMRPMNQLY-PIDLLTELPPPITDLTLPPPPLVIPPERML 169

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 47.5 bits (112), Expect = 8e-06
 Identities = 16/164 (9%), Positives = 35/164 (21%), Gaps = 1/164 (0%)

Query: 3   QEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTT 62
           Q     P Q       +          +  +  Q    +    Q  QQ     ++ +   
Sbjct: 25  QPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMH 84

Query: 63  IPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSS 122
           +             P        P +        P     S       +  +    +   
Sbjct: 85  LHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLL 144

Query: 123 SSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSS 166
           +   P       +P PP       +  P   + +       + +
Sbjct: 145 TELPPPI-TDLTLPPPPLVIPPERMLVPSELSNASPDYIRSTLN 187

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 46.4 bits (109), Expect = 2e-05
 Identities = 24/169 (14%), Positives = 41/169 (24%), Gaps = 4/169 (2%)

Query: 3   QEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPS----SQPPQQQQQTPPTPSTP 58
           Q Q Q  Q               + A++ ++  Q+  P         QQQ  TP      
Sbjct: 11  QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLH 70

Query: 59  SSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSS 118
                 T++      +  P   P+     +       P +            Q  +    
Sbjct: 71  QQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQ 130

Query: 119 LPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSF 167
                +          +P P         P   P      PS   ++S 
Sbjct: 131 NMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASP 179

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 41.7 bits (97), Expect = 6e-04
 Identities = 20/179 (11%), Positives = 43/179 (24%), Gaps = 2/179 (1%)

Query: 137 SPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVM 196
              +             A   Q    F         G+    + +P     P++     +
Sbjct: 3   HHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFL 62

Query: 197 GSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSP 256
                    +    +        +    L  P +    Q P       Q   +     + 
Sbjct: 63  TP-AQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAY 121

Query: 257 GSSSPNTSQSVQSFNQPWLSSGSQGKP-PLAPPSTYRPQMNTPSMQQRSHIPQQHSPLS 314
           G  S    Q+++  NQ +        P P+   +   P +  P  +        ++   
Sbjct: 122 GQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPD 180

>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A* Length = 422

 Score = 46.8 bits (110), Expect = 9e-06
 Identities = 19/125 (15%), Positives = 37/125 (29%), Gaps = 6/125 (4%)

Query: 29  SSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSR 88
           S +   + +        Q+ Q  PP PS  S    P S         +   + + AP + 
Sbjct: 10  SDSNFMANLPNGYMTDLQRPQPPPPPPSAASPGATPGSAA------ASAERASTAAPVAS 63

Query: 89  PTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVP 148
           P + +P       F        +  +  ++   S      +  +    +  R  + I  P
Sbjct: 64  PAAPSPGSSGGGGFFSSLSNAVKQTTAAAAATFSEQVGGGSGGAGRGGAAARVLLVIDEP 123

Query: 149 APRPT 153
                
Sbjct: 124 HTDWA 128

>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A* Length = 422

 Score = 45.6 bits (107), Expect = 2e-05
 Identities = 20/125 (16%), Positives = 31/125 (24%), Gaps = 17/125 (13%)

Query: 38  TAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPP 97
             P+      Q+  PP P   +                  SP  +P   +          
Sbjct: 17  NLPNGYMTDLQRPQPPPPPPSA-----------------ASPGATPGSAAASAERASTAA 59

Query: 98  RPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSP 157
              S + P          FSSL ++   T + +A+        G    G        L  
Sbjct: 60  PVASPAAPSPGSSGGGGFFSSLSNAVKQTTAAAAATFSEQVGGGSGGAGRGGAAARVLLV 119

Query: 158 QPSPP 162
              P 
Sbjct: 120 IDEPH 124

>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane fusion, viral P glycoprotein B, HSV-1, membrane; HET: NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A* 3nwd_A* Length = 703

 Score = 47.3 bits (112), Expect = 1e-05
 Identities = 20/104 (19%), Positives = 30/104 (28%), Gaps = 7/104 (6%)

Query: 51  TPPTPSTPSSTTIPTSTPTTNT-PNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPP 109
           +P TP   ++T      P T   P    +P+  P P        P PPRP   +      
Sbjct: 7   SPGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKKNKKPKNPTPPRPAGDNATVAAG 66

Query: 110 QQHFSHFSSLPSSSSATPSTSASPP-IPSPPRGGIAIGVPAPRP 152
                               + +   +  PP G   +    PR 
Sbjct: 67  HATLR-----EHLRDIKAENTDANFYVCPPPTGATVVQFEQPRR 105

>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane fusion, viral P glycoprotein B, HSV-1, membrane; HET: NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A* 3nwd_A* Length = 703

 Score = 43.0 bits (101), Expect = 2e-04
 Identities = 16/100 (16%), Positives = 27/100 (27%), Gaps = 1/100 (1%)

Query: 5   QPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIP 64
            P  P    TP  +  T       + T     + A  +  P+ ++   P   TP      
Sbjct: 1   DPAAPTSPGTPGVAAATQAANGGPA-TPAPPALGAAPTGDPKPKKNKKPKNPTPPRPAGD 59

Query: 65  TSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSR 104
            +T                A  +       PPP   +  +
Sbjct: 60  NATVAAGHATLREHLRDIKAENTDANFYVCPPPTGATVVQ 99

>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane fusion, viral P glycoprotein B, HSV-1, membrane; HET: NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A* 3nwd_A* Length = 703

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 18/107 (16%), Positives = 28/107 (26%), Gaps = 8/107 (7%)

Query: 39  APSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAP----PSRPTSLTP 94
           AP+S  P        T +       P        P  +P P  +  P    P RP     
Sbjct: 4   APTS--PGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKKNKKPKNPTPPRPAGDNA 61

Query: 95  PPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSA--SPPIPSPP 139
                 +  R      +  +  ++       T +T      P   P 
Sbjct: 62  TVAAGHATLREHLRDIKAENTDANFYVCPPPTGATVVQFEQPRRCPT 108

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 46.7 bits (110), Expect = 1e-05
 Identities = 12/119 (10%), Positives = 20/119 (16%), Gaps = 3/119 (2%)

Query: 2   DQEQPQQPQQTQTPTPSTTTTTTANTASSTVTT---SQITAPSSQPPQQQQQTPPTPSTP 58
                  P  + T   S          +            A  + P      +       
Sbjct: 17  RGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGDSVLQRILR 76

Query: 59  SSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFS 117
             T   T++              +PA          P         P     +  S   
Sbjct: 77  GPTGPGTTSLAPAVRYGRQPGPEAPASAPPAAGRAVPGLYHHPVPEPDPVRVEEVSRRI 135

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 46.7 bits (110), Expect = 1e-05
 Identities = 18/114 (15%), Positives = 27/114 (23%), Gaps = 6/114 (5%)

Query: 1   MDQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSS 60
           M          +      +     +  AS T   S   A    P       PP P  P++
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMVIPS--ASVTSAASDFLAALHPPVTVPDPAPPPPPAPAA 58

Query: 61  TTIPTSTPTTNTPNPNPS----PSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQ 110
              P +    +           P  +   P+      P P  P S         
Sbjct: 59  GNPPDTVTGDSVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPAAGRAV 112

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 45.9 bits (108), Expect = 2e-05
 Identities = 25/139 (17%), Positives = 36/139 (25%), Gaps = 18/139 (12%)

Query: 33  TTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSL 92
           +       S   P+      P+ S  S+     S        P   P P+P PP  P + 
Sbjct: 4   SHHHHHHSSGLVPRGSHMVIPSASVTSAA----SDFLAALHPPVTVPDPAPPPPPAPAAG 59

Query: 93  TPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRP 152
            PP       S   +                   P T++  P     R       PA  P
Sbjct: 60  NPPDTVT-GDSVLQRIL------------RGPTGPGTTSLAPAVRYGRQP-GPEAPASAP 105

Query: 153 TALSPQPSPPFSSSFGQPF 171
            A        +     +P 
Sbjct: 106 PAAGRAVPGLYHHPVPEPD 124

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 45.3 bits (107), Expect = 3e-05
 Identities = 17/105 (16%), Positives = 27/105 (25%), Gaps = 3/105 (2%)

Query: 6   PQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPT 65
               ++T+    + T      ++ +  +             Q+ Q       P     P 
Sbjct: 338 QFDDKETEDDKDAETEIPAGESSDAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPP 397

Query: 66  STPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQ 110
                    P   P     P   P    PP   P   + P  PPQ
Sbjct: 398 QGYPPQGYPPQGYPPQGYPPQGYP---PPPQGAPPQGAPPAAPPQ 439

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 40.7 bits (95), Expect = 8e-04
 Identities = 19/98 (19%), Positives = 31/98 (31%)

Query: 2   DQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSST 61
           D ++ +  +  +T  P+  ++  A +A +      +        QQ    P   + P   
Sbjct: 340 DDKETEDDKDAETEIPAGESSDAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQG 399

Query: 62  TIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRP 99
             P   P    P     P   P PP        PP  P
Sbjct: 400 YPPQGYPPQGYPPQGYPPQGYPPPPQGAPPQGAPPAAP 437

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 40.7 bits (95), Expect = 8e-04
 Identities = 17/99 (17%), Positives = 28/99 (28%), Gaps = 6/99 (6%)

Query: 3   QEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTT 62
            ++  +  +          ++ A  ++      ++ A   +  QQQ   PP    P    
Sbjct: 340 DDKETEDDKDAETEIPAGESSDAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQG 399

Query: 63  IPTSTPTTN------TPNPNPSPSPSPAPPSRPTSLTPP 95
            P              P     P P  APP       PP
Sbjct: 400 YPPQGYPPQGYPPQGYPPQGYPPPPQGAPPQGAPPAAPP 438

>3sv0_A Casein kinase I-like; typical kinase domain fold, cytosol, transferase; 2.00A {Oryza sativa japonica group} Length = 483

 Score = 43.8 bits (103), Expect = 8e-05
 Identities = 21/155 (13%), Positives = 38/155 (24%), Gaps = 10/155 (6%)

Query: 12  TQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTN 71
           T      +   +    A          AP +    +Q       ++  S+      P   
Sbjct: 291 TILKYQQSQIASAPPRAVGHGAGPSGLAPPALQNDRQSGVDEGRTSGWSSMDRRRAPPPI 350

Query: 72  TPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSA 131
                 +   +P       S  P         R     ++      ++ SS    P  ++
Sbjct: 351 ASVGTLAKQKAPVGNDASFSKEPVISASNFLGRSSGSSRR-----PAVSSSRDVMPIDTS 405

Query: 132 SPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSS 166
            P              P        PQ S P +S+
Sbjct: 406 EPSRTRATDAS-----PGAFRRTSGPQKSSPVNSA 435

>1id3_B Histone H4; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1 Length = 102

 Score = 38.1 bits (88), Expect = 8e-04
 Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDIL 461
           +TK +I+ L  +    +R+   + + +  + + F+ES+     +  +H K  T+ + D++
Sbjct: 29  ITKPAIRRLARRGG-VKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVV 87

Query: 462 VHLERNWNMTLPGFSG 477
             L+R    TL GF G
Sbjct: 88  YALKRQGR-TLYGFGG 102

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	496
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	100.0
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	99.06
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	99.0
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	98.94
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	98.9
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	98.82
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	98.72
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	98.72
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	98.67
1taf_A	68	TFIID TBP associated factor 42; transcription init	98.51
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	98.48
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	98.47
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	98.46
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	98.35
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	98.32
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	98.27
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	98.22
3r45_A	156	Histone H3-like centromeric protein A; histone fol	98.2
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	98.17
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	98.15
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	98.14
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	98.09
1taf_B	70	TFIID TBP associated factor 62; transcription init	98.07
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	98.04
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	98.0
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	98.0
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	97.82
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	97.81
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	97.68
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	97.65
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	97.57
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	97.52
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	97.43
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	97.31
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	97.26
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	97.26
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	97.04
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	96.9
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	96.85
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	96.8
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	96.77
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	96.76
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	96.49
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	96.45
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	96.29
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	96.21
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	93.63
3v9r_B	88	MHF2, uncharacterized protein YDL160C-A; histone f	92.18
2r44_A	331	Uncharacterized protein; putative ATPase, structur	92.03
1h3o_A	75	Transcription initiation factor TFIID 135 kDa subu	91.95
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	91.22
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	90.88
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	90.51
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	89.55
3kw6_A	78	26S protease regulatory subunit 8; structural geno	85.95
3bos_A	242	Putative DNA replication factor; P-loop containing	85.9
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	85.72
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	85.49
3ox6_A	153	Calcium-binding protein 1; EF-hand, calcium-sensor	85.0
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	84.84
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	84.67
1fh1_A	92	NODF, nodulation protein F; ROOT nodulation factor	83.94
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	83.91
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	83.41
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	83.08
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	82.81
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	82.57
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	81.6

>1h3o_B Transcription initiation factor TFIID 20/15 kDa subunits; transcription/TBP-associated factors, TBP-associated factors; 2.3A {Homo sapiens} SCOP: a.22.1.3

Probab=100.00  E-value=1.1e-33  Score=230.40  Aligned_cols=75  Identities=53%  Similarity=0.960  Sum_probs=73.1

Q ss_pred             CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992          398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I  472 (496)
                      +.+||+|++|++||++||+++.||+||||+|++|||||||+|+++||+||||||+++||+|||+|||||+|||+|
T Consensus         2 s~~vl~k~~L~~Lv~~idp~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s~~le~kDvql~Ler~wni~i   76 (76)
T 1h3o_B            2 SHMVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQWNMWI   76 (76)
T ss_dssp             -CCSSCHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHHTCCCC
T ss_pred             CcccccHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHhhcCCcC
Confidence            578999999999999999999999999999999999999999999999999999999999999999999999987

>2hue_C Histone H4; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} SCOP: a.22.1.1 PDB: 3nqj_B 1aoi_B 3kwq_B* 1hio_D 2yfv_B

Probab=99.06  E-value=2.9e-10  Score=92.52  Aligned_cols=79  Identities=24%  Similarity=0.313  Sum_probs=72.9

Q ss_pred             cCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCC
Q 010992          397 FGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFS  476 (496)
Q Consensus       397 ~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFs  476 (496)
                      +..+.|+|..+.+|+++.+. ..|.+|+.|.|.++.++|++.|+..|+.+|+|.|-.||+..||.+.|+|. |..+.||+
T Consensus         6 ~~~~~ip~~~I~Riar~~Gv-~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~-g~~lYgf~   83 (84)
T 2hue_C            6 DNIQGITKPAIRRLARRGGV-KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ-GRTLYGFG   83 (84)
T ss_dssp             GGCCSSCHHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTT-CEEEESCC
T ss_pred             ccCCCCCHHHHHHHHHHcCc-hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc-CCCCCCCC
Confidence            45677999999999999854 88999999999999999999999999999999999999999999999998 78899996


Q ss_pred             c
Q 010992          477 G  477 (496)
Q Consensus       477 s  477 (496)
                      +
T Consensus        84 ~   84 (84)
T 2hue_C           84 G   84 (84)
T ss_dssp             -
T ss_pred             C
Confidence            3

>1id3_B Histone H4; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1

Probab=99.00  E-value=6.7e-10  Score=93.86  Aligned_cols=79  Identities=23%  Similarity=0.313  Sum_probs=72.6

Q ss_pred             CcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992          396 EFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF  475 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF  475 (496)
                      .+..+.|+|..|.+|++++. -..|.+|+.|.|.+++++|+++|+..|+.+|+|-+-.||+..||.+.|+|. +..+.||
T Consensus        23 r~~i~~ip~~~I~Rlar~~G-v~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~ALkr~-g~~lYGf  100 (102)
T 1id3_B           23 RDNIQGITKPAIRRLARRGG-VKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ-GRTLYGF  100 (102)
T ss_dssp             -CCGGGSCHHHHHHHHHHTT-CCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHT-TCCEESS
T ss_pred             HhccCCCCHHHHHHHHHHcC-chhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc-CCCCCCC
Confidence            35566799999999999985 488999999999999999999999999999999999999999999999998 6788899


Q ss_pred             C
Q 010992          476 S  476 (496)
Q Consensus       476 s  476 (496)
                      +
T Consensus       101 ~  101 (102)
T 1id3_B          101 G  101 (102)
T ss_dssp             C
T ss_pred             C
Confidence            6

>1tzy_D Histone H4-VI; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1f66_B 1eqz_D 1hq3_D 1u35_B 2aro_D 2cv5_B* 2f8n_B 3nqu_B 3r45_B 3azg_B 3a6n_B 3an2_B 3av1_B 3av2_B 3ayw_B 3aze_B 3azf_B 3afa_B 3azh_B 3azk_B ...

Probab=98.94  E-value=1.5e-09  Score=91.16  Aligned_cols=80  Identities=24%  Similarity=0.311  Sum_probs=72.9

Q ss_pred             CcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992          396 EFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF  475 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF  475 (496)
                      .+..+.|++..|.+|++.... ..|.+|+.|.|.++.++|+++|+..|..+|+|-|-.||+.+||.+.|++. +..+.||
T Consensus        24 r~~~~gip~~~I~Rlar~~G~-~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktIt~~DV~~Alr~~-g~~lYGf  101 (103)
T 1tzy_D           24 RDNIQGITKPAIRRLARRGGV-KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ-GRTLYGF  101 (103)
T ss_dssp             CCGGGGSCHHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHT-TCEEESC
T ss_pred             hhhcccCCHHHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHc-CCCCcCC
Confidence            344555999999999999866 79999999999999999999999999999999999999999999999998 6788899


Q ss_pred             Cc
Q 010992          476 SG  477 (496)
Q Consensus       476 ss  477 (496)
                      ++
T Consensus       102 ~~  103 (103)
T 1tzy_D          102 GG  103 (103)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl y-1140}

Probab=98.90  E-value=2.1e-09  Score=90.50  Aligned_cols=78  Identities=23%  Similarity=0.321  Sum_probs=63.8

Q ss_pred             cCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCC
Q 010992          397 FGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFS  476 (496)
Q Consensus       397 ~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFs  476 (496)
                      +..+.|++..|.+|++.... ..|.+|+.|.|.++.++|+++|+..|..+|+|-|-.||+.+||.+.|++. |..+-||+
T Consensus        25 ~~~~gip~~~I~Rlar~~G~-~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktvt~~DV~~Alr~~-g~~lYGf~  102 (103)
T 2yfw_B           25 DNIQGITKPAIRRLARRGGV-KRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQ-GRTLYGFG  102 (103)
T ss_dssp             -----CCHHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH-C-------
T ss_pred             hhhccCCHHHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc-CCCCcCCC
Confidence            44555999999999999866 79999999999999999999999999999999999999999999999998 57788986

>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2

Probab=98.82  E-value=8.1e-09  Score=80.79  Aligned_cols=64  Identities=19%  Similarity=0.368  Sum_probs=61.1

Q ss_pred             cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      .|+|..+.+|+|++ +..++++++.+.|.+++++|+++|+..|+.+|+|.|..||+.+||++.++
T Consensus         6 ~lp~a~v~Rl~r~~-g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakRkTI~~~DV~lA~~   69 (70)
T 1ku5_A            6 ELPIAPVDRLIRKA-GAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   69 (70)
T ss_dssp             CSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             cCChHHHHHHHHHc-CcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence            58999999999998 46899999999999999999999999999999999999999999999986

>1b67_A Protein (histone HMFA); DNA binding protein; 1.48A {Methanothermus fervidus} SCOP: a.22.1.2 PDB: 1hta_A 1a7w_A 1b6w_A 1bfm_A

Probab=98.72  E-value=2.9e-08  Score=76.76  Aligned_cols=65  Identities=26%  Similarity=0.322  Sum_probs=62.0

Q ss_pred             cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      -|.|..+..||+++ +...+..|+.++|.+.+++||..+++.|..+|+|.|..||..+||++.+++
T Consensus         2 ~lP~a~v~Ri~k~~-~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~~kRkTI~~~Di~~A~~~   66 (68)
T 1b67_A            2 ELPIAPIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKM   66 (68)
T ss_dssp             CSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHGGG
T ss_pred             CCCccHHHHHHhcC-CcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            37899999999999 678999999999999999999999999999999999999999999999986

>3b0c_W CENP-W, centromere protein W; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_W* 3vh5_W 3vh6_W

Probab=98.72  E-value=2.4e-08  Score=79.62  Aligned_cols=71  Identities=13%  Similarity=0.191  Sum_probs=65.3

Q ss_pred             CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc
Q 010992          398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNW  468 (496)
Q Consensus       398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW  468 (496)
                      |.+.|.+..+..+++++.++..|..|+.++|.+.+++||+.|...|..+|+|.|..||..+||+..||.-+
T Consensus         1 g~~~LP~A~V~rI~K~~~p~~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A~~~ll   71 (76)
T 3b0c_W            1 GRRTVPRGTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAAAKVIL   71 (76)
T ss_dssp             ---CCCHHHHHHHHHHHCTTCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHHHH
T ss_pred             CCCcccccHHHHHHHHhCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence            34679999999999999999999999999999999999999999999999999999999999999998754

>3b0c_T CENP-T, centromere protein T; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_T* 3vh5_T 3vh6_T

Probab=98.67  E-value=3.3e-08  Score=84.64  Aligned_cols=72  Identities=15%  Similarity=0.201  Sum_probs=63.4

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcc
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMT  471 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~  471 (496)
                      ...|+|..|.+|+++. ...+|.+|+.+.|.+++++|+++|+..|+.+|+|.|.+||+..||.+.|+|+-.+.
T Consensus         5 d~~lP~a~I~Ri~r~~-g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~lalrr~g~~~   76 (111)
T 3b0c_T            5 EPEIASSLIKQIFSHY-VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRRQGLVT   76 (111)
T ss_dssp             -----CHHHHHHHHHH-HCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTSSB
T ss_pred             CCCCCHHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHCCCcc
Confidence            4568999999999998 67899999999999999999999999999999999999999999999999985543

>1taf_A TFIID TBP associated factor 42; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3

Probab=98.51  E-value=3.2e-07  Score=73.36  Aligned_cols=63  Identities=19%  Similarity=0.331  Sum_probs=57.3

Q ss_pred             HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc
Q 010992          405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNW  468 (496)
Q Consensus       405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW  468 (496)
                      +.|..|++..+- +.++++|...|+|++.+|+.+|+..|..+|+|.|.++|++.||+|.++...
T Consensus         5 ~~i~~iLk~~G~-~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLAi~~~~   67 (68)
T 1taf_A            5 QVIMSILKELNV-QEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEVTL   67 (68)
T ss_dssp             HHHHHHHHHTTC-CCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTC
T ss_pred             HHHHHHHHHCCC-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcc
Confidence            457788888644 799999999999999999999999999999999999999999999998753

>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3

Probab=98.48  E-value=4.2e-07  Score=74.49  Aligned_cols=70  Identities=14%  Similarity=0.278  Sum_probs=63.5

Q ss_pred             cCCccCCHHHHHHHHHhh-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          397 FGNRILTKRSIQELVNQI-DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       397 ~~nrILtKrKLqELVrqI-DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +....|.+..+..|+|++ .....+..|+.++|.+.+++||..++..|..+|+|.|..||..+||..+|++
T Consensus         4 ~~d~~LP~a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~Al~~   74 (93)
T 1n1j_A            4 EQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMST   74 (93)
T ss_dssp             ---CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             cccccCChhHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHH
Confidence            356689999999999999 4468999999999999999999999999999999999999999999999983

>1f1e_A Histone fold protein; archaeal histone protein, DNA binding protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP: a.22.1.2

Probab=98.47  E-value=3.9e-07  Score=82.46  Aligned_cols=73  Identities=11%  Similarity=0.249  Sum_probs=68.2

Q ss_pred             CCcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc
Q 010992          395 DEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNW  468 (496)
Q Consensus       395 ~e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW  468 (496)
                      .+.+...|++..+.+|+|+. +.+++..|+.+.|.+++++|++.|+..|+.+|+|-|..||..+||+++|+++.
T Consensus        76 ~d~~~l~lP~a~V~Ri~k~~-g~~RVS~~A~~~l~~~le~f~~~I~~~A~~~a~ha~RKTIt~eDV~~Al~~~~  148 (154)
T 1f1e_A           76 EDYDGELFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYSM  148 (154)
T ss_dssp             TTCCSCCCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHS
T ss_pred             CccccccCCccHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhcC
Confidence            34566689999999999998 77899999999999999999999999999999999999999999999999974

>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae}

Probab=98.46  E-value=2.4e-07  Score=81.30  Aligned_cols=62  Identities=26%  Similarity=0.405  Sum_probs=58.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCc
Q 010992          415 DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSG  477 (496)
Q Consensus       415 DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFss  477 (496)
                      .+-++|..++.|.|.++.++|+++|+..|+.+|+|.|.+||++.||.+.|+|. |..+-||++
T Consensus        60 gGvkRIS~~iy~e~r~vl~~~l~~i~rdav~yaehA~RKTVta~DV~~Alkr~-G~~lygf~~  121 (121)
T 2ly8_A           60 RGSKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ-GRTLYGFGG  121 (121)
T ss_dssp             CCSSCCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCBCHHHHHHHHHHT-TCGGGGCCC
T ss_pred             cCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhC-CCcCCCCCC
Confidence            34578999999999999999999999999999999999999999999999996 779999984

>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A single chain of CSE4+SCM3+H4, fusion protein; NMR {Saccharomyces cerevisiae}

Probab=98.35  E-value=1.3e-06  Score=83.87  Aligned_cols=75  Identities=21%  Similarity=0.384  Sum_probs=67.7

Q ss_pred             cCCHHHHHHHHHhhC--------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992          401 ILTKRSIQELVNQID--------PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       401 ILtKrKLqELVrqID--------PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I  472 (496)
                      .=-++.|.|++. |+        +-+.|..++.|.|.++.++|+++|+..|+.+|+|.+..||++.||.|.|+|. |..+
T Consensus       153 ~r~~~vLrD~i~-i~~~RlaRrgGVkRIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~ALKr~-gr~l  230 (235)
T 2l5a_A          153 TKYTSVLRDIID-ISDEEDGDKGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ-GRTL  230 (235)
T ss_dssp             STHHHHHHHHHH-HTCCTTSCCTTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHH-HHHH
T ss_pred             hhHHHHHHHhhc-ccHHHHhhcCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhc-CCcc
Confidence            344778888887 75        5679999999999999999999999999999999999999999999999997 5889


Q ss_pred             cCCCc
Q 010992          473 PGFSG  477 (496)
Q Consensus       473 PGFss  477 (496)
                      .||++
T Consensus       231 YGf~~  235 (235)
T 2l5a_A          231 YGFGG  235 (235)
T ss_dssp             TTCCC
T ss_pred             ccCCC
Confidence            99974

>1jfi_B DR1 protein, transcription regulator NC2 beta chain; histone, H2A/H2B, tata-DNA, transcription initiation, NC2, negative cofactor, structural genomics, PSI; 2.62A {Homo sapiens} SCOP: a.22.1.3

Probab=98.32  E-value=1.3e-06  Score=80.80  Aligned_cols=72  Identities=14%  Similarity=0.353  Sum_probs=66.5

Q ss_pred             CCcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          395 DEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       395 ~e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      .++....|.+..|..||+++-++.+|.+|+.++|.+++.+||.-|+..|..+|+|.+..||..+||...|++
T Consensus         9 ~~~eD~~LP~A~V~RImK~alp~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~~   80 (179)
T 1jfi_B            9 GNDDDLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALES   80 (179)
T ss_dssp             ---CCCCCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             CchhhhhcCHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHh
Confidence            566778999999999999997789999999999999999999999999999999999999999999999995

>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.10A {Homo sapiens}

Probab=98.27  E-value=1.9e-06  Score=71.25  Aligned_cols=65  Identities=20%  Similarity=0.147  Sum_probs=61.0

Q ss_pred             cCCHHHHHHHHHhhC------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          401 ILTKRSIQELVNQID------PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       401 ILtKrKLqELVrqID------PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      +|.|--+++|||+|.      ...++..++.++|.|.+|+|+.++.+.+...|+|.|--||..|||+|+..
T Consensus         3 LI~klPF~RLVREI~~~~~~~~~~R~q~~Al~aLQea~E~ylv~Lfeda~lcAiHAkRvTi~~kDiqLa~r   73 (82)
T 3nqj_A            3 LIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARR   73 (82)
T ss_dssp             SSCHHHHHHHHHHHHHHHHSSCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             CcccccHHHHHHHHHHHhccCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHHHH
Confidence            678999999999997      46899999999999999999999999999999999999999999999754

>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis}

Probab=98.22  E-value=3e-06  Score=69.33  Aligned_cols=66  Identities=23%  Similarity=0.222  Sum_probs=61.0

Q ss_pred             cCCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          401 ILTKRSIQELVNQID----PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       401 ILtKrKLqELVrqID----PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +|.|--+++|||+|.    ....+..++.++|.+.+|+|+..+.+.+..+|+|.|.-||..|||+|...-
T Consensus         3 li~k~PF~RLVRei~~~~~~~~R~q~~Al~aLQea~Eaylv~lfeda~l~A~HAkRvTi~~kDiqLa~ri   72 (77)
T 2hue_B            3 LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRI   72 (77)
T ss_dssp             CSCHHHHHHHHHHHHHTTCSSCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             ccccchHHHHHHHHHHHcCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHhhHHHHHHH
Confidence            688999999999992    468999999999999999999999999999999999999999999998743

>3r45_A Histone H3-like centromeric protein A; histone fold, centromere, CENP-A, histone chaperone, hjurp; 2.60A {Homo sapiens}

Probab=98.20  E-value=1.7e-06  Score=78.93  Aligned_cols=70  Identities=19%  Similarity=0.119  Sum_probs=62.5

Q ss_pred             CcCCccCCHHHHHHHHHhhC------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          396 EFGNRILTKRSIQELVNQID------PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqID------PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      ...+-+|.|--++.||++|.      .+..+..++.++|.|.+|+|+.++.+.+..+|+|.|--||..|||+|+..
T Consensus        72 kSteLLIpKlPF~RLVREIa~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEdanLcAiHAkRVTIm~kDIqLArr  147 (156)
T 3r45_A           72 KSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARR  147 (156)
T ss_dssp             ---CCCSCHHHHHHHHHHHHHTTTTTCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHH
T ss_pred             cccccccccccHHHHHHHHHHHhccCccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHH
Confidence            35777899999999999996      35688999999999999999999999999999999999999999999753

>3nqu_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.50A {Homo sapiens} PDB: 3an2_A

Probab=98.17  E-value=2.4e-06  Score=76.75  Aligned_cols=70  Identities=19%  Similarity=0.119  Sum_probs=63.1

Q ss_pred             CcCCccCCHHHHHHHHHhhC------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          396 EFGNRILTKRSIQELVNQID------PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqID------PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      .+.+-+|.|--++.||++|.      .+..+..++.++|.|.+|+|+.++.+.+..+|+|.|--||..|||+|+..
T Consensus        56 kst~LLIpKlPF~RLVREI~~~~~~~~~~Rfq~~Al~ALQEAaEayLv~LFEdanlcAiHAkRVTIm~kDiqLArr  131 (140)
T 3nqu_A           56 KSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARR  131 (140)
T ss_dssp             ---CCCSCTTHHHHHHHHHHHHHHTTCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             cccccccccccHHHHHHHHHHHhcccccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHH
Confidence            46778899999999999996      46899999999999999999999999999999999999999999999764

>2yfv_A Histone H3-like centromeric protein CSE4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.32A {Kluyveromyces lactis nrrl y-1140} PDB: 2yfw_A

Probab=98.15  E-value=3.2e-06  Score=72.00  Aligned_cols=70  Identities=17%  Similarity=0.193  Sum_probs=59.5

Q ss_pred             CcCCccCCHHHHHHHHHhhCC-------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          396 EFGNRILTKRSIQELVNQIDP-------SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqIDP-------sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      .+.+-+|.|--+..||++|.-       ...+..++.++|.|.+|+|+..+.+.+..+|+|.|--||..|||+|+..
T Consensus        22 kst~llIpk~PF~RLVREI~~~~~~~~~~~R~q~~Al~ALQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~r   98 (100)
T 2yfv_A           22 RSTDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARR   98 (100)
T ss_dssp             ------CCHHHHHHHHHHHHHTTC-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             ccchhhhccccHHHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHH
Confidence            356778999999999999962       5789999999999999999999999999999999999999999999863

>1tzy_C Histone H3; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_C 1hq3_C 2aro_C 2f8n_A 2hio_C 3av1_A 3lel_A 3afa_A 3azi_A 3azj_A 3azk_A 3azl_A 3azm_A 3azn_A 2cv5_A* 1u35_A* 2nqb_A 2io5_B 2pyo_A* 3c9k_C ...

Probab=98.14  E-value=5.5e-06  Score=73.95  Aligned_cols=71  Identities=21%  Similarity=0.185  Sum_probs=65.2

Q ss_pred             CcCCccCCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          396 EFGNRILTKRSIQELVNQID----PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqID----PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      .+.+-+|.|--++.||++|.    .+..+..++.++|.|.+|+|+..+.+.+..+|+|.|--||..|||+|+..-
T Consensus        57 kst~lLIpk~PF~RLVREI~~~~~~~~R~q~~Al~aLQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~ri  131 (136)
T 1tzy_C           57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI  131 (136)
T ss_dssp             HCCSCCSCHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             cchhhhhccchHHHHHHHHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHhHHHHHHH
Confidence            35778999999999999992    468999999999999999999999999999999999999999999998743

>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus}

Probab=98.09  E-value=2.7e-06  Score=73.19  Aligned_cols=61  Identities=15%  Similarity=0.148  Sum_probs=54.2

Q ss_pred             HHHHHHhhCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          407 IQELVNQIDP--SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       407 LqELVrqIDP--sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      +..+++++..  ++.+.++|...|.+++.+|+++|...+..+|||.|.+||+..||.|.++|+
T Consensus        25 V~rI~~~~g~~~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~La~Rrn   87 (107)
T 3b0b_B           25 TGCLCQDVAEDKGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLARRS   87 (107)
T ss_dssp             HHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTC
T ss_pred             HHHHHHHHhhhcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHHHHHhC
Confidence            3455555533  578999999999999999999999999999999999999999999999996

>1taf_B TFIID TBP associated factor 62; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3

Probab=98.07  E-value=1.7e-05  Score=63.77  Aligned_cols=66  Identities=18%  Similarity=0.240  Sum_probs=61.8

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      +-+|++..+.++++.++- +.|.+|+.+.|.+-++..+..|+..|++++||-|..+|...||.+.|+
T Consensus         4 ~s~lp~~~v~~iaes~Gi-~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk~Lt~~DI~~Alk   69 (70)
T 1taf_B            4 GSSISAESMKVIAESIGV-GSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             SCCCCHHHHHHHHHHTTC-CCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             cccCCHHHHHHHHHHCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHc
Confidence            457899999999999855 799999999999999999999999999999999999999999999885

>3v9r_A MHF1, uncharacterized protein YOL086W-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae}

Probab=98.04  E-value=1.1e-05  Score=67.64  Aligned_cols=60  Identities=15%  Similarity=0.225  Sum_probs=53.6

Q ss_pred             HHHHHhhCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          408 QELVNQIDP--SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       408 qELVrqIDP--sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      ..++.++..  +..+++++...|.+++.+|+++|...+..+|||-|.+||+..||.|.++||
T Consensus        19 ~ki~~e~~~~~g~~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAgRkTI~~eDV~L~~Rrn   80 (90)
T 3v9r_A           19 EERLQQVLSSEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRKQ   80 (90)
T ss_dssp             HHHHHHHSCSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTC
T ss_pred             HHHHHHHHHhcCceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhC
Confidence            355566533  367999999999999999999999999999999999999999999999997

>1f1e_A Histone fold protein; archaeal histone protein, DNA binding protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP: a.22.1.2

Probab=98.00  E-value=1.3e-05  Score=72.55  Aligned_cols=66  Identities=20%  Similarity=0.206  Sum_probs=62.3

Q ss_pred             cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      .|.+..+.+|+|+.=+.+++..|+.|.|.+++++|+..|+..|..+|+|.|..||..+||+..|.+
T Consensus         4 ~LP~a~V~Riik~~lg~~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~ha~RKTv~a~DV~~a~~~   69 (154)
T 1f1e_A            4 ELPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADV   69 (154)
T ss_dssp             CCCHHHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH
T ss_pred             cCCccHHHHHHHhcCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHh
Confidence            478999999999985569999999999999999999999999999999999999999999999976

>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_B

Probab=98.00  E-value=1.3e-05  Score=70.20  Aligned_cols=71  Identities=24%  Similarity=0.288  Sum_probs=62.2

Q ss_pred             cCCccCCHHHHHHHHHhhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          397 FGNRILTKRSIQELVNQIDP-SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       397 ~~nrILtKrKLqELVrqIDP-sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      .....|.+..|..|++++++ ...|..|+.++|.+.++.||..|+..|..+|+|.+..||..+||...|++.
T Consensus         5 ~~d~~LP~A~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~Al~~l   76 (128)
T 2byk_B            5 IEDLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTEL   76 (128)
T ss_dssp             ------CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHT
T ss_pred             cccccCCHHHHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHc
Confidence            45678999999999998776 679999999999999999999999999999999999999999999999985

>4dra_A Centromere protein S; DNA binding complex, DNA damage repair, histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB: 4drb_A

Probab=97.82  E-value=2.7e-05  Score=67.94  Aligned_cols=60  Identities=13%  Similarity=0.154  Sum_probs=52.8

Q ss_pred             HHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc
Q 010992          409 ELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNW  468 (496)
Q Consensus       409 ELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW  468 (496)
                      .+|++..  -+..+++++...|.+++++|+++|...+..+|||-|.+||+..||+|.++|+=
T Consensus        35 rIvke~gaer~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr~~   96 (113)
T 4dra_A           35 CLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSN   96 (113)
T ss_dssp             HHHHHHHHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCH
T ss_pred             HHHHHHHHHcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHhCH
Confidence            3444442  25679999999999999999999999999999999999999999999999973

>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3

Probab=97.81  E-value=4.4e-05  Score=63.38  Aligned_cols=78  Identities=14%  Similarity=0.242  Sum_probs=64.3

Q ss_pred             CCcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992          395 DEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       395 ~e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I  472 (496)
                      .+.++..|.-.++..+++.-.....+..|+-.+|.+.++.||..+++.|+..|++.|..+|..+||..++++...+.|
T Consensus        13 ~~~~~~~lP~arIkrImK~~~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~krktI~~~di~~Av~~~e~~~F   90 (97)
T 1n1j_B           13 KDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDF   90 (97)
T ss_dssp             -------CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGG
T ss_pred             CCcCCCcCCHHHHHHHHccCccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHhcCcHHHH
Confidence            455677889999999999754447899999999999999999999999999999999999999999999998755544

>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus, binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A

Probab=97.68  E-value=4.6e-05  Score=68.61  Aligned_cols=51  Identities=16%  Similarity=0.156  Sum_probs=49.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          417 SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       417 sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      +..+++++...|.+++++|+++|...+..+|||-|..||+..||.|.++|+
T Consensus        37 ~~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rrn   87 (140)
T 3vh5_A           37 GVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARRS   87 (140)
T ss_dssp             TCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTS
T ss_pred             CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhC
Confidence            568999999999999999999999999999999999999999999999997

>2nqb_D Histone H2B; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_D*

Probab=97.65  E-value=8.2e-05  Score=65.83  Aligned_cols=63  Identities=19%  Similarity=0.287  Sum_probs=59.4

Q ss_pred             HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      .-|..+|++|.+...|..++.++|-.+++|+.|.|...|++||+|.|..||..+||+..++-.
T Consensus        37 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLl   99 (123)
T 2nqb_D           37 IYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLL   99 (123)
T ss_dssp             HHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHHHh
Confidence            458999999999999999999999999999999999999999999999999999999987654

>1tzy_B Histone H2B; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_B 1hq3_B 2aro_B 2hio_B 3c9k_B 3azg_D 3a6n_D 3an2_D 3av1_D 3av2_D 3ayw_D 3aze_D 3azf_D 3afa_D 3azh_D 3azi_D 3azj_D 3azk_D 3azl_D 3azm_D ...

Probab=97.57  E-value=0.00012  Score=65.06  Aligned_cols=63  Identities=17%  Similarity=0.272  Sum_probs=59.3

Q ss_pred             HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      .-|..+|++|.+...|..++.++|-.+++|+.|.|...|++||+|.|..||..+||+..++-.
T Consensus        40 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLl  102 (126)
T 1tzy_B           40 IYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLL  102 (126)
T ss_dssp             HHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            348999999999999999999999999999999999999999999999999999999987654

>4g92_C HAPE; transcription factor, nucleosome, minor groove binding, CCAA complex, histone fold motif, specific binding to the ccaat- nucleus; HET: DNA; 1.80A {Aspergillus nidulans} PDB: 4g91_C*

Probab=97.52  E-value=0.00028  Score=60.74  Aligned_cols=75  Identities=16%  Similarity=0.212  Sum_probs=66.4

Q ss_pred             CcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCc
Q 010992          396 EFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNM  470 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI  470 (496)
                      +....-|...+|..+++.-.....+..|+-.+|.+.++.||..+++.|...|+.+|..+|..+||..++++.-.+
T Consensus        36 d~k~~~lPvaRIkrImK~d~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~krktI~~~di~~Av~~~e~~  110 (119)
T 4g92_C           36 DYKIHQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDIAAALSKSDMF  110 (119)
T ss_dssp             CSSCCSSCHHHHHHHHHTSTTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGG
T ss_pred             ccccCCCCHHHHHHHHhhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccCHHHHHHHHhcCchh
Confidence            344566999999999997555679999999999999999999999999999999999999999999999885333

>3b0b_C CENP-X, centromere protein X; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} PDB: 3vh5_D 3vh6_D

Probab=97.43  E-value=0.00039  Score=57.35  Aligned_cols=69  Identities=14%  Similarity=0.202  Sum_probs=59.8

Q ss_pred             CcCCccCCHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992          396 EFGNRILTKRSIQELVNQI--DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL  464 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqI--DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL  464 (496)
                      |+.+..|.++-|.+|++..  |.+.+|.+|+-+++.++.|-||...+.+|+..||-++.+.||+.|++-++
T Consensus         3 ~~~~~~~~~~lI~ril~~~f~~~ktrI~~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~~~LEki~   73 (81)
T 3b0b_C            3 EEREGGFRKETVERLLRLHFRDGRTRVNGDALLLMAELLKVFVREAAARAARQAQAEDLEKVDIEHVEKVL   73 (81)
T ss_dssp             ----CCCCHHHHHHHHHHHCCSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHH
T ss_pred             CccCCCCCHHHHHHHHHHHhccCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeecHHHHHHHH
Confidence            4557789999999999987  45789999999999999999999999999999999999999999986554

>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A single chain of CSE4+SCM3+H4, fusion protein; NMR {Saccharomyces cerevisiae}

Probab=97.31  E-value=0.00043  Score=66.67  Aligned_cols=82  Identities=20%  Similarity=0.150  Sum_probs=68.1

Q ss_pred             CccCCHHHHHHHHHhhCC-------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcc
Q 010992          399 NRILTKRSIQELVNQIDP-------SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMT  471 (496)
Q Consensus       399 nrILtKrKLqELVrqIDP-------sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~  471 (496)
                      .-+|.|--+++||++|.-       ..++..++..+|.|.+|.|+-.+.+.+...|.|.|--||..|||+|+. |-.|.+
T Consensus         9 ~~lI~KlPFqRLVREIaq~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEd~nLcaiHAkRVTim~kDiqLar-rirg~~   87 (235)
T 2l5a_A            9 KLLISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLAR-RIRGQF   87 (235)
T ss_dssp             --CCSCCHHHHHHHHHHHTSCGGGTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTSGGGTTHHHHHH-TSSCSC
T ss_pred             cccccCccHHHHHHHHHHHhccCCccceecHHHHHHHHHHHHHHHHHHHhhhHHHHhcccccccchhhHHHHH-HHhhcc
Confidence            347889999999999932       468999999999999999999999999999999999999999999986 445666


Q ss_pred             ccCCCccccc
Q 010992          472 LPGFSGDEIK  481 (496)
Q Consensus       472 IPGFssDEIr  481 (496)
                      +.++...|.+
T Consensus        88 ~~p~evme~~   97 (235)
T 2l5a_A           88 LVPRGSMERH   97 (235)
T ss_dssp             CCCSSSCHHH
T ss_pred             CCchhHHHHH
Confidence            6555554433

>1jfi_A Transcription regulator NC2 alpha chain; histone, H2A/H2B, tata-DNA, transcription initiation, NC2, negative cofactor, structural genomics, PSI; 2.62A {Homo sapiens} SCOP: a.22.1.3

Probab=97.26  E-value=0.00039  Score=58.02  Aligned_cols=74  Identities=16%  Similarity=0.238  Sum_probs=57.3

Q ss_pred             CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcc
Q 010992          398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMT  471 (496)
Q Consensus       398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~  471 (496)
                      .+-.|.-.+|..+++.-+....+..|+--+|...+|-||.++++.|+..|+++|..+|..+||+++++++-.+.
T Consensus         8 ~~~~fPvaRIkrimK~~~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~~krktI~~~di~~av~~~e~l~   81 (98)
T 1jfi_A            8 YNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIELEGDPA   81 (98)
T ss_dssp             --CCCCHHHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC------
T ss_pred             cCCCCChHHHHHHHHcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHhcCchhh
Confidence            34567788899999974334799999999999999999999999999999999999999999999998864443

>2jss_A Chimera of histone H2B.1 and histone H2A.Z; histone/chaperone complex, intrinsically unfolded protein, chaperone/structural protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.22.1.1 a.22.1.1

Probab=97.26  E-value=0.00084  Score=61.78  Aligned_cols=64  Identities=22%  Similarity=0.287  Sum_probs=59.6

Q ss_pred             HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      +--|..++++|.+...|..++.+.|-.|.+|+++.|+..|++|+++.+..||..+||+..++..
T Consensus         6 ~~yi~kvLkqv~p~~~iS~~Am~~m~s~v~di~~rIa~eA~~L~~~~~r~Tit~~eIq~Avrl~   69 (192)
T 2jss_A            6 SSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLI   69 (192)
T ss_dssp             HHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHcccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHh
Confidence            3458899999999999999999999999999999999999999999999999999999888754

>4dra_E Centromere protein X; DNA binding complex, DNA damage repair, histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB: 4drb_J

Probab=97.04  E-value=0.002  Score=53.62  Aligned_cols=67  Identities=15%  Similarity=0.237  Sum_probs=58.9

Q ss_pred             CCccCCHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992          398 GNRILTKRSIQELVNQI--DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL  464 (496)
Q Consensus       398 ~nrILtKrKLqELVrqI--DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL  464 (496)
                      .+..|.++-|.+|++..  |.+.+|.+|+-.++.++.|-||...+.+|+..|+-.+...||+.|++-+|
T Consensus         9 ~~~~i~~~li~ril~~~F~~~kTkIs~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~e~LEki~   77 (84)
T 4dra_E            9 AGSGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEKVL   77 (84)
T ss_dssp             --CCCCHHHHHHHHHTTCSSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Confidence            45578899999999965  46789999999999999999999999999999999999999999986554

>2nqb_C Histone H2A; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_C*

Probab=96.90  E-value=0.0022  Score=56.00  Aligned_cols=68  Identities=12%  Similarity=0.190  Sum_probs=62.5

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +-.|.-.+|+.++++-...+++..++-..|..+.|.|+.+|++.|..+|+|.|..+|..+||++.++.
T Consensus        21 gL~fPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~n   88 (123)
T 2nqb_C           21 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN   88 (123)
T ss_dssp             TCSSCHHHHHHHHHHTTSCSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             CeeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHhc
Confidence            34578889999999987778999999999999999999999999999999999999999999998764

>2f8n_G Core histone macro-H2A.1; nucleosome, NCP, macroh2A, histone variant, chromatin, X- RAY structure, crystallography, structural protein/DNA complex; 2.90A {Homo sapiens} SCOP: a.22.1.1 PDB: 1u35_C

Probab=96.85  E-value=0.0024  Score=55.55  Aligned_cols=68  Identities=13%  Similarity=0.231  Sum_probs=62.2

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +-.|.-.++++++++-.-.+++..++-..|..+.|.|+.+|++.|..+|+|.|..+|..+||++.++.
T Consensus        20 gLqfPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp~hi~lAI~n   87 (120)
T 2f8n_G           20 GVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVAN   87 (120)
T ss_dssp             TCSSCHHHHHHHHHHHSSSCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             CccCChHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHhc
Confidence            34567788999999987678999999999999999999999999999999999999999999998764

>1tzy_A Histone H2A-IV; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_A 1hq3_A 2aro_A 2hio_A 3c9k_A 3azg_C 3a6n_C 3an2_C 3av1_C 3av2_C 3ayw_C 3aze_C 3azf_C 3afa_C 3azh_C 3azi_C 3azj_C 3azk_C 3azl_C 3azm_C ...

Probab=96.80  E-value=0.0028  Score=55.82  Aligned_cols=68  Identities=12%  Similarity=0.187  Sum_probs=62.5

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +-.|.-.+|+.++++-...+++..++-..|..+.|.|+.+|++.|..+|+|.+..+|..+||++.++.
T Consensus        23 gLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~n   90 (129)
T 1tzy_A           23 GLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN   90 (129)
T ss_dssp             TCSSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             ceeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHhc
Confidence            44678889999999987778999999999999999999999999999999999999999999997763

>1id3_C Histone H2A.1; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1

Probab=96.77  E-value=0.0023  Score=56.45  Aligned_cols=69  Identities=10%  Similarity=0.189  Sum_probs=63.1

Q ss_pred             CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      .+-.|.-.+|++++++-...+++..++-..|..+.|.|+.+|++.|..+|+|.+..+|..+||++.++.
T Consensus        22 agLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hI~lAI~n   90 (131)
T 1id3_C           22 AGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRN   90 (131)
T ss_dssp             GTCSSCHHHHHHHHHTTCSCSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             CCeecCHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHhc
Confidence            344678899999999976778999999999999999999999999999999999999999999998763

>2f8n_K Histone H2A type 1; nucleosome, NCP, macroh2A, histone variant, chromatin, X- RAY structure, crystallography, structural protein/DNA complex; 2.90A {Mus musculus} SCOP: a.22.1.1

Probab=96.76  E-value=0.0027  Score=57.46  Aligned_cols=68  Identities=13%  Similarity=0.193  Sum_probs=62.5

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +-.|.-.+|.+++++-.-.++|+.++-..|..+.|.|+.+|++.|..+|+|.|..+|..+||++.++.
T Consensus        42 gLqFPVgrI~R~LK~~~~a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~krkrItprhI~lAI~n  109 (149)
T 2f8n_K           42 GLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN  109 (149)
T ss_dssp             TCSSCHHHHHHHHHHTTSCSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             CeeccHHHHHHHHHccccccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHhc
Confidence            44567889999999987778999999999999999999999999999999999999999999998764

>1f66_C Histone H2A.Z; nucleosome, chromatin, histone variant, protein DNA interaction, nucleoprotein, supercoiled DNA, complex (nucleosome core/DNA); 2.60A {Homo sapiens} SCOP: a.22.1.1

Probab=96.49  E-value=0.0057  Score=53.77  Aligned_cols=68  Identities=9%  Similarity=0.107  Sum_probs=61.1

Q ss_pred             CccCCHHHHHHHHHhhC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          399 NRILTKRSIQELVNQID-PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       399 nrILtKrKLqELVrqID-PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +-.|.-.+|++++++-. ..++++.++-..|..+.|.|+.+|++.|...|||.|..+|..+||++.+..
T Consensus        25 gLqfPV~ri~R~Lk~~~~a~~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItprhi~lAI~n   93 (128)
T 1f66_C           25 GLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG   93 (128)
T ss_dssp             TCSSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH
T ss_pred             CccCChHHHHHHHHHcccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHhc
Confidence            44577889999999865 346999999999999999999999999999999999999999999998764

>1bh9_B TAFII28; histone fold, tata binding protein, transcription regulation complex; HET: PMB; 2.60A {Homo sapiens} SCOP: a.22.1.3 PDB: 1bh8_B*

Probab=96.45  E-value=0.011  Score=49.22  Aligned_cols=66  Identities=17%  Similarity=0.245  Sum_probs=56.8

Q ss_pred             cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC-CCcchhhHHHHHhhh
Q 010992          401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS-DTLEAKDILVHLERN  467 (496)
Q Consensus       401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS-dTLEvKDVQLhLERn  467 (496)
                      -|+|+++..|++.|. +..+.++|..+|--||..||-++++.|..+.+.++. .-|..+.|.-.+.|.
T Consensus        16 ~f~k~~vKrl~~~~~-~~~v~~~v~i~v~glaKvfVgelVE~A~~V~~~~~~~~Pl~P~HireA~rrl   82 (89)
T 1bh9_B           16 AFPKAAIKRLIQSIT-GTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRL   82 (89)
T ss_dssp             CCCHHHHHHHHHHHH-SSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHc-CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHHH
Confidence            479999999999995 668999999999999999999999999999998864 367777776666653

>2byk_A Chrac-16; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_A

Probab=96.29  E-value=0.0051  Score=54.74  Aligned_cols=76  Identities=12%  Similarity=0.183  Sum_probs=54.2

Q ss_pred             cCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhh-hhcCCCCcchhhHHHHHhhhcCccc
Q 010992          397 FGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLA-KHRKSDTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       397 ~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLA-KHRKSdTLEvKDVQLhLERnWNI~I  472 (496)
                      .....|.-.+|..+++.-.-...|..++-.+|...++.||..++..|+..| +.+|..+|..+||..++++.-.+.|
T Consensus        15 ~~~~~LPlaRIKrIMK~dpdv~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~AV~~~e~~dF   91 (140)
T 2byk_A           15 TAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEF   91 (140)
T ss_dssp             --------------CCSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCSTTGG
T ss_pred             ccCCCCCHHHHHHHHhcCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHHHhcCchhhh
Confidence            455677888888888864344689999999999999999999999999999 9999999999999999997644433

>2jss_A Chimera of histone H2B.1 and histone H2A.Z; histone/chaperone complex, intrinsically unfolded protein, chaperone/structural protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.22.1.1 a.22.1.1

Probab=96.21  E-value=0.012  Score=54.13  Aligned_cols=68  Identities=10%  Similarity=0.155  Sum_probs=61.4

Q ss_pred             CccCCHHHHHHHHHhhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          399 NRILTKRSIQELVNQIDP-SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       399 nrILtKrKLqELVrqIDP-sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +-.|.-.++++++++-.. .++++.++-..|..+.|.|+.+|++.|..+|||.|..+|..+||++.+..
T Consensus       103 gl~fPv~ri~R~lk~~~~a~~Rv~~~A~vyLaavLEyl~~eIlelA~n~a~~~~~~~I~p~~i~lAi~n  171 (192)
T 2jss_A          103 GLQFPVGRIKRYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRG  171 (192)
T ss_dssp             SCCSCHHHHHHHHHHTTCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHHHHT
T ss_pred             CCcCCHHHHHHHHHhcCccccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhc
Confidence            446788899999998744 47999999999999999999999999999999999999999999998764

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=93.63  E-value=0.23  Score=45.96  Aligned_cols=68  Identities=10%  Similarity=0.188  Sum_probs=55.9

Q ss_pred             CCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHH----HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcC
Q 010992          402 LTKRSIQELVNQID--PSERLDPDVEDILVDIAED----FVESITMFGCSLAKHRKSDTLEAKDILVHLERNWN  469 (496)
Q Consensus       402 LtKrKLqELVrqID--PsesLDpDVEELLLeIADD----FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWN  469 (496)
                      +++..+.++++..-  .+..+++++.+.|.++++.    .+.+++..++.+|..++.+.|+.+||.-.|+...+
T Consensus       259 ~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~~A~~~~~~~It~~~v~~a~~~~~~  332 (368)
T 3uk6_A          259 YSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLD  332 (368)
T ss_dssp             CCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHSBC
T ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhcC
Confidence            46777777777542  3467999999999999984    77889999999999999999999999988886444

>3v9r_B MHF2, uncharacterized protein YDL160C-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae}

Probab=92.18  E-value=0.16  Score=42.93  Aligned_cols=61  Identities=13%  Similarity=0.237  Sum_probs=45.9

Q ss_pred             cCCHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC-------CCcchhhHH
Q 010992          401 ILTKRSIQELVNQI--DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS-------DTLEAKDIL  461 (496)
Q Consensus       401 ILtKrKLqELVrqI--DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS-------dTLEvKDVQ  461 (496)
                      .|.|.-|.+|+..-  +.+.+|..|+-+++.++.|-||...+-+|..-.+--+.       -+|++.|+.
T Consensus         1 ~ip~~llaRIL~~~F~~~kTrIt~da~~lv~kY~diFVrEAv~Rs~e~ke~~~~~~~~~~d~~LeveDLE   70 (88)
T 3v9r_B            1 MLSKEALIKILSQNEGGNDMKIADEVVPMIQKYLDIFIDEAVLRSLQSHKDINGERGDKSPLELSHQDLE   70 (88)
T ss_dssp             CCCSHHHHHHHTTTSCSSCCEECTTTHHHHHHHHHHHHHHHHHHHHHHHHCC-----------CCHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCCCceecHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCeeehHHHH
Confidence            36777788888754  56779999999999999999999999999655444223       278888874

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=92.03  E-value=0.42  Score=44.00  Aligned_cols=73  Identities=15%  Similarity=0.210  Sum_probs=55.4

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHH-----------------------HHHHHHHHHHhhhhcCCCCc
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDF-----------------------VESITMFGCSLAKHRKSDTL  455 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDF-----------------------VDsVvt~ACrLAKHRKSdTL  455 (496)
                      ..++..+.|.++.+.+ .+..+++++.+.|.+++.+.                       ...++..+..+|+.++.+.|
T Consensus       207 ~~~~~~~~i~~~~~~~-~~v~~~~~~~~~i~~~~~~~r~~~~~~~~~~~~~~~~~~s~R~~~~ll~~a~a~A~l~g~~~v  285 (331)
T 2r44_A          207 QKIVSKNDVLEIRNEI-NKVTISESLEKYIIELVFATRFPAEYGLEAEASYILYGASTRAAINLNRVAKAMAFFNNRDYV  285 (331)
T ss_dssp             CCCSCHHHHHHHHHHH-HTCBCCHHHHHHHHHHHHHHHSGGGGTCHHHHHHEEECCCHHHHHHHHHHHHHHHHHTTCSBC
T ss_pred             cccCCHHHHHHHHHHh-ccCCCCHHHHHHHHHHHHHHhccccccccccccccccCcChhHHHHHHHHHHHHHHHcCCCCC
Confidence            4566777777766554 46789999999999988543                       34567777888999999999


Q ss_pred             chhhHHHHHhhhcCccc
Q 010992          456 EAKDILVHLERNWNMTL  472 (496)
Q Consensus       456 EvKDVQLhLERnWNI~I  472 (496)
                      +..||+-.++.-+..++
T Consensus       286 ~~~dv~~~~~~vl~~r~  302 (331)
T 2r44_A          286 LPEDIKEVAYDILNHRI  302 (331)
T ss_dssp             CHHHHHHHHHHHHTTTS
T ss_pred             CHHHHHHHHHHHhHhhc
Confidence            99999888877665444

>1h3o_A Transcription initiation factor TFIID 135 kDa subunit; transcription/TBP-associated factors, TBP-associated factors; 2.3A {Homo sapiens} SCOP: a.22.1.3

Probab=91.95  E-value=0.17  Score=41.56  Aligned_cols=49  Identities=16%  Similarity=0.221  Sum_probs=34.1

Q ss_pred             HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992          404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD  453 (496)
Q Consensus       404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd  453 (496)
                      ++||.++.++ .+-..+.+||+++|---+++-+.++++.-+.+|+||...
T Consensus         9 qkri~~I~~k-~gl~~~~~dv~~~iS~a~qeRLr~llekl~~~a~~R~~~   57 (75)
T 1h3o_A            9 QRRILEIGKK-HGITELHPDVVSYVSHATQQRLQNLVEKISETAQQKNFS   57 (75)
T ss_dssp             HHHHHHHHHT-TTCCEECTTHHHHHHHHHHHHHHHHHHHHHC--------
T ss_pred             HHHHHHHHHh-cCCCcCChhHHHHhHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            3556666665 345678999999999999999999999999999999876

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=91.22  E-value=0.6  Score=42.58  Aligned_cols=56  Identities=5%  Similarity=-0.142  Sum_probs=46.7

Q ss_pred             CCCCCHHHHHHHHHHHHH-------HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992          417 SERLDPDVEDILVDIAED-------FVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       417 sesLDpDVEELLLeIADD-------FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I  472 (496)
                      ...|++++.++|.+++..       -+.+++..|+.+|+.++.++|+.+||...++..+.-++
T Consensus       265 ~~~ls~~~~~~l~~~~~~~~~~~~R~~~~ll~~a~~~A~~~~~~~v~~~~v~~a~~~~l~~r~  327 (350)
T 1g8p_A          265 KVEAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEGATAVGRDHLKRVATMALSHRL  327 (350)
T ss_dssp             GCBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTTCSBCCHHHHHHHHHHHHGGGC
T ss_pred             CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHhhcc
Confidence            458999999999999875       57889999999999999999999999877776554443

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B*

Probab=90.88  E-value=0.11  Score=40.18  Aligned_cols=54  Identities=17%  Similarity=0.116  Sum_probs=34.3

Q ss_pred             HHHHHHHHHH----HHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCcccccccC
Q 010992          426 DILVDIAEDF----VESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFR  484 (496)
Q Consensus       426 ELLLeIADDF----VDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~r  484 (496)
                      +.|.+.++.|    |..++..|+..|-.|+...|+.+|+.-.|++.    .|+.. ++++-|+
T Consensus        26 ~~la~~t~G~SGADi~~l~~eA~~~a~~~~~~~i~~~df~~Al~~~----~ps~~-~~l~~y~   83 (83)
T 3aji_B           26 EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTV----IKKDE-QEHEFYK   83 (83)
T ss_dssp             HHHHTSSCCCCHHHHHHHHHHHHHGGGTSCCSSBCHHHHHHHHHHH----CC-----------
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHHHhccCCcCHHHHHHHHHHH----ccCch-HHHHhcC
Confidence            3444444433    77899999999999999999999999888874    57767 7777664

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=90.51  E-value=1.1  Score=40.64  Aligned_cols=65  Identities=9%  Similarity=0.135  Sum_probs=51.0

Q ss_pred             CCHHHHHHHHHhh----CCCCCCCHHHHHHHHHHHH------HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          402 LTKRSIQELVNQI----DPSERLDPDVEDILVDIAE------DFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       402 LtKrKLqELVrqI----DPsesLDpDVEELLLeIAD------DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +++..+.++++..    .....+++++.+.|.++++      .++.+++..++.+|..++...|+.+||.-.+++
T Consensus       197 l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a~~~a~~~~~~~i~~~~v~~a~~~  271 (386)
T 2qby_A          197 YNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAERMKDTKVKEEYVYMAKEE  271 (386)
T ss_dssp             CCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Confidence            4677777777653    2346899999999999998      345678999999999888888999999865554

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=89.55  E-value=0.5  Score=43.05  Aligned_cols=66  Identities=14%  Similarity=0.234  Sum_probs=53.5

Q ss_pred             CCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHH------HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          402 LTKRSIQELVNQID----PSERLDPDVEDILVDIAE------DFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       402 LtKrKLqELVrqID----PsesLDpDVEELLLeIAD------DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      +++..+.++++..-    ....+++++.+.|.++++      .++.+++..++.+|..++.+.|+.+||.-.+++.
T Consensus       201 l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~a~~~~  276 (387)
T 2v1u_A          201 YTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLLRVAGEIAERRREERVRREHVYSARAEI  276 (387)
T ss_dssp             CCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCHHHHHHHHHHHHHHHHHTTCSCBCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            46777887776541    346899999999999998      5677999999999998888999999998777654

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=85.95  E-value=0.35  Score=37.04  Aligned_cols=45  Identities=7%  Similarity=0.069  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHH----HHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcC
Q 010992          425 EDILVDIAEDF----VESITMFGCSLAKHRKSDTLEAKDILVHLERNWN  469 (496)
Q Consensus       425 EELLLeIADDF----VDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWN  469 (496)
                      .+.|.+.++.|    |..|+..|+..|-.|+...|+.+|+.-.|++..+
T Consensus        27 l~~la~~t~G~SGADi~~l~~eA~~~a~~~~~~~i~~~d~~~Al~~v~~   75 (78)
T 3kw6_A           27 LRKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAKVMQ   75 (78)
T ss_dssp             HHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Confidence            35566677777    8999999999999999999999999999998643

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=85.90  E-value=1.5  Score=37.03  Aligned_cols=62  Identities=10%  Similarity=-0.051  Sum_probs=43.6

Q ss_pred             CHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHH---HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          403 TKRSIQELVNQI--DPSERLDPDVEDILVDIAE---DFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       403 tKrKLqELVrqI--DPsesLDpDVEELLLeIAD---DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      +.+.+.++++.+  ..+..+++++.+.|.+.++   .-+.++++.+|.+|...+. .|+.+||.-+|+
T Consensus       175 ~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~l~~~l~~~~~~a~~~~~-~It~~~v~~~l~  241 (242)
T 3bos_A          175 MDDEKLAALQRRAAMRGLQLPEDVGRFLLNRMARDLRTLFDVLDRLDKASMVHQR-KLTIPFVKEMLR  241 (242)
T ss_dssp             CGGGHHHHHHHHHHHTTCCCCHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHTC-CCCHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCC-CCcHHHHHHHhh
Confidence            334444444443  1245799999999998876   3566788888888876664 589999987775

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=85.72  E-value=1.8  Score=39.63  Aligned_cols=66  Identities=14%  Similarity=0.185  Sum_probs=52.0

Q ss_pred             CCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHH---------H---HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          402 LTKRSIQELVNQID----PSERLDPDVEDILVDIA---------E---DFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       402 LtKrKLqELVrqID----PsesLDpDVEELLLeIA---------D---DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      +++..+.++++..-    ....+++++.+.|.+++         +   .++.+++..++.+|..++.+.|+.+||...++
T Consensus       193 l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~~~~  272 (389)
T 1fnn_A          193 YTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSK  272 (389)
T ss_dssp             CBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHHH
Confidence            45667777776542    23479999999999999         2   34788999999999999999999999987777


Q ss_pred             hh
Q 010992          466 RN  467 (496)
Q Consensus       466 Rn  467 (496)
                      ..
T Consensus       273 ~~  274 (389)
T 1fnn_A          273 EV  274 (389)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=85.49  E-value=3  Score=38.35  Aligned_cols=64  Identities=6%  Similarity=0.088  Sum_probs=49.7

Q ss_pred             CCHHHHHHHHHhh----CCCCCCCHHHHHHHHHHHH---H---HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          402 LTKRSIQELVNQI----DPSERLDPDVEDILVDIAE---D---FVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       402 LtKrKLqELVrqI----DPsesLDpDVEELLLeIAD---D---FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      +++..+.++++..    -....+++++.+.|.++++   -   .+.+++..++.+|.  +...|+.+||.-.|++.
T Consensus       197 l~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~~a~--~~~~i~~~~v~~~~~~~  270 (384)
T 2qby_B          197 YDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQLAS--GGGIIRKEHVDKAIVDY  270 (384)
T ss_dssp             CCHHHHHHHHHHHHHHTSCTTSCCSHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHTT--SSSCCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhhcccCCcCHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhc--CCCccCHHHHHHHHHHH
Confidence            4778888888764    1346799999999999987   2   45678888888888  66788999998777654

>3ox6_A Calcium-binding protein 1; EF-hand, calcium-sensor; 2.40A {Homo sapiens} PDB: 3ox5_A 2lan_A 2lap_A 2k7b_A 2k7c_A 2k7d_A

Probab=85.00  E-value=3.7  Score=31.81  Aligned_cols=75  Identities=8%  Similarity=0.061  Sum_probs=45.8

Q ss_pred             CcCCccCCHHHHHHHHHhhCCCCCCCHH-HHHHHHHH---------HHHHHHHH----------------HHHHHHhhhh
Q 010992          396 EFGNRILTKRSIQELVNQIDPSERLDPD-VEDILVDI---------AEDFVESI----------------TMFGCSLAKH  449 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqIDPsesLDpD-VEELLLeI---------ADDFVDsV----------------vt~ACrLAKH  449 (496)
                      .+++..|++..|..+++.++-  .++.+ +++++..+         .++|+.-+                +..++++.-.
T Consensus        22 ~d~~G~i~~~el~~~l~~~~~--~~~~~~~~~l~~~~d~~~~g~i~~~eF~~~~~~~~~~~~~~~~~~~~~~~~F~~~D~   99 (153)
T 3ox6_A           22 KDKDGYINCRDLGNCMRTMGY--MPTEMELIELSQQINMNLGGHVDFDDFVELMGPKLLAETADMIGVKELRDAFREFDT   99 (153)
T ss_dssp             HHCSSSCCHHHHHHHHHHTTC--CCCHHHHHHHHHHHHTTSTTCCCHHHHHHHHHHHHTTCCHHHHCHHHHHHHHHHHCT
T ss_pred             CCCCCcCcHHHHHHHHHHcCC--CCCHHHHHHHHHHhCCCCCccCcHHHHHHHHHHHhhccccccccHHHHHHHHHHhCC
Confidence            345667777778777777643  23333 33333332         34565443                4555666655


Q ss_pred             cCCCCcchhhHHHHHhhhcCccc
Q 010992          450 RKSDTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       450 RKSdTLEvKDVQLhLERnWNI~I  472 (496)
                      .+...|+..++.-.|...+|..+
T Consensus       100 d~~G~i~~~el~~~l~~~~~~~~  122 (153)
T 3ox6_A          100 NGDGEISTSELREAMRALLGHQV  122 (153)
T ss_dssp             TCSSSBCHHHHHHHHHHHHSSCC
T ss_pred             CCCCcCcHHHHHHHHHHHhcCCC
Confidence            67778999999888887566544

>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B*

Probab=84.84  E-value=0.36  Score=38.39  Aligned_cols=56  Identities=11%  Similarity=0.252  Sum_probs=37.2

Q ss_pred             HHHHHHHHHH----HHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCcc-cccccCC
Q 010992          426 DILVDIAEDF----VESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGD-EIKTFRK  485 (496)
Q Consensus       426 ELLLeIADDF----VDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssD-EIr~~rk  485 (496)
                      +.|.+..+.|    |..||..|+..|-+|+...|+.+|+.-.|++.    ++|.... .+..|.+
T Consensus        26 ~~lA~~t~G~SGADl~~l~~eAa~~a~r~~~~~i~~~df~~Al~~v----~~~~~~~~~~~~y~~   86 (88)
T 3vlf_B           26 ELISRLCPNSTGAELRSVCTEAGMFAIRARRKVATEKDFLKAVDKV----ISGYKKFSSTSRYMQ   86 (88)
T ss_dssp             HHHHHTCSSCCHHHHHHHHHHHHHHHHHHSCSSBCHHHHHHHHHHH----TC-------------
T ss_pred             HHHHHHcCCCcHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHH----hcCcccccchhHHhc
Confidence            4556666667    89999999999999999999999999999885    4555432 3444443

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=84.67  E-value=1.1  Score=39.90  Aligned_cols=68  Identities=13%  Similarity=0.082  Sum_probs=48.5

Q ss_pred             CCHHHHHHHHHhhCCCCCCCHH-HHHHHHHHHHH----HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcC
Q 010992          402 LTKRSIQELVNQIDPSERLDPD-VEDILVDIAED----FVESITMFGCSLAKHRKSDTLEAKDILVHLERNWN  469 (496)
Q Consensus       402 LtKrKLqELVrqIDPsesLDpD-VEELLLeIADD----FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWN  469 (496)
                      .+.+...++++..-....++.+ ..+.|.++++.    -|+.++..|+..|..++.+.|+.+||.-+|++...
T Consensus       188 p~~~~r~~il~~~~~~~~~~~~~~~~~l~~~~~g~~~~~i~~l~~~a~~~a~~~~~~~I~~~d~~~al~~~~~  260 (285)
T 3h4m_A          188 PDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIRELRDYVTMDDFRKAVEKIME  260 (285)
T ss_dssp             CCHHHHHHHHHHHHTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhccCcCCHHHHHHHHHHHHh
Confidence            4666677777766544444333 23445555544    47789999999999999999999999999987643

>1fh1_A NODF, nodulation protein F; ROOT nodulation factor, protein backbone fold, lipid binding protein; NMR {Rhizobium leguminosarum} SCOP: i.11.1.1

Probab=83.94  E-value=0.55  Score=37.03  Aligned_cols=39  Identities=15%  Similarity=0.215  Sum_probs=15.2

Q ss_pred             hhcCCCCcchhhHHHHHhhhcCcccc---CCCcccccccCCc
Q 010992          448 KHRKSDTLEAKDILVHLERNWNMTLP---GFSGDEIKTFRKP  486 (496)
Q Consensus       448 KHRKSdTLEvKDVQLhLERnWNI~IP---GFssDEIr~~rk~  486 (496)
                      ..-|-+.|++-+|...||+.||+.|+   -....++++++..
T Consensus        39 ~dlg~DSl~~vel~~~lE~~fgi~i~~~~~~~~~~~~Tv~~l   80 (92)
T 1fh1_A           39 TSLGIDSLGLADVLWDLEQLYGIKIEMNTADAWSNLNNIGDV   80 (92)
T ss_dssp             -------CTTTTHHHHHHHC-----------------CTTTS
T ss_pred             hhcCCChHHHHHHHHHHHHHhCCccCCccHhHHhhcCCHHHH
Confidence            34567889999999999999999998   4444555555543

>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae}

Probab=83.91  E-value=1.8  Score=38.08  Aligned_cols=50  Identities=18%  Similarity=0.221  Sum_probs=43.6

Q ss_pred             cCCHHHHHHHHHhhC----C---CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 010992          401 ILTKRSIQELVNQID----P---SERLDPDVEDILVDIAEDFVESITMFGCSLAKHR  450 (496)
Q Consensus       401 ILtKrKLqELVrqID----P---sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHR  450 (496)
                      +|.|--+++|||+|.    .   ..++..++..+|.|.+|+|+-...+.+-..|.|.
T Consensus         1 LI~klPF~RLVREI~~~~~~~~~~lRfq~~Al~ALQeAsEayLV~lFEd~nlcaiHA   57 (121)
T 2ly8_A            1 LISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHL   57 (121)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTCCSSCCBCHHHHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCccchHHHHHHHHHHhcCCCCCccccHHHHHHHHHHHHHHHHHHHHHHhHHHHcC
Confidence            467778899999882    2   5689999999999999999999999999999986

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=83.41  E-value=1.2  Score=39.59  Aligned_cols=65  Identities=9%  Similarity=0.088  Sum_probs=44.3

Q ss_pred             CHHHHHHHHHhhCCCCCCCHHH-HHHHHHHHHH----HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          403 TKRSIQELVNQIDPSERLDPDV-EDILVDIAED----FVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       403 tKrKLqELVrqIDPsesLDpDV-EELLLeIADD----FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      +.+...++++..-....+++++ .++|.+..+.    -|++++..|+.+|..++.+.|+.+|+.-.+++.
T Consensus       183 ~~~~r~~il~~~~~~~~l~~~~~~~~la~~~~G~~~~dl~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~  252 (257)
T 1lv7_A          183 DVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRVVSMVEFEKAKDKI  252 (257)
T ss_dssp             CHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhcCCCCccccHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHH
Confidence            4444455665554444555554 3344333333    467899999999999999999999999888874

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=83.08  E-value=3.2  Score=42.63  Aligned_cols=52  Identities=12%  Similarity=0.144  Sum_probs=44.0

Q ss_pred             CCCCCCHHHHHHHHHHHH-------------HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          416 PSERLDPDVEDILVDIAE-------------DFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       416 PsesLDpDVEELLLeIAD-------------DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      ....|++++.+.|++.+.             ..+.+++..|+.+|+.++.+.|+.+||.-.+++.
T Consensus       311 ~~~~ls~eAl~~Li~~~~r~~g~r~~l~~~~R~l~~llr~A~~~A~~~~~~~I~~edv~~A~~~~  375 (604)
T 3k1j_A          311 KIPHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLGGIVRAAGDIAVKKGKKYVEREDVIEAVKMA  375 (604)
T ss_dssp             SSCCBBHHHHHHHHHHHHHTTCSTTEEECCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHT
T ss_pred             CcccCCHHHHHHHHHHHhhhhccccccccCHHHHHHHHHHHHHHHHhcCcccccHHHHHHHHHhh
Confidence            345799999999988763             4678899999999999999999999998888663

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=82.81  E-value=4.5  Score=41.54  Aligned_cols=62  Identities=10%  Similarity=0.071  Sum_probs=53.3

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHH-------------HHHHHHHHHHHhhhhcCCCCcchhhHH
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAED-------------FVESITMFGCSLAKHRKSDTLEAKDIL  461 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADD-------------FVDsVvt~ACrLAKHRKSdTLEvKDVQ  461 (496)
                      ..+++.+.|.++.+.+. ...++++|.|++.+++.+             ....++..|..+|+.++.+.|+..||.
T Consensus       206 ~~~~~~e~l~~~~~~~~-~v~v~d~v~e~i~~l~~~lr~~r~~~~iS~R~~~~llr~A~A~A~l~gr~~Vt~eDv~  280 (500)
T 3nbx_X          206 ALQVTDEEYERWQKEIG-EITLPDHVFELIFMLRQQLDKLPDAPYVSDRRWKKAIRLLQASAFFSGRSAVAPVDLI  280 (500)
T ss_dssp             TTSBCHHHHHHHHHHHT-TCBCCHHHHHHHHHHHHHHHHCSSSCCCCHHHHHHHHHHHHHHHHHTTCSBCCGGGGG
T ss_pred             cceecHHHHHHHHhcCC-cccCchHHHHHHHHHHHHhhcCCCCCccchhHHHHHHHHHHHHHhhcCCccccchHHH
Confidence            56788999999888874 478999999999999853             455688899999999999999999998

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=82.57  E-value=3.8  Score=42.58  Aligned_cols=65  Identities=14%  Similarity=0.125  Sum_probs=50.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHH---------HHHHHHHHHHhhhh----cCCCCcchhhHHHHHhhhcCccccCCCcccc
Q 010992          416 PSERLDPDVEDILVDIAEDF---------VESITMFGCSLAKH----RKSDTLEAKDILVHLERNWNMTLPGFSGDEI  480 (496)
Q Consensus       416 PsesLDpDVEELLLeIADDF---------VDsVvt~ACrLAKH----RKSdTLEvKDVQLhLERnWNI~IPGFssDEI  480 (496)
                      ....+++++.+.+.++++.|         +.+++..+|..++.    .+...|+.+||.-++++..++.+..+..+|+
T Consensus       369 ~~v~~~~~al~~~~~~s~~~i~~~~lp~~~i~lld~a~~~~~~~~~~~~~~~v~~~di~~~~~~~~~ip~~~~~~~~~  446 (758)
T 1r6b_X          369 HDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPVSKRKKTVNVADIESVVARIARIPEKSVSQSDR  446 (758)
T ss_dssp             HTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHHHHHHHHSSSCCCCCSCCHHHHHHHHHHHSCCCCCCSSSSHH
T ss_pred             cCCCCCHHHHHHHHHHhhhhcccccCchHHHHHHHHHHHHHhcccccccCCccCHHHHHHHHHHhcCCCccccchhHH
Confidence            35679999999999999886         44678888888776    3456789999999999887777766665554

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=81.60  E-value=2.8  Score=41.33  Aligned_cols=69  Identities=13%  Similarity=0.173  Sum_probs=55.3

Q ss_pred             CCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHH-H---HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCc
Q 010992          402 LTKRSIQELVNQIDP--SERLDPDVEDILVDIA-E---DFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNM  470 (496)
Q Consensus       402 LtKrKLqELVrqIDP--sesLDpDVEELLLeIA-D---DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI  470 (496)
                      +++..|.++++.+..  +..+++++.++|.+++ +   ....++++.|..+|..++.+.|+.+||.-.++.-+|.
T Consensus       366 ~~~~e~~~iL~~~~~~~~~~~~~~~~~~i~~~a~~g~~r~a~~ll~~a~~~A~~~~~~~v~~~~v~~~~~~~~d~  440 (456)
T 2c9o_A          366 YTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYDA  440 (456)
T ss_dssp             CCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHSCHHHHHHTHHHHHHHHHHTTCSSBCHHHHHHHHHHSCCH
T ss_pred             CCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhcCCCccCHHHHHHHHHHhcCh
Confidence            477788888876532  3569999999999998 4   2566788888899999999999999999888876554

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	496
d1h3ob_	74	a.22.1.3 (B:) TAF(II)-20, (TAF(II)-15, hTAF12), hi	4e-45
d1htaa_	68	a.22.1.2 (A:) Archaeal histone {Archaeon Methanoth	9e-07
d1ku5a_	66	a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococc	2e-06
d2huec1	82	a.22.1.1 (C:20-101) Histone H4 {African clawed fro	2e-06
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	5e-06
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	3e-05

>d1h3ob_ a.22.1.3 (B:) TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  150 bits (380), Expect = 4e-45
 Identities = 40/74 (54%), Positives = 59/74 (79%)

Query: 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAK 458
           + +LTK+ +Q+LV ++DP+E+LD DVE++L+ IA+DF+ES+    C LA+HRKS TLE K
Sbjct: 1   HMVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVK 60

Query: 459 DILVHLERNWNMTL 472
           D+ +HLER WNM +
Sbjct: 61  DVQLHLERQWNMWI 74

>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]} Length = 68

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanothermus fervidus, histone A [TaxId: 2180]

 Score = 44.0 bits (104), Expect = 9e-07
 Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDIL 461
           L    I  ++      ER+  D    L  + E+  E I      LAKH    T++A+DI 
Sbjct: 4   LPIAPIGRIIKNAGA-ERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIE 62

Query: 462 VHLER 466
           +  + 
Sbjct: 63  LARKM 67

>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]} Length = 66

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon (Pyrococcus horikoshii) [TaxId: 53953]

 Score = 43.2 bits (102), Expect = 2e-06
 Identities = 12/58 (20%), Positives = 24/58 (41%), Gaps = 5/58 (8%)

Query: 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDIL 461
            R I++       +ER+      +L +  E++   I       A+H    T++ +DI 
Sbjct: 9   DRLIRK-----AGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIK 61

>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 82

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H4
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

 Score = 43.2 bits (102), Expect = 2e-06
 Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDIL 461
           +TK +I+ L  +    +R+   + +    + + F+E++     +  +H K  T+ A D++
Sbjct: 10  ITKPAIRRLARRGG-VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVV 68

Query: 462 VHLERNWNMTLPGF 475
             L+R    TL GF
Sbjct: 69  YALKRQ-GRTLYGF 81

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

 Score = 44.4 bits (105), Expect = 5e-06
 Identities = 13/59 (22%), Positives = 22/59 (37%)

Query: 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460
           L K +I+ +  Q     RL  D +D + D      E +     S+       TL  + +
Sbjct: 2   LPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHL 60

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 8/69 (11%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 393 ESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS 452
             +++   +  + +++ ++ +    ER   D  D+   +     E +       A     
Sbjct: 71  GVEDYDGELFGRATVRRILKRAGI-ERASSDAVDLYNKLICRATEELGEKAAEYADEDGR 129

Query: 453 DTLEAKDIL 461
            T++ +D+ 
Sbjct: 130 KTVQGEDVE 138

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	496
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	100.0
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	98.9
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	98.76
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	98.52
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	98.2
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	98.19
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	98.16
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	98.08
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	97.97
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	97.84
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	97.71
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	97.62
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	97.31
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	97.05
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	96.82
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	96.67
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	95.72
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	94.92
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	93.13
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	93.02
d1tzya_	106	Histone H2A {Chicken (Gallus gallus), erythrocytes	89.73
d1f66c_	103	Histone H2A {Human (Homo sapiens), variant H2A.Z [	88.38
d1u35c1	106	macro-H2A.1, histone domain {Human (Homo sapiens)	87.17

>d1h3ob_ a.22.1.3 (B:) TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.9e-34  Score=230.46  Aligned_cols=74  Identities=54%  Similarity=0.971  Sum_probs=72.9

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I  472 (496)
                      |+||+|++|++||++||+++.||+||||+|++|||||||+|+++||+||||||+++||+|||+|||||+|||+|
T Consensus         1 ~~il~K~~L~eLv~~idp~~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s~~le~kDvql~LeR~wNm~i   74 (74)
T d1h3ob_           1 HMVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQWNMWI   74 (74)
T ss_dssp             CCSSCHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHHTCCCC
T ss_pred             CccccHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHhhcCccC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999987

>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H4
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=98.90  E-value=1.3e-09  Score=87.10  Aligned_cols=77  Identities=23%  Similarity=0.294  Sum_probs=71.2

Q ss_pred             CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCC
Q 010992          398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFS  476 (496)
Q Consensus       398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFs  476 (496)
                      .-+.|+|..|..|++.. +-..|.+|+.|.|.++.++|++.|+..|+.+|+|-|.+||+..||.+.|+| .+..+-|||
T Consensus         6 ~i~gI~k~~i~Riar~~-Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr-~g~plyGfg   82 (82)
T d2huec1           6 NIQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKR-QGRTLYGFG   82 (82)
T ss_dssp             GCCSSCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT-TCEEEESCC
T ss_pred             hhcCcCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHh-cCCCCCCCC
Confidence            33569999999999986 557899999999999999999999999999999999999999999999997 589999997

>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanothermus fervidus, histone A [TaxId: 2180]

Probab=98.76  E-value=1.5e-08  Score=76.65  Aligned_cols=64  Identities=27%  Similarity=0.345  Sum_probs=61.1

Q ss_pred             CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      |.+..|..|+++.+. .+|..|+.++|.+++++||..|+..|+.+|+|.|..||..+||...|||
T Consensus         4 LP~a~I~ri~k~~~~-~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk~   67 (68)
T d1htaa_           4 LPIAPIGRIIKNAGA-ERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKM   67 (68)
T ss_dssp             SCHHHHHHHHHHTTC-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHCCc-chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHh
Confidence            889999999999654 6899999999999999999999999999999999999999999999998

>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon (Pyrococcus horikoshii) [TaxId: 53953]

Probab=98.52  E-value=1.1e-07  Score=71.86  Aligned_cols=63  Identities=19%  Similarity=0.397  Sum_probs=59.3

Q ss_pred             CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      |.+..|..|+++.+ ..+|..|+.++|.+.+++||+.++..|+.+|+|.|..||..+||...||
T Consensus         3 LP~a~I~rI~k~~~-~~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~~~~RKTI~~~Dv~~Al~   65 (66)
T d1ku5a_           3 LPIAPVDRLIRKAG-AERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   65 (66)
T ss_dssp             SCHHHHHHHHHHTT-CSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             CCHHHHHHHHHhCc-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHh
Confidence            78899999999864 4699999999999999999999999999999999999999999999987

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

Probab=98.20  E-value=2e-06  Score=74.21  Aligned_cols=71  Identities=11%  Similarity=0.248  Sum_probs=65.8

Q ss_pred             CcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          396 EFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       396 e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      +..+.+++|..+.+|++.. ....|..|+.++|.+++++||..++..|+.+|+|.|..||..+||++.|.+.
T Consensus        74 ~~~~~~fp~a~IkRi~k~~-g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~~kRkTI~~~DI~~Av~~~  144 (151)
T d1f1ea_          74 DYDGELFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYS  144 (151)
T ss_dssp             TCCSCCCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             ccccCccCHHHHHHHHHcC-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHc
Confidence            4567899999999999975 4678999999999999999999999999999999999999999999999875

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

Probab=98.19  E-value=1.6e-06  Score=74.72  Aligned_cols=66  Identities=20%  Similarity=0.205  Sum_probs=62.7

Q ss_pred             CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      |.+..|..|++++-+...|+.|+.++|.+++.||++.|...|+.+|+|.|..||..+||+..++-.
T Consensus         2 lP~a~I~rilk~~~~~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a~~~~   67 (151)
T d1f1ea_           2 LPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVL   67 (151)
T ss_dssp             CCHHHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhc
Confidence            678999999999989999999999999999999999999999999999999999999999987654

>d1tzyc_ a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H3
species: Chicken (Gallus gallus), erythrocytes [TaxId: 9031]

Probab=98.16  E-value=2.5e-06  Score=70.15  Aligned_cols=69  Identities=22%  Similarity=0.200  Sum_probs=63.6

Q ss_pred             cCCccCCHHHHHHHHHhh----CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          397 FGNRILTKRSIQELVNQI----DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       397 ~~nrILtKrKLqELVrqI----DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      +.+-+|.|--++.||++|    ..+..+..++.++|.+.+|+|+-++.+.|-.+|.|+|--||..|||+|+..
T Consensus        17 st~lLIpk~pF~RLVRei~~~~~~~~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~Larr   89 (95)
T d1tzyc_          17 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR   89 (95)
T ss_dssp             CCSCCSCHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             CcccccccccHHHHHHHHHHhcCCCCEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHHHHH
Confidence            456789999999999998    456899999999999999999999999999999999999999999999764

>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Nuclear transcription factor Y subunit beta (Nf-Yb3)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.08  E-value=5.5e-06  Score=65.35  Aligned_cols=67  Identities=16%  Similarity=0.324  Sum_probs=63.1

Q ss_pred             cCCHHHHHHHHHhhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          401 ILTKRSIQELVNQIDP-SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       401 ILtKrKLqELVrqIDP-sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      +|.+..+..++++.|+ ...+..|+.++|.+.|+.||..+++.|...|+..+..||..+||.-+|++.
T Consensus         2 ~LP~a~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~rKTI~~~dv~~Al~~~   69 (87)
T d1n1ja_           2 YLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTL   69 (87)
T ss_dssp             CCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHT
T ss_pred             CCcHhHHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHc
Confidence            5889999999998865 578999999999999999999999999999999999999999999999985

>d1n1jb_ a.22.1.3 (B:) Nuclear transcription factor Y subunit gamma (Nf-Yc2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Nuclear transcription factor Y subunit gamma (Nf-Yc2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.97  E-value=8.4e-06  Score=62.73  Aligned_cols=71  Identities=14%  Similarity=0.238  Sum_probs=63.5

Q ss_pred             CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992          402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I  472 (496)
                      |...++..+++.-+....+..|+-.+|.+.++.||..+++.|+..|+..|..+|..+||..+++++..+.|
T Consensus         1 LP~srVkrImK~~~~~~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~~~rkti~~~dl~~av~~~~~~~F   71 (78)
T d1n1jb_           1 LPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDF   71 (78)
T ss_dssp             CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGG
T ss_pred             CCHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHhcCChhHH
Confidence            56778999999755567999999999999999999999999999999999999999999999998755543

>d1jfib_ a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Negative cofactor 2, NC2, beta chain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.84  E-value=3.1e-05  Score=65.73  Aligned_cols=69  Identities=14%  Similarity=0.370  Sum_probs=65.3

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      ...|.+..|..||+...++..|..|+.++|.+.+..||..|+..|...|+..+..||..+||.-.|++.
T Consensus         2 dl~LP~a~I~kI~K~~~~~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~Al~~~   70 (135)
T d1jfib_           2 DLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESL   70 (135)
T ss_dssp             CCCCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHhhCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHc
Confidence            356899999999999988999999999999999999999999999999999999999999999999973

>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)42
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=97.71  E-value=6.2e-05  Score=58.91  Aligned_cols=63  Identities=19%  Similarity=0.318  Sum_probs=57.0

Q ss_pred             HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc
Q 010992          405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNW  468 (496)
Q Consensus       405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW  468 (496)
                      +.|..|+++. +-...|+.|.-.|||++-.|+-+|+..|.-+|+|.|..+|++.||+|.+.-..
T Consensus         5 ~~i~~iL~~~-GV~~yeprV~~qlLef~yRYtt~VL~DA~vys~HA~k~~id~dDVkLAi~~r~   67 (68)
T d1tafa_           5 QVIMSILKEL-NVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEVTL   67 (68)
T ss_dssp             HHHHHHHHHT-TCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTC
T ss_pred             HHHHHHHHHc-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhcc
Confidence            4577888887 56789999999999999999999999999999999999999999999987543

>d1jfia_ a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Negative cofactor 2, NC2, alpha chain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.62  E-value=3.7e-05  Score=57.81  Aligned_cols=64  Identities=17%  Similarity=0.317  Sum_probs=54.4

Q ss_pred             CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      |...++..+++.-+....+..|+-.+|...++.||..+++.|+..|+..|..+|..+||..++|
T Consensus         3 fP~srVkkimk~~~~~~~is~~A~~~~~~a~E~Fi~~l~~~A~~~a~~~krktI~~~dl~~ai~   66 (66)
T d1jfia_           3 FPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIE   66 (66)
T ss_dssp             CCHHHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC
T ss_pred             CChHHHHHHHhcCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHhC
Confidence            4567888999976566799999999999999999999999999999999999999999987654

>d2bykb1 a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Chrac-14
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=97.31  E-value=0.00024  Score=56.01  Aligned_cols=63  Identities=25%  Similarity=0.332  Sum_probs=58.1

Q ss_pred             HHHHHHHHHhhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          404 KRSIQELVNQIDP-SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       404 KrKLqELVrqIDP-sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +.++..|+++.|| +..+..|+.++|.+.|+.||..+++.|-..|+..+..||..+||.-.|+.
T Consensus         2 ~a~i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~Al~~   65 (89)
T d2bykb1           2 NAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTE   65 (89)
T ss_dssp             CSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             ccHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence            3568899998765 57899999999999999999999999999999999999999999999986

>d1tzyb_ a.22.1.1 (B:) Histone H2B {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H2B
species: Chicken (Gallus gallus), erythrocytes [TaxId: 9031]

Probab=97.05  E-value=0.00056  Score=55.76  Aligned_cols=61  Identities=18%  Similarity=0.310  Sum_probs=57.1

Q ss_pred             HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      -|..++++|-|+..|...+.++|-.+.+|..|.|+..|++||++.|..||..+||+-...-
T Consensus         8 Yi~kVLKqVhp~~giS~kam~imnsfvndiferIa~EA~~La~~~kr~TitsreIqtAvrL   68 (92)
T d1tzyb_           8 YVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRL   68 (92)
T ss_dssp             HHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             HHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHH
Confidence            3678999999999999999999999999999999999999999999999999999887654

>d1tafb_ a.22.1.3 (B:) TAF(II)62 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)62
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=96.82  E-value=0.0029  Score=49.57  Aligned_cols=66  Identities=18%  Similarity=0.235  Sum_probs=60.6

Q ss_pred             CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE  465 (496)
Q Consensus       399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE  465 (496)
                      +.+++++.+..+...| +-..|.+||.+.|.+=++=-|..|+..|+++.+|-|..+|...||-..|+
T Consensus         4 ~S~~~~esik~iAeS~-Gi~~l~de~a~~LA~DveYRl~eiiQeA~KFMrhskR~~Ltt~Did~ALk   69 (70)
T d1tafb_           4 GSSISAESMKVIAESI-GVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             SCCCCHHHHHHHHHHT-TCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             cccCCHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcCcHHHHHHHHc
Confidence            5678999999999988 55679999999999999999999999999999999999999999988874

>d1q9ca_ a.22.1.3 (A:) Histone domain of Son of sevenless protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Histone domain of Son of sevenless protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.67  E-value=0.0022  Score=57.00  Aligned_cols=66  Identities=17%  Similarity=0.232  Sum_probs=61.4

Q ss_pred             ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      -++.-.+++.|+|+. ...++++++-..|..+.|.+..+|++.|+.+|||.|..+|..+||++.+..
T Consensus        98 L~fPV~rv~rlLk~~-~a~RVs~~A~vyLaavLEyl~aeILelAgn~a~~~krkrItp~dI~lAi~n  163 (172)
T d1q9ca_          98 LSLPVEKIHPLLKEV-LGYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIKVAMCA  163 (172)
T ss_dssp             -CCCHHHHHHHHHHH-HSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSBCCHHHHHHHHHT
T ss_pred             ceecHHHHHHHHHhc-cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCceecHHHHHHHHhC
Confidence            467888999999998 678999999999999999999999999999999999999999999999875

>d2byka1 a.22.1.3 (A:29-100) Chrac-16 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Chrac-16
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.72  E-value=0.012  Score=44.81  Aligned_cols=55  Identities=15%  Similarity=0.206  Sum_probs=49.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHhh-hhcCCCCcchhhHHHHHhhhcCccc
Q 010992          418 ERLDPDVEDILVDIAEDFVESITMFGCSLA-KHRKSDTLEAKDILVHLERNWNMTL  472 (496)
Q Consensus       418 esLDpDVEELLLeIADDFVDsVvt~ACrLA-KHRKSdTLEvKDVQLhLERnWNI~I  472 (496)
                      ..+..|+--++-.-+|-||++++..|+..| ++|+..+|..+||.-+++++..+.|
T Consensus         8 ~~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~~ktl~~~dl~~aV~~~~~f~F   63 (72)
T d2byka1           8 GLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEF   63 (72)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCSTTGG
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccHHHHHHHHccCchhhH
Confidence            368889999999999999999999999888 6778899999999999999987765

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=94.92  E-value=0.049  Score=44.72  Aligned_cols=65  Identities=14%  Similarity=0.166  Sum_probs=49.4

Q ss_pred             CHHHHHHHH----HhhCCCCCCCHHHHHHHHHHHH------------HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          403 TKRSIQELV----NQIDPSERLDPDVEDILVDIAE------------DFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       403 tKrKLqELV----rqIDPsesLDpDVEELLLeIAD------------DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      +...+.+++    +.+.....+++++.++|.+++.            .-+.+++..|..+|+.++..+|+.+||+..+|+
T Consensus       193 ~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~~~~~~~~~~~~G~~R~a~~ll~~a~~~A~~~~~~~I~~edv~~A~~~  272 (276)
T d1fnna2         193 TKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKE  272 (276)
T ss_dssp             BHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhhhhhhhhhcCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHH
Confidence            455554443    3334567799999998877752            135678889999999999999999999999987


Q ss_pred             h
Q 010992          467 N  467 (496)
Q Consensus       467 n  467 (496)
                      -
T Consensus       273 ~  273 (276)
T d1fnna2         273 V  273 (276)
T ss_dssp             H
T ss_pred             H
Confidence            5

>d1bh9b_ a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)28
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.13  E-value=0.18  Score=40.38  Aligned_cols=64  Identities=17%  Similarity=0.260  Sum_probs=53.9

Q ss_pred             CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC-CcchhhHHHHHhh
Q 010992          402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD-TLEAKDILVHLER  466 (496)
Q Consensus       402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd-TLEvKDVQLhLER  466 (496)
                      |.|..|..|++.|- +..+.+.|.-+|..||.-||-+||+.|..+...++.. -|-.+.|.-.+.|
T Consensus        17 ~~K~~vkrl~~~~~-g~sv~~~v~i~v~giaKvFvGEiVE~A~~V~~~~~e~~PL~P~HireA~rr   81 (89)
T d1bh9b_          17 FPKAAIKRLIQSIT-GTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRR   81 (89)
T ss_dssp             CCHHHHHHHHHHHH-SSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHc-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHH
Confidence            89999999999995 5789999999999999999999999999998877643 5555666555554

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=93.02  E-value=0.19  Score=41.28  Aligned_cols=67  Identities=13%  Similarity=0.208  Sum_probs=52.2

Q ss_pred             cCCHHHHHHHHHhh----CCCCCCCHHHHHHHHHHHHH---------HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992          401 ILTKRSIQELVNQI----DPSERLDPDVEDILVDIAED---------FVESITMFGCSLAKHRKSDTLEAKDILVHLERN  467 (496)
Q Consensus       401 ILtKrKLqELVrqI----DPsesLDpDVEELLLeIADD---------FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn  467 (496)
                      -.++..|.+++++.    .....+|+++.+++.+++..         -+.+++..|..+|...+.+.|+.+||+-+++.+
T Consensus       208 ~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~~~It~~~V~~A~~e~  287 (287)
T d1w5sa2         208 AYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSEN  287 (287)
T ss_dssp             CCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC
T ss_pred             CCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcC
Confidence            34677777777643    34567999999999887732         345788899999999999999999999888753

>d1tzya_ a.22.1.1 (A:) Histone H2A {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H2A
species: Chicken (Gallus gallus), erythrocytes [TaxId: 9031]

Probab=89.73  E-value=0.45  Score=39.04  Aligned_cols=66  Identities=12%  Similarity=0.202  Sum_probs=60.6

Q ss_pred             cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      .+.-.+++.|+++-.-..+++..+--.|..+-|-...+|++.|...||..|...|..+||++.+..
T Consensus        12 ~FpV~rv~r~Lk~~~~~~rv~~~apVylaAVLEYLtaEiLELAgn~a~~~k~~rItPrhi~lAirn   77 (106)
T d1tzya_          12 QFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN   77 (106)
T ss_dssp             SSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             cCChHHHHHHHHcCccccccCCCchHHHHHHHHHHHHHHHHHhhHHHHhcCCceecchhhhhcccC
Confidence            466778999999987788999999999999999999999999999999999999999999988754

>d1f66c_ a.22.1.1 (C:) Histone H2A {Human (Homo sapiens), variant H2A.Z [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H2A
species: Human (Homo sapiens), variant H2A.Z [TaxId: 9606]

Probab=88.38  E-value=0.72  Score=37.34  Aligned_cols=66  Identities=11%  Similarity=0.136  Sum_probs=58.2

Q ss_pred             cCCHHHHHHHHHhhCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          401 ILTKRSIQELVNQIDPSE-RLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       401 ILtKrKLqELVrqIDPse-sLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      .+.-.+++.++++..-.. +++..+--.|.-+-|-++.+|++.|+..|+..|...|..+||++.+..
T Consensus        11 ~FpVgrv~r~L~~~~~~~~rv~~~A~VyLaAvLEYL~aEILelagn~a~~~~~~rItpr~l~lai~n   77 (103)
T d1f66c_          11 QFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG   77 (103)
T ss_dssp             SSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH
T ss_pred             ccChHHHHHHHhccCccceecCCCceeeHHHHHHHHHHHHHHHhhhhhccCCCCeeechhhhccccC
Confidence            466778999999876554 599999999999999999999999999999999999999999887754

>d1u35c1 a.22.1.1 (C:814-919) macro-H2A.1, histone domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: macro-H2A.1, histone domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.17  E-value=0.74  Score=37.63  Aligned_cols=67  Identities=13%  Similarity=0.232  Sum_probs=60.3

Q ss_pred             ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992          400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER  466 (496)
Q Consensus       400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER  466 (496)
                      -.+.-.+++.|+++-.-..+++..+--.|..+-|-.+.+|++.|...|+..|...|..+||++.+..
T Consensus        10 L~FpV~ri~r~Lk~~~~~~rv~~~apVylaAVLEYL~aEILELAgn~a~~~k~~rItprhi~lairn   76 (106)
T d1u35c1          10 VIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVAN   76 (106)
T ss_dssp             CSSCHHHHHHHHHHHSTTSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             cccCHHHHHHHHhCCCCccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCeeecchhhhcccC
Confidence            3566778999999876778999999999999999999999999999999999999999999988754