Psyllid ID: psy6534

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------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-------31
MNINKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLNGSDLSTMIGPGRGDASFDGFGMSKYQNRRTMNSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPIHELPQL
cccccccccccccccEEEEcccccEEcccccEEEccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHHccHHHHHHHHHHHHHHHccccccccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHcccccccccccccccccccc
ccccEEEccccccccEEEccccccEEcHHccEEEcccEccccccEEEccccccccccccccccccccccccccEEEEcccccccccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHcccccccccccccHHccccc
mninkvccyehpdapliedyragdqicsecglvvgDRVIDVGsewrtfsneksgvdpsrvggpenpllngsdlstmigpgrgdasfdgfgmskyqnrrtmnSSDRALLNAIREINSMADRINLTKTIVDRANNLfkqvhdgknlkgrsnDAIASACLYIACrqegvprtfKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMsrfcsnlslpNMVQKAATHIARKAVEldivpgrspiSVAAAAIYMASQassdkrsqkeigdiAGVAEVTIRQSYklmyphasklfpqdfvfhtpihelpql
mninkvccyehpDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRtfsneksgvdpsrvggPENPLLNGSDLSTMIGPGRGDASFDGFGMSKYQNRRTMNSSDRALLNAIREINSMADRINLTKTIVDRANNLfkqvhdgknlkgrsNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASqassdkrsqkeigDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPIHELPQL
MNINKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLNGSDLSTMIGPGRGDASFDGFGMSKYQNRRTMNSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPIsvaaaaiymasqassDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPIHELPQL
***NKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTF**********************************************************LLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYM*************IGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPI******
***NKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWR*******************PLLN*SDL**********************************LNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPIHELPQL
MNINKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLNGSDLSTMIGPGRGDASFDGFGMSKYQNRRTMNSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMA***********EIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPIHELPQL
**INKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSN***********GPENPLLNGSDLSTMIGPGRGDASFDGFGMSKYQNRRTMNSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPIHEL***
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MNINKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLNGSDLSTMIGPGRGDASFDGFGMSKYQNRRTMNSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPIHELPQL
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query309 2.2.26 [Sep-21-2011]
P29052315 Transcription initiation yes N/A 1.0 0.980 0.864 1e-160
P29054316 Transcription initiation N/A N/A 0.987 0.965 0.8 1e-145
P62916316 Transcription initiation yes N/A 0.987 0.965 0.803 1e-144
P62915316 Transcription initiation yes N/A 0.987 0.965 0.803 1e-144
Q5R886316 Transcription initiation yes N/A 0.987 0.965 0.803 1e-144
Q4R3J5316 Transcription initiation N/A N/A 0.987 0.965 0.803 1e-144
Q00403316 Transcription initiation yes N/A 0.987 0.965 0.803 1e-144
Q2KIN8316 Transcription initiation yes N/A 0.987 0.965 0.8 1e-144
Q9NHP7293 Transcription initiation N/A N/A 0.919 0.969 0.784 1e-139
O16991306 Transcription initiation yes N/A 0.970 0.980 0.622 1e-110
>sp|P29052|TF2B_DROME Transcription initiation factor IIB OS=Drosophila melanogaster GN=TfIIB PE=2 SV=1 Back     alignment and function desciption
 Score =  564 bits (1453), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 267/309 (86%), Positives = 288/309 (93%)

Query: 1   MNINKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRV 60
           ++ NKVCCY HP++PLIEDYRAGD ICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRV
Sbjct: 7   LDNNKVCCYAHPESPLIEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRV 66

Query: 61  GGPENPLLNGSDLSTMIGPGRGDASFDGFGMSKYQNRRTMNSSDRALLNAIREINSMADR 120
           GGPENPLL+G DLST+IGPG G ASFD FG  KYQNRRTM+SSDR+L++A +EI+SMADR
Sbjct: 67  GGPENPLLSGGDLSTIIGPGTGSASFDAFGAPKYQNRRTMSSSDRSLISAFKEISSMADR 126

Query: 121 INLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKIS 180
           INL KTIVDRANNLFKQVHDGKNLKGRSNDA ASACLYIACRQEGVPRTFKEICAVSKIS
Sbjct: 127 INLPKTIVDRANNLFKQVHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKIS 186

Query: 181 KKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPG 240
           KKEIGRCFKL LKALETSVDLITT DFM RFC+NL LPNMVQ+AATHIA+KAVE+DIVPG
Sbjct: 187 KKEIGRCFKLTLKALETSVDLITTADFMCRFCANLDLPNMVQRAATHIAKKAVEMDIVPG 246

Query: 241 RSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFH 300
           RSPISVAAAAIYMASQAS  KRSQKEIGDIAGVA+VTIRQSYKLMYPHA+KLFP+DF F 
Sbjct: 247 RSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSYKLMYPHAAKLFPEDFKFT 306

Query: 301 TPIHELPQL 309
           TPI +LPQ+
Sbjct: 307 TPIDQLPQM 315
General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.
Drosophila melanogaster (taxid: 7227)
>sp|P29054|TF2B_XENLA Transcription initiation factor IIB OS=Xenopus laevis GN=gtf2b PE=2 SV=1 Back     alignment and function description
>sp|P62916|TF2B_RAT Transcription initiation factor IIB OS=Rattus norvegicus GN=Gtf2b PE=2 SV=1 Back     alignment and function description
>sp|P62915|TF2B_MOUSE Transcription initiation factor IIB OS=Mus musculus GN=Gtf2b PE=1 SV=1 Back     alignment and function description
>sp|Q5R886|TF2B_PONAB Transcription initiation factor IIB OS=Pongo abelii GN=GTF2B PE=2 SV=1 Back     alignment and function description
>sp|Q4R3J5|TF2B_MACFA Transcription initiation factor IIB OS=Macaca fascicularis GN=GTF2B PE=2 SV=1 Back     alignment and function description
>sp|Q00403|TF2B_HUMAN Transcription initiation factor IIB OS=Homo sapiens GN=GTF2B PE=1 SV=1 Back     alignment and function description
>sp|Q2KIN8|TF2B_BOVIN Transcription initiation factor IIB OS=Bos taurus GN=GTF2B PE=2 SV=1 Back     alignment and function description
>sp|Q9NHP7|TF2B_DROVI Transcription initiation factor IIB OS=Drosophila virilis GN=TfIIB PE=3 SV=1 Back     alignment and function description
>sp|O16991|TF2B_CAEEL Transcription initiation factor IIB OS=Caenorhabditis elegans GN=ttb-1 PE=3 SV=2 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query309
242013902313 transcription initiation factor iib, put 0.990 0.977 0.921 1e-167
383862315315 PREDICTED: transcription initiation fact 0.990 0.971 0.921 1e-167
48102797315 PREDICTED: transcription initiation fact 0.990 0.971 0.921 1e-166
307179392315 Transcription initiation factor IIB [Cam 0.996 0.977 0.905 1e-166
270006604315 hypothetical protein TcasGA2_TC010900 [T 0.996 0.977 0.905 1e-166
307197188373 Transcription initiation factor IIB [Har 0.990 0.820 0.918 1e-166
350417950315 PREDICTED: transcription initiation fact 0.990 0.971 0.918 1e-165
322794062321 hypothetical protein SINV_13223 [Solenop 0.990 0.953 0.918 1e-165
332376975315 unknown [Dendroctonus ponderosae] 0.990 0.971 0.901 1e-164
156546454315 PREDICTED: transcription initiation fact 0.996 0.977 0.886 1e-163
>gi|242013902|ref|XP_002427639.1| transcription initiation factor iib, putative [Pediculus humanus corporis] gi|212512060|gb|EEB14901.1| transcription initiation factor iib, putative [Pediculus humanus corporis] Back     alignment and taxonomy information
 Score =  592 bits (1527), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 282/306 (92%), Positives = 293/306 (95%)

Query: 4   NKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGP 63
           NKVCCY HPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEK+G DPSRVGGP
Sbjct: 8   NKVCCYAHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKAGTDPSRVGGP 67

Query: 64  ENPLLNGSDLSTMIGPGRGDASFDGFGMSKYQNRRTMNSSDRALLNAIREINSMADRINL 123
           ENPLLNGSDL TMIGPGRGDASFDG G+SKYQNRRTM+SSDRAL+NA REIN+MADRINL
Sbjct: 68  ENPLLNGSDLCTMIGPGRGDASFDGLGVSKYQNRRTMSSSDRALINAFREINAMADRINL 127

Query: 124 TKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKE 183
            KTIVDRANNLFKQVHDGKNLKGR+NDAIASA LYIACRQEGVPRTFKEICAVSKISKKE
Sbjct: 128 PKTIVDRANNLFKQVHDGKNLKGRANDAIASAALYIACRQEGVPRTFKEICAVSKISKKE 187

Query: 184 IGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSP 243
           IGRCFKLILKALETSVDLITTGDFMSRFCSNL LPNMVQ+AATHIARKAVELDIVPGRSP
Sbjct: 188 IGRCFKLILKALETSVDLITTGDFMSRFCSNLGLPNMVQRAATHIARKAVELDIVPGRSP 247

Query: 244 ISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPI 303
           ISVAAAAIYMASQAS DKR QKEIGDIAGVA+VTIRQSYKLMYPHA+KLFP+DF F TPI
Sbjct: 248 ISVAAAAIYMASQASDDKRVQKEIGDIAGVADVTIRQSYKLMYPHATKLFPEDFQFSTPI 307

Query: 304 HELPQL 309
            ELPQ+
Sbjct: 308 EELPQM 313

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|383862315|ref|XP_003706629.1| PREDICTED: transcription initiation factor IIB-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|48102797|ref|XP_395432.1| PREDICTED: transcription initiation factor IIB isoform 1 [Apis mellifera] gi|380019249|ref|XP_003693523.1| PREDICTED: transcription initiation factor IIB-like [Apis florea] Back     alignment and taxonomy information
>gi|307179392|gb|EFN67722.1| Transcription initiation factor IIB [Camponotus floridanus] Back     alignment and taxonomy information
>gi|270006604|gb|EFA03052.1| hypothetical protein TcasGA2_TC010900 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|307197188|gb|EFN78510.1| Transcription initiation factor IIB [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|350417950|ref|XP_003491660.1| PREDICTED: transcription initiation factor IIB-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|322794062|gb|EFZ17278.1| hypothetical protein SINV_13223 [Solenopsis invicta] Back     alignment and taxonomy information
>gi|332376975|gb|AEE63627.1| unknown [Dendroctonus ponderosae] Back     alignment and taxonomy information
>gi|156546454|ref|XP_001607291.1| PREDICTED: transcription initiation factor IIB-like [Nasonia vitripennis] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query309
FB|FBgn0004915315 TfIIB "Transcription factor II 0.990 0.971 0.826 4.1e-136
UNIPROTKB|F1NXP2306 GTF2B "Uncharacterized protein 0.987 0.996 0.760 1.9e-122
MGI|MGI:2385191316 Gtf2b "general transcription f 0.987 0.965 0.757 6.5e-122
RGD|619735316 Gtf2b "general transcription f 0.987 0.965 0.757 6.5e-122
UNIPROTKB|F2Z4J6316 LOC786656 "Uncharacterized pro 0.987 0.965 0.757 8.3e-122
UNIPROTKB|E2RPG1316 GTF2B "Uncharacterized protein 0.987 0.965 0.757 8.3e-122
UNIPROTKB|Q00403316 GTF2B "Transcription initiatio 0.987 0.965 0.757 8.3e-122
UNIPROTKB|Q2KIN8316 GTF2B "Transcription initiatio 0.987 0.965 0.757 1.1e-121
ZFIN|ZDB-GENE-030131-3544316 gtf2b "general transcription f 0.996 0.974 0.75 1.3e-121
UNIPROTKB|F2Z5J6316 GTF2B "Uncharacterized protein 0.987 0.965 0.744 2.3e-119
FB|FBgn0004915 TfIIB "Transcription factor IIB" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 1333 (474.3 bits), Expect = 4.1e-136, P = 4.1e-136
 Identities = 253/306 (82%), Positives = 272/306 (88%)

Query:     4 NKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGP 63
             NKVCCY HP++PLIEDYRAGD ICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGP
Sbjct:    10 NKVCCYAHPESPLIEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGP 69

Query:    64 ENPLLNGSDLSTMIGPGRGDASFDGFGMSKYQNRRTMNSSDRALLNAIREINSMADRINL 123
             ENPLL+G DLST+IGPG G ASFD FG  KYQNRRTM+SSDR+L++A +EI+SMADRINL
Sbjct:    70 ENPLLSGGDLSTIIGPGTGSASFDAFGAPKYQNRRTMSSSDRSLISAFKEISSMADRINL 129

Query:   124 TKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKE 183
              KTIVDRANNLFKQVHDGKNLKGRSNDA ASACLYIACRQEGVPRTFKEICAVSKISKKE
Sbjct:   130 PKTIVDRANNLFKQVHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKISKKE 189

Query:   184 IGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSP 243
             IGRCFKL LKALETSVDLITT DFM RFC+NL LPNMVQ+AATHIA+KAVE+DIVPGRSP
Sbjct:   190 IGRCFKLTLKALETSVDLITTADFMCRFCANLDLPNMVQRAATHIAKKAVEMDIVPGRSP 249

Query:   244 IXXXXXXXXXXXXXXXDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPI 303
             I                KRSQKEIGDIAGVA+VTIRQSYKLMYPHA+KLFP+DF F TPI
Sbjct:   250 ISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSYKLMYPHAAKLFPEDFKFTTPI 309

Query:   304 HELPQL 309
              +LPQ+
Sbjct:   310 DQLPQM 315
GO:0005634 "nucleus" evidence=NAS;IDA
GO:0001174 "transcriptional start site selection at RNA polymerase II promoter" evidence=IDA
GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=NAS;IDA
GO:0008134 "transcription factor binding" evidence=IPI
GO:0051101 "regulation of DNA binding" evidence=IDA
GO:0005667 "transcription factor complex" evidence=ISS
GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISS
GO:0008270 "zinc ion binding" evidence=IEA
GO:0017025 "TBP-class protein binding" evidence=IEA
UNIPROTKB|F1NXP2 GTF2B "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
MGI|MGI:2385191 Gtf2b "general transcription factor IIB" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|619735 Gtf2b "general transcription factor IIB" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F2Z4J6 LOC786656 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RPG1 GTF2B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q00403 GTF2B "Transcription initiation factor IIB" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q2KIN8 GTF2B "Transcription initiation factor IIB" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-3544 gtf2b "general transcription factor IIB" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|F2Z5J6 GTF2B "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q8W0W3TF2B_ORYSJNo assigned EC number0.47880.94820.9391yesN/A
Q8TT29TF2B_METACNo assigned EC number0.37580.90290.8278yesN/A
A8MCX6TF2B_CALMQNo assigned EC number0.34190.86400.7946yesN/A
Q05959TF2B_KLULANo assigned EC number0.37060.95140.8235yesN/A
O59151TF2B_PYRHONo assigned EC number0.33330.90290.93yesN/A
P58111TF2B1_SULSONo assigned EC number0.36200.90290.9029yesN/A
A0B5T8TF2B_METTPNo assigned EC number0.38960.88990.8160yesN/A
A9A8Q0TF2B_METM6No assigned EC number0.37450.88020.8023yesN/A
P62915TF2B_MOUSENo assigned EC number0.80320.98700.9651yesN/A
P62916TF2B_RATNo assigned EC number0.80320.98700.9651yesN/A
Q4R3J5TF2B_MACFANo assigned EC number0.80320.98700.9651N/AN/A
P61998TF2B_PYRFUNo assigned EC number0.34020.90290.93yesN/A
O28970TF2B_ARCFUNo assigned EC number0.38810.88990.8435yesN/A
P0CW15TF2B_METMANo assigned EC number0.37580.90290.8278yesN/A
A6VI28TF2B_METM7No assigned EC number0.37450.88020.8023yesN/A
P0CW14TF2B_METMZNo assigned EC number0.37580.90290.8278yesN/A
Q9UWN6TF2B_SULACNo assigned EC number0.35460.87700.8827yesN/A
Q2KIN8TF2B_BOVINNo assigned EC number0.80.98700.9651yesN/A
Q54FD6TF2B_DICDINo assigned EC number0.50490.95790.9107yesN/A
A3CSQ6TF2B_METMJNo assigned EC number0.38110.88990.8160yesN/A
Q5R886TF2B_PONABNo assigned EC number0.80320.98700.9651yesN/A
P29052TF2B_DROMENo assigned EC number0.86401.00.9809yesN/A
P29054TF2B_XENLANo assigned EC number0.80.98700.9651N/AN/A
P29055TF2B_YEASTNo assigned EC number0.35690.95140.8521yesN/A
Q6M176TF2B_METMPNo assigned EC number0.37450.88020.8023yesN/A
A7IAR4TF2B_METB6No assigned EC number0.38010.90930.8413yesN/A
B8GJQ9TF2B_METPENo assigned EC number0.38460.88990.8233yesN/A
Q2NEL6TF2B_METSTNo assigned EC number0.34570.90610.9003yesN/A
Q9HJM7TF2B1_THEACNo assigned EC number0.34370.88340.875yesN/A
A5UKA1TF2B_METS3No assigned EC number0.34580.89640.8935yesN/A
Q9NHP7TF2B_DROVINo assigned EC number0.78430.91900.9692N/AN/A
O16991TF2B_CAEELNo assigned EC number0.62250.97080.9803yesN/A
Q5JGN1TF2B1_PYRKONo assigned EC number0.35740.85430.88yesN/A
Q8SRP3TF2B_ENCCUNo assigned EC number0.42660.92880.9198yesN/A
O13749TF2B_SCHPONo assigned EC number0.44060.94170.8558yesN/A
P48512TF2B1_ARATHNo assigned EC number0.48670.93850.9294yesN/A
P48513TF2B_SOYBNNo assigned EC number0.48330.92880.9169yesN/A
Q9HRE6TF2B2_HALSANo assigned EC number0.34160.86730.8246yesN/A
Q979Q3TF2B1_THEVONo assigned EC number0.34370.88340.875yesN/A
A6UW60TF2B_META3No assigned EC number0.36740.88020.8143yesN/A
Q00403TF2B_HUMANNo assigned EC number0.80320.98700.9651yesN/A
A4G0F2TF2B_METM5No assigned EC number0.37100.88020.8023yesN/A
Q9V0V5TF2B_PYRABNo assigned EC number0.33210.86400.89yesN/A
O26971TF2B_METTHNo assigned EC number0.34650.84780.8451yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query309
COG1405285 COG1405, SUA7, Transcription initiation factor TFI 1e-89
PRK00423310 PRK00423, tfb, transcription initiation factor IIB 1e-81
pfam0038271 pfam00382, TFIIB, Transcription factor TFIIB repea 2e-27
pfam0038271 pfam00382, TFIIB, Transcription factor TFIIB repea 3e-25
cd0004388 cd00043, CYCLIN, Cyclin box fold 7e-15
cd0004388 cd00043, CYCLIN, Cyclin box fold 2e-13
smart0038583 smart00385, CYCLIN, domain present in cyclins, TFI 5e-13
COG1405285 COG1405, SUA7, Transcription initiation factor TFI 3e-11
smart0038583 smart00385, CYCLIN, domain present in cyclins, TFI 2e-10
pfam0827140 pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding 3e-09
PRK00423310 PRK00423, tfb, transcription initiation factor IIB 4e-09
COG1405285 COG1405, SUA7, Transcription initiation factor TFI 8e-08
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information 
 Score =  268 bits (687), Expect = 1e-89
 Identities = 104/269 (38%), Positives = 163/269 (60%), Gaps = 8/269 (2%)

Query: 16  LIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLNGSDLST 75
           +I DY  G+ +C++CGLV+ D +ID G EWR F          RVG P  P ++   LST
Sbjct: 12  IITDYERGEIVCADCGLVLEDSLIDPGPEWRAFDER----HERRVGAPLTPSIHDKGLST 67

Query: 76  MIGPGRGDASFDGFGMSKYQNR-RTMNSSDRALLNAIREINSMADRINLTKTIVDRANNL 134
           +IG G  D  +    + K+Q R R  ++ +R L+ A+ E+  +A  + L +++ + A  +
Sbjct: 68  IIGWGDKDKMYR---LRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARI 124

Query: 135 FKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKA 194
           +++  D   L+GRS +++A+AC+Y ACR  GVPRT  EI     +SKKEIGR ++L+++ 
Sbjct: 125 YRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVSKKEIGRTYRLLVRE 184

Query: 195 LETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMA 254
           L+  +  +   D++ RF S L L + V++ A  I +KA    +  G+SP  +AAAAIY+A
Sbjct: 185 LKLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLA 244

Query: 255 SQASSDKRSQKEIGDIAGVAEVTIRQSYK 283
           S    ++R+QKE+  +AGV EVTIR  YK
Sbjct: 245 SLLLGERRTQKEVAKVAGVTEVTIRNRYK 273

Length = 285
>gnl|CDD|234758 PRK00423, tfb, transcription initiation factor IIB; Reviewed Back     alignment and domain information
>gnl|CDD|109440 pfam00382, TFIIB, Transcription factor TFIIB repeat Back     alignment and domain information
>gnl|CDD|109440 pfam00382, TFIIB, Transcription factor TFIIB repeat Back     alignment and domain information
>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold Back     alignment and domain information
>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold Back     alignment and domain information
>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>gnl|CDD|203895 pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding Back     alignment and domain information
>gnl|CDD|234758 PRK00423, tfb, transcription initiation factor IIB; Reviewed Back     alignment and domain information
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 309
KOG1597|consensus308 100.0
PRK00423310 tfb transcription initiation factor IIB; Reviewed 100.0
COG1405285 SUA7 Transcription initiation factor TFIIIB, Brf1 100.0
KOG1598|consensus 521 100.0
PF0038271 TFIIB: Transcription factor TFIIB repeat; InterPro 99.75
PF0038271 TFIIB: Transcription factor TFIIB repeat; InterPro 99.73
KOG0835|consensus 367 99.69
TIGR00569305 ccl1 cyclin ccl1. University). 99.69
KOG0834|consensus323 99.65
PF0827143 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013 99.62
COG5333297 CCL1 Cdk activating kinase (CAK)/RNA polymerase II 99.52
KOG0794|consensus264 99.46
PRK00423310 tfb transcription initiation factor IIB; Reviewed 99.44
COG1405285 SUA7 Transcription initiation factor TFIIIB, Brf1 99.36
cd0004388 CYCLIN Cyclin box fold. Protein binding domain fun 99.14
cd0004388 CYCLIN Cyclin box fold. Protein binding domain fun 99.12
smart0038583 CYCLIN domain present in cyclins, TFIIB and Retino 99.11
KOG0656|consensus335 99.06
smart0038583 CYCLIN domain present in cyclins, TFIIB and Retino 99.02
KOG1597|consensus308 98.91
KOG4557|consensus262 98.81
COG5024440 Cyclin [Cell division and chromosome partitioning] 98.54
KOG0653|consensus391 98.49
KOG2496|consensus325 98.48
PF00134127 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR 98.45
KOG1598|consensus 521 98.3
PF02984118 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR 98.07
PF01857135 RB_B: Retinoblastoma-associated protein B domain; 97.79
KOG0655|consensus408 97.64
PF1178136 RRN7: RNA polymerase I-specific transcription init 97.35
PRK0041559 rps27e 30S ribosomal protein S27e; Reviewed 96.83
PHA0062659 hypothetical protein 96.82
COG205167 RPS27A Ribosomal protein S27E [Translation, riboso 96.64
KOG0835|consensus367 96.62
PF0166755 Ribosomal_S27e: Ribosomal protein S27; InterPro: I 96.57
PF01857135 RB_B: Retinoblastoma-associated protein B domain; 96.49
TIGR00569 305 ccl1 cyclin ccl1. University). 96.48
PF00134127 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR 96.32
PLN0020986 ribosomal protein S27; Provisional 96.28
PTZ0008385 40S ribosomal protein S27; Provisional 96.18
PF02984118 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR 95.9
KOG0834|consensus 323 95.86
PRK00420112 hypothetical protein; Validated 95.63
PF0827430 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01 95.52
PRK0043250 30S ribosomal protein S27ae; Validated 95.42
TIGR0209838 MJ0042_CXXC MJ0042 family finger-like domain. This 95.35
PF1324023 zinc_ribbon_2: zinc-ribbon domain 95.14
smart0077837 Prim_Zn_Ribbon Zinc-binding domain of primase-heli 95.11
PF0879233 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I 95.09
COG1645131 Uncharacterized Zn-finger containing protein [Gene 94.99
KOG4164|consensus497 94.96
PF1324826 zf-ribbon_3: zinc-ribbon domain 94.96
COG199789 RPL43A Ribosomal protein L37AE/L43A [Translation, 94.9
PRK1182760 hypothetical protein; Provisional 94.83
PF1480334 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C. 94.76
PF0396668 Trm112p: Trm112p-like protein; InterPro: IPR005651 94.75
COG5333 297 CCL1 Cdk activating kinase (CAK)/RNA polymerase II 94.71
COG199851 RPS31 Ribosomal protein S27AE [Translation, riboso 94.7
PF08613149 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu 94.61
PF1435461 Lar_restr_allev: Restriction alleviation protein L 94.56
TIGR0120654 lysW lysine biosynthesis protein LysW. This very s 94.43
PF0215035 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I 94.42
PRK10220111 hypothetical protein; Provisional 94.1
PF0827340 Prim_Zn_Ribbon: Zinc-binding domain of primase-hel 93.87
PF08613149 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu 93.83
COG283560 Uncharacterized conserved protein [Function unknow 93.82
PF1276046 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int 93.81
COG4888104 Uncharacterized Zn ribbon-containing protein [Gene 93.75
smart0066152 RPOL9 RNA polymerase subunit 9. 93.69
KOG2496|consensus 325 93.51
TIGR00686109 phnA alkylphosphonate utilization operon protein P 93.3
PRK00464154 nrdR transcriptional regulator NrdR; Validated 93.28
PF1340442 HTH_AsnC-type: AsnC-type helix-turn-helix domain; 93.21
PRK0039846 rpoP DNA-directed RNA polymerase subunit P; Provis 93.16
PF09538108 FYDLN_acid: Protein of unknown function (FYDLN_aci 93.07
PF05460 353 ORC6: Origin recognition complex subunit 6 (ORC6); 92.99
PF0032532 Crp: Bacterial regulatory proteins, crp family; In 92.94
PF0667741 Auto_anti-p27: Sjogren's syndrome/scleroderma auto 92.93
PF1057126 UPF0547: Uncharacterised protein family UPF0547; I 92.89
COG2824112 PhnA Uncharacterized Zn-ribbon-containing protein 92.72
COG347868 Predicted nucleic-acid-binding protein containing 92.62
TIGR0365553 anti_R_Lar restriction alleviation protein, Lar fa 92.58
PF0827955 HTH_11: HTH domain; InterPro: IPR013196 Winged hel 92.51
PF0178090 Ribosomal_L37ae: Ribosomal L37ae protein family; I 92.49
KOG4557|consensus262 92.47
KOG1010|consensus920 92.41
PTZ0025590 60S ribosomal protein L37a; Provisional 92.21
KOG1779|consensus84 92.17
TIGR02300129 FYDLN_acid conserved hypothetical protein TIGR0230 92.14
PF0132560 Fe_dep_repress: Iron dependent repressor, N-termin 92.11
PRK05901509 RNA polymerase sigma factor; Provisional 92.07
PF1371937 zinc_ribbon_5: zinc-ribbon domain 92.06
TIGR02393238 RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter 92.03
KOG0654|consensus359 91.98
smart0034284 HTH_ARAC helix_turn_helix, arabinose operon contro 91.93
PF1341248 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 91.85
PF1373055 HTH_36: Helix-turn-helix domain 91.77
TIGR0028091 L37a ribosomal protein L37a. This model finds euka 91.64
PF0728269 OrfB_Zn_ribbon: Putative transposase DNA-binding d 91.19
PRK1489299 putative transcription elongation factor Elf1; Pro 91.14
PF0035646 LacI: Bacterial regulatory proteins, lacI family; 91.01
PF0929732 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do 90.96
PF1066860 Phage_terminase: Phage terminase small subunit; In 90.91
PRK09210367 RNA polymerase sigma factor RpoD; Validated 90.79
COG288861 Predicted Zn-ribbon RNA-binding protein with a fun 90.59
TIGR0161095 phage_O_Nterm phage replication protein O, N-termi 90.34
PRK0397690 rpl37ae 50S ribosomal protein L37Ae; Reviewed 90.29
PRK05911257 RNA polymerase sigma factor sigma-28; Reviewed 90.16
PF0822057 HTH_DeoR: DeoR-like helix-turn-helix domain; Inter 90.0
cd0009267 HTH_CRP helix_turn_helix, cAMP Regulatory protein 89.91
PF1354576 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 89.86
PF1361353 HTH_Tnp_4: Helix-turn-helix of DDE superfamily end 89.79
KOG0794|consensus 264 89.44
PF0454550 Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763 89.31
PF1393644 HTH_38: Helix-turn-helix domain; PDB: 2W48_A. 89.29
smart0034284 HTH_ARAC helix_turn_helix, arabinose operon contro 89.27
PF0279645 HTH_7: Helix-turn-helix domain of resolvase; Inter 88.94
PF1371736 zinc_ribbon_4: zinc-ribbon domain 88.93
PRK07405317 RNA polymerase sigma factor SigD; Validated 88.89
smart0041948 HTH_CRP helix_turn_helix, cAMP Regulatory protein. 88.61
PF0137187 Trp_repressor: Trp repressor protein; InterPro: IP 88.56
cd0657190 Bac_DnaA_C C-terminal domain of bacterial DnaA pro 88.5
smart0034560 HTH_GNTR helix_turn_helix gluconate operon transcr 88.46
smart0044040 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo 88.39
PRK0971064 lar restriction alleviation and modification prote 88.21
COG5349126 Uncharacterized protein conserved in bacteria [Fun 88.17
TIGR00244147 transcriptional regulator NrdR. Members of this al 88.05
PRK07406373 RNA polymerase sigma factor RpoD; Validated 88.03
PF1354252 HTH_Tnp_ISL3: Helix-turn-helix domain of transposa 87.68
TIGR03697193 NtcA_cyano global nitrogen regulator NtcA, cyanoba 87.64
PRK11169164 leucine-responsive transcriptional regulator; Prov 87.54
PRK02935110 hypothetical protein; Provisional 87.51
COG1191247 FliA DNA-directed RNA polymerase specialized sigma 87.49
TIGR0244359 conserved hypothetical metal-binding protein. Memb 87.43
PF0512981 Elf1: Transcription elongation factor Elf1 like; I 87.33
PRK00135188 scpB segregation and condensation protein B; Revie 87.25
COG1725125 Predicted transcriptional regulators [Transcriptio 86.98
PF0360432 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa 86.9
PF0496753 HTH_10: HTH DNA binding domain; InterPro: IPR00705 86.87
COG1326201 Uncharacterized archaeal Zn-finger protein [Genera 86.83
PF1444654 Prok-RING_1: Prokaryotic RING finger family 1 86.81
PRK05949327 RNA polymerase sigma factor; Validated 86.76
PF0032532 Crp: Bacterial regulatory proteins, crp family; In 86.71
PRK14088440 dnaA chromosomal replication initiation protein; P 86.55
PRK1313056 H/ACA RNA-protein complex component Nop10p; Review 86.55
PF0952671 DUF2387: Probable metal-binding protein (DUF2387); 86.46
PRK05978148 hypothetical protein; Provisional 86.44
PRK1489059 putative Zn-ribbon RNA-binding protein; Provisiona 86.33
PRK11179153 DNA-binding transcriptional regulator AsnC; Provis 86.25
PF0039264 GntR: Bacterial regulatory proteins, gntR family; 86.13
PF0381136 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0 86.03
PRK12495226 hypothetical protein; Provisional 86.02
TIGR01384104 TFS_arch transcription factor S, archaeal. There h 85.94
PF0016542 HTH_AraC: Bacterial regulatory helix-turn-helix pr 85.93
PF1338450 HTH_23: Homeodomain-like domain; PDB: 2X48_C. 85.38
PF0519136 ADK_lid: Adenylate kinase, active site lid; InterP 85.35
PF1280262 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP 85.35
PF1450248 HTH_41: Helix-turn-helix domain 85.15
smart0083441 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C 85.14
PF0208283 Rrf2: Transcriptional regulator; InterPro: IPR0009 85.05
COG1510177 Predicted transcriptional regulators [Transcriptio 85.04
TIGR0132194 TrpR trp operon repressor, proteobacterial. This m 84.97
PF0829970 Bac_DnaA_C: Bacterial dnaA protein helix-turn-heli 84.66
smart0065944 RPOLCX RNA polymerase subunit CX. present in RNA p 84.54
PRK1228657 rpmF 50S ribosomal protein L32; Reviewed 84.24
PF0522545 HTH_psq: helix-turn-helix, Psq domain; InterPro: I 83.82
PF0102247 HTH_5: Bacterial regulatory protein, arsR family; 83.72
PRK14086617 dnaA chromosomal replication initiation protein; P 83.71
PF1341362 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_ 83.25
PF1277350 DZR: Double zinc ribbon 83.25
COG1594113 RPB9 DNA-directed RNA polymerase, subunit M/Transc 83.08
PF0985564 DUF2082: Nucleic-acid-binding protein containing Z 82.93
TIGR0387973 near_KaiC_dom probable regulatory domain. This mod 82.85
TIGR0012269 birA_repr_reg BirA biotin operon repressor domain. 82.83
cd0657190 Bac_DnaA_C C-terminal domain of bacterial DnaA pro 82.65
TIGR02395429 rpoN_sigma RNA polymerase sigma-54 factor. A sigma 82.6
PF11023114 DUF2614: Protein of unknown function (DUF2614); In 82.59
PF0311928 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f 82.52
PRK11161235 fumarate/nitrate reduction transcriptional regulat 82.46
PF0178356 Ribosomal_L32p: Ribosomal L32p protein family; Int 82.41
PF15616131 TerY-C: TerY-C metal binding domain 82.2
smart0042158 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo 82.19
PRK06266178 transcription initiation factor E subunit alpha; V 82.13
PF0208283 Rrf2: Transcriptional regulator; InterPro: IPR0009 82.05
TIGR02010135 IscR iron-sulfur cluster assembly transcription fa 81.56
smart0055068 Zalpha Z-DNA-binding domain in adenosine deaminase 81.4
PF0109639 TFIIS_C: Transcription factor S-II (TFIIS); InterP 81.34
COG3877122 Uncharacterized protein conserved in bacteria [Fun 81.28
COG165479 BirA Biotin operon repressor [Transcription] 80.8
PRK07122264 RNA polymerase sigma factor SigF; Reviewed 80.41
PF0827955 HTH_11: HTH domain; InterPro: IPR013196 Winged hel 80.31
PRK07408256 RNA polymerase sigma factor SigF; Reviewed 80.25
PF0019658 GerE: Bacterial regulatory proteins, luxR family; 80.24
PRK11014141 transcriptional repressor NsrR; Provisional 80.22
KOG3507|consensus62 80.16
PHA0259183 hypothetical protein; Provisional 80.13
PF14319111 Zn_Tnp_IS91: Transposase zinc-binding domain 80.12
>KOG1597|consensus Back     alignment and domain information 
Probab=100.00  E-value=1.9e-75  Score=502.10  Aligned_cols=303  Identities=61%  Similarity=0.955  Sum_probs=285.4

Q ss_pred             ccCCCCCCC--CeeeeCCCCceecCCCCccccCcccccCCCcccccCCCCCCCCCCCCCCCCCcccCCCCceeeccCCCC
Q psy6534           6 VCCYEHPDA--PLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLNGSDLSTMIGPGRGD   83 (309)
Q Consensus         6 ~~Cp~C~~~--~~v~D~~~G~~vC~~CG~V~~e~~id~~~ewr~f~~~~~~~~~sr~g~~~~~~~~~~~l~t~i~~~~~~   83 (309)
                      +.||+|+..  ++|+|+.+|+++|..||+|+++++||+++|||+|++++++.||||+|+++||++.+++|+|+|+++.|.
T Consensus         1 ~~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~Id~~sEwrtfsnd~~~~DPsrvG~~sNPlL~~g~L~T~I~~g~g~   80 (308)
T KOG1597|consen    1 MTCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRIIDEGSEWRTFSNDDSDADPSRVGASSNPLLDGGDLSTFISKGTGT   80 (308)
T ss_pred             CCCCCCCCCCCCeeeeccCCceecccCCeeeccccccccccccccccCCCCCCccccCCCCCCCCCCCCcceeeecCCCC
Confidence            368888643  589999999999999999999999999999999999998999999999999999999999999998876


Q ss_pred             CCCCCCCcccccccccCChhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHh
Q psy6534          84 ASFDGFGMSKYQNRRTMNSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQ  163 (309)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~  163 (309)
                      ++....+..+||++..+++.|+.+..+|..|..|++.++||..+.++|.++|+++.+.+.++||+.++++|||||+|||+
T Consensus        81 ~s~~~s~l~~~Q~~~sm~~~d~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq  160 (308)
T KOG1597|consen   81 SSSFASSLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQ  160 (308)
T ss_pred             CHHHHHHHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHh
Confidence            54433334568888888899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCC--CChHHHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCC
Q psy6534         164 EGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDL--ITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGR  241 (309)
Q Consensus       164 ~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~--~~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr  241 (309)
                      ++.|||++||+.++++++++|++.++.|.+.|+..++.  ++..+|++|||+.|+||+.++++|.++++++.+..+..||
T Consensus       161 ~~~pRT~kEI~~~anv~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gR  240 (308)
T KOG1597|consen  161 EDVPRTFKEISAVANVSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGR  240 (308)
T ss_pred             cCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCC
Confidence            99999999999999999999999999999999987664  4588999999999999999999999999999999999999


Q ss_pred             ChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCcCCCCCCCCCCC
Q psy6534         242 SPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPIHELPQ  308 (309)
Q Consensus       242 ~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~~~~~~~~~~~~~~~~  308 (309)
                      +|.+||||+|||+++++..+++++||.+++||+++|||+.||+|++++.+|+|.||.+..|++.||.
T Consensus       241 sPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~~liP~~~a~~~~lk~Lp~  307 (308)
T KOG1597|consen  241 SPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLYPHADKLIPSWYANAVPLKNLPG  307 (308)
T ss_pred             CchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHHHHhhchhhhChhhhccccchhhcCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999996

>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>KOG1598|consensus Back     alignment and domain information
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) Back     alignment and domain information
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) Back     alignment and domain information
>KOG0835|consensus Back     alignment and domain information
>TIGR00569 ccl1 cyclin ccl1 Back     alignment and domain information
>KOG0834|consensus Back     alignment and domain information
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair] Back     alignment and domain information
>KOG0794|consensus Back     alignment and domain information
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>cd00043 CYCLIN Cyclin box fold Back     alignment and domain information
>cd00043 CYCLIN Cyclin box fold Back     alignment and domain information
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>KOG0656|consensus Back     alignment and domain information
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>KOG1597|consensus Back     alignment and domain information
>KOG4557|consensus Back     alignment and domain information
>COG5024 Cyclin [Cell division and chromosome partitioning] Back     alignment and domain information
>KOG0653|consensus Back     alignment and domain information
>KOG2496|consensus Back     alignment and domain information
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) Back     alignment and domain information
>KOG1598|consensus Back     alignment and domain information
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) Back     alignment and domain information
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation Back     alignment and domain information
>KOG0655|consensus Back     alignment and domain information
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[] Back     alignment and domain information
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed Back     alignment and domain information
>PHA00626 hypothetical protein Back     alignment and domain information
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG0835|consensus Back     alignment and domain information
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation Back     alignment and domain information
>TIGR00569 ccl1 cyclin ccl1 Back     alignment and domain information
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) Back     alignment and domain information
>PLN00209 ribosomal protein S27; Provisional Back     alignment and domain information
>PTZ00083 40S ribosomal protein S27; Provisional Back     alignment and domain information
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) Back     alignment and domain information
>KOG0834|consensus Back     alignment and domain information
>PRK00420 hypothetical protein; Validated Back     alignment and domain information
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues Back     alignment and domain information
>PRK00432 30S ribosomal protein S27ae; Validated Back     alignment and domain information
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain Back     alignment and domain information
>PF13240 zinc_ribbon_2: zinc-ribbon domain Back     alignment and domain information
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase Back     alignment and domain information
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [] Back     alignment and domain information
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only] Back     alignment and domain information
>KOG4164|consensus Back     alignment and domain information
>PF13248 zf-ribbon_3: zinc-ribbon domain Back     alignment and domain information
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK11827 hypothetical protein; Provisional Back     alignment and domain information
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C Back     alignment and domain information
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function Back     alignment and domain information
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair] Back     alignment and domain information
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) Back     alignment and domain information
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar Back     alignment and domain information
>TIGR01206 lysW lysine biosynthesis protein LysW Back     alignment and domain information
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PRK10220 hypothetical protein; Provisional Back     alignment and domain information
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4 Back     alignment and domain information
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs) Back     alignment and domain information
>COG2835 Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc Back     alignment and domain information
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only] Back     alignment and domain information
>smart00661 RPOL9 RNA polymerase subunit 9 Back     alignment and domain information
>KOG2496|consensus Back     alignment and domain information
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA Back     alignment and domain information
>PRK00464 nrdR transcriptional regulator NrdR; Validated Back     alignment and domain information
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B Back     alignment and domain information
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional Back     alignment and domain information
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues Back     alignment and domain information
>PF05460 ORC6: Origin recognition complex subunit 6 (ORC6); InterPro: IPR008721 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 [] Back     alignment and domain information
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif Back     alignment and domain information
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) Back     alignment and domain information
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines Back     alignment and domain information
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism] Back     alignment and domain information
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only] Back     alignment and domain information
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family Back     alignment and domain information
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets Back     alignment and domain information
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>KOG4557|consensus Back     alignment and domain information
>KOG1010|consensus Back     alignment and domain information
>PTZ00255 60S ribosomal protein L37a; Provisional Back     alignment and domain information
>KOG1779|consensus Back     alignment and domain information
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300 Back     alignment and domain information
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family Back     alignment and domain information
>PRK05901 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PF13719 zinc_ribbon_5: zinc-ribbon domain Back     alignment and domain information
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain Back     alignment and domain information
>KOG0654|consensus Back     alignment and domain information
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein Back     alignment and domain information
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A Back     alignment and domain information
>PF13730 HTH_36: Helix-turn-helix domain Back     alignment and domain information
>TIGR00280 L37a ribosomal protein L37a Back     alignment and domain information
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins Back     alignment and domain information
>PRK14892 putative transcription elongation factor Elf1; Provisional Back     alignment and domain information
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif Back     alignment and domain information
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains Back     alignment and domain information
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes Back     alignment and domain information
>PRK09210 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain Back     alignment and domain information
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed Back     alignment and domain information
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed Back     alignment and domain information
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism Back     alignment and domain information
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family Back     alignment and domain information
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A Back     alignment and domain information
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease Back     alignment and domain information
>KOG0794|consensus Back     alignment and domain information
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A Back     alignment and domain information
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein Back     alignment and domain information
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms Back     alignment and domain information
>PF13717 zinc_ribbon_4: zinc-ribbon domain Back     alignment and domain information
>PRK07405 RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein Back     alignment and domain information
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression Back     alignment and domain information
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins Back     alignment and domain information
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor Back     alignment and domain information
>smart00440 ZnF_C2C2 C2C2 Zinc finger Back     alignment and domain information
>PRK09710 lar restriction alleviation and modification protein; Reviewed Back     alignment and domain information
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>TIGR00244 transcriptional regulator NrdR Back     alignment and domain information
>PRK07406 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3 Back     alignment and domain information
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial Back     alignment and domain information
>PRK11169 leucine-responsive transcriptional regulator; Provisional Back     alignment and domain information
>PRK02935 hypothetical protein; Provisional Back     alignment and domain information
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription] Back     alignment and domain information
>TIGR02443 conserved hypothetical metal-binding protein Back     alignment and domain information
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines Back     alignment and domain information
>PRK00135 scpB segregation and condensation protein B; Reviewed Back     alignment and domain information
>COG1725 Predicted transcriptional regulators [Transcription] Back     alignment and domain information
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates Back     alignment and domain information
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif Back     alignment and domain information
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only] Back     alignment and domain information
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1 Back     alignment and domain information
>PRK05949 RNA polymerase sigma factor; Validated Back     alignment and domain information
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif Back     alignment and domain information
>PRK14088 dnaA chromosomal replication initiation protein; Provisional Back     alignment and domain information
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed Back     alignment and domain information
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC Back     alignment and domain information
>PRK05978 hypothetical protein; Provisional Back     alignment and domain information
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional Back     alignment and domain information
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional Back     alignment and domain information
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities Back     alignment and domain information
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases Back     alignment and domain information
>PRK12495 hypothetical protein; Provisional Back     alignment and domain information
>TIGR01384 TFS_arch transcription factor S, archaeal Back     alignment and domain information
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A Back     alignment and domain information
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C Back     alignment and domain information
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2 Back     alignment and domain information
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B Back     alignment and domain information
>PF14502 HTH_41: Helix-turn-helix domain Back     alignment and domain information
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein Back     alignment and domain information
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp Back     alignment and domain information
>COG1510 Predicted transcriptional regulators [Transcription] Back     alignment and domain information
>TIGR01321 TrpR trp operon repressor, proteobacterial Back     alignment and domain information
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication Back     alignment and domain information
>smart00659 RPOLCX RNA polymerase subunit CX Back     alignment and domain information
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed Back     alignment and domain information
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster [] Back     alignment and domain information
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities Back     alignment and domain information
>PRK14086 dnaA chromosomal replication initiation protein; Provisional Back     alignment and domain information
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A Back     alignment and domain information
>PF12773 DZR: Double zinc ribbon Back     alignment and domain information
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription] Back     alignment and domain information
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins Back     alignment and domain information
>TIGR03879 near_KaiC_dom probable regulatory domain Back     alignment and domain information
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain Back     alignment and domain information
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins Back     alignment and domain information
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor Back     alignment and domain information
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins Back     alignment and domain information
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional Back     alignment and domain information
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PF15616 TerY-C: TerY-C metal binding domain Back     alignment and domain information
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon Back     alignment and domain information
>PRK06266 transcription initiation factor E subunit alpha; Validated Back     alignment and domain information
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp Back     alignment and domain information
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR Back     alignment and domain information
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases Back     alignment and domain information
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>COG1654 BirA Biotin operon repressor [Transcription] Back     alignment and domain information
>PRK07122 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets Back     alignment and domain information
>PRK07408 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators Back     alignment and domain information
>PRK11014 transcriptional repressor NsrR; Provisional Back     alignment and domain information
>KOG3507|consensus Back     alignment and domain information
>PHA02591 hypothetical protein; Provisional Back     alignment and domain information
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query309
1c9b_A207 Crystal Structure Of A Human Tbp Core Domain-Human 2e-90
1tfb_A208 Nmr Studies Of Human General Transcription Factor T 2e-89
2phg_A206 Model For Vp16 Binding To Tfiib Length = 206 3e-89
1vol_A204 Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEME 6e-87
3k7a_M345 Crystal Structure Of An Rna Polymerase Ii-Tfiib Com 5e-44
1ais_B200 Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA- 2e-22
1d3u_B201 Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+T 2e-22
1rly_A60 Rdc-Derived Models Of The Zinc Ribbon Domain Of Hum 5e-18
1dl6_A58 Solution Structure Of Human Tfiib N-Terminal Domain 8e-18
3k1f_M197 Crystal Structure Of Rna Polymerase Ii In Complex W 2e-06
1pft_A50 N-Terminal Domain Of Tfiib, Nmr Length = 50 3e-04
>pdb|1C9B|A Chain A, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib Core Domain Complex Bound To An Extended, Modified Adenoviral Major Late Promoter (Admlp) Length = 207 Back     alignment and structure 
Iteration: 1

 Score =  328 bits (841), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 157/207 (75%), Positives = 175/207 (84%)
Query: 103 SDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACR 162
           SDRA++NA +EI +MADRINL + IVDR NNLFKQV++ K+LKGR+NDAIASACLYIACR
Sbjct: 1   SDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACR 60
Query: 163 QEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQ 222
           QEGVPRTFKEICAVS+ISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNL LP  VQ
Sbjct: 61  QEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQ 120
Query: 223 KAATHIARKAVELDIVPGRSPIXXXXXXXXXXXXXXXDKRSQKEIGDIAGVAEVTIRQSY 282
            AATHIARKAVELD+VPGRSPI               +KR+QKEIGDIAGVA+VTIRQSY
Sbjct: 121 MAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSY 180
Query: 283 KLMYPHASKLFPQDFVFHTPIHELPQL 309
           +L+YP A  LFP DF F TP+ +LPQL
Sbjct: 181 RLIYPRAPDLFPTDFKFDTPVDKLPQL 207
>pdb|1TFB|A Chain A, Nmr Studies Of Human General Transcription Factor Tfiib: Dynamics And Interaction With Vp16 Activation Domain, 20 Structures Length = 208 Back     alignment and structure
>pdb|2PHG|A Chain A, Model For Vp16 Binding To Tfiib Length = 206 Back     alignment and structure
>pdb|1VOL|A Chain A, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT Ternary Complex Length = 204 Back     alignment and structure
>pdb|3K7A|M Chain M, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex Length = 345 Back     alignment and structure
>pdb|1AIS|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-Box Complex From Pyrococcus Woesei Length = 200 Back     alignment and structure
>pdb|1D3U|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+TATA- Box Complex From Pyrococcus Woesei Length = 201 Back     alignment and structure
>pdb|1RLY|A Chain A, Rdc-Derived Models Of The Zinc Ribbon Domain Of Human General Transcription Tfiib (Zinc Bound Structures) Length = 60 Back     alignment and structure
>pdb|1DL6|A Chain A, Solution Structure Of Human Tfiib N-Terminal Domain Length = 58 Back     alignment and structure
>pdb|3K1F|M Chain M, Crystal Structure Of Rna Polymerase Ii In Complex With Tfiib Length = 197 Back     alignment and structure
>pdb|1PFT|A Chain A, N-Terminal Domain Of Tfiib, Nmr Length = 50 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query309
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 6e-93
1c9b_A207 General transcription factor IIB; protein-DNA comp 2e-76
1c9b_A207 General transcription factor IIB; protein-DNA comp 9e-14
1ais_B200 TFB TFIIB, protein (transcription initiation facto 7e-69
1ais_B200 TFB TFIIB, protein (transcription initiation facto 1e-13
3k1f_M197 Transcription initiation factor IIB; RNA polymeras 4e-29
1dl6_A58 Transcription factor II B (TFIIB); zinc ribbon, ge 3e-19
1pft_A50 TFIIB, PFTFIIBN; N-terminal domain, transcription 8e-16
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 2e-07
1f5q_B252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 5e-07
2ivx_A257 Cyclin-T2; transcription regulation, cell division 6e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-07
2pk2_A358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 2e-06
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 3e-06
3g33_B306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 7e-06
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 9e-06
2w96_A271 G1/S-specific cyclin-D1; serine/threonine-protein 1e-05
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 2e-05
2r7g_A347 PP110, retinoblastoma-associated protein, P105-RB, 3e-05
4ell_A411 Retinoblastoma-associated protein; cyclin fold, tu 1e-04
2cch_B260 Cyclin A2, cyclin-A; complex(transferase/cell divi 1e-04
4elj_A656 Retinoblastoma-associated protein; cyclin fold, tu 2e-04
2b9r_A269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 4e-04
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae} Length = 345 Back     alignment and structure
 Score =  278 bits (712), Expect = 6e-93
 Identities = 107/326 (32%), Positives = 168/326 (51%), Gaps = 18/326 (5%)

Query: 1   MNINKVC--CYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNE-KSGVDP 57
           +NI   C  C +     ++E +  GD +C+ CGLV+ D+++D  SEWRTFSN+  +G DP
Sbjct: 18  LNIVLTCPEC-KVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDP 76

Query: 58  SRVGGPENPLLNGSDLSTMIGPGRGDASFDGFGMSKYQNRRTMNSSDRALLNAIREINSM 117
           SRVG   NPLL+G++LST IG G          ++K Q +  M+  D  +  A  +I  +
Sbjct: 77  SRVGEASNPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMDKKDNEVQAAFAKITML 136

Query: 118 ADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVS 177
            D   L K + D A   +K  HD K LKG+S ++I +A + I CR+  V RTFKEI ++ 
Sbjct: 137 CDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLI 196

Query: 178 KISKKEIGRCFKLILKALE------------TSVDLITTGDFMSRFCSNLSLPNMVQKAA 225
            +  KE G+   ++   L              ++       ++ RFCS+L LP  V  +A
Sbjct: 197 HVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSA 256

Query: 226 THIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLM 285
            + A+K  E+  + G+SPI++A  +IY+         +  ++G    V E TI+  YK++
Sbjct: 257 EYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSGYKIL 316

Query: 286 YPHASKLFPQDFV--FHTPIHELPQL 309
           Y H  KL     +      +  LP +
Sbjct: 317 YEHRDKLVDPQLIANGVVSLDNLPGV 342
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A* Length = 207 Back     alignment and structure
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A* Length = 207 Back     alignment and structure
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Length = 200 Back     alignment and structure
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Length = 200 Back     alignment and structure
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197 Back     alignment and structure
>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A Length = 58 Back     alignment and structure
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1 Length = 50 Back     alignment and structure
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Length = 258 Back     alignment and structure
>1f5q_B Gamma herpesvirus cyclin; herpesviral cyclin, cyclin dependent kinase. protein/protein complex, transferase; 2.50A {Murid herpesvirus 4} SCOP: a.74.1.1 a.74.1.1 Length = 252 Back     alignment and structure
>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B* Length = 257 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C Length = 358 Back     alignment and structure
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Length = 235 Back     alignment and structure
>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens} Length = 306 Back     alignment and structure
>1g3n_C V-cyclin; cyclin-dependent kinase, INK4 inhibitor, viral cyclin, cell cycle, signaling protein; 2.90A {Human herpesvirus 8} SCOP: a.74.1.1 a.74.1.1 Length = 257 Back     alignment and structure
>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A Length = 271 Back     alignment and structure
>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A Length = 254 Back     alignment and structure
>2r7g_A PP110, retinoblastoma-associated protein, P105-RB, RB; retinoblastoma protein, E2F displacement, transcription repressor; 1.67A {Homo sapiens} SCOP: a.74.1.3 a.74.1.3 PDB: 1n4m_A 3pom_A 1gh6_B 1gux_A 1o9k_A 1ad6_A 1gux_B 1o9k_B Length = 347 Back     alignment and structure
>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor, cell cycle; 1.98A {Homo sapiens} Length = 411 Back     alignment and structure
>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ... Length = 260 Back     alignment and structure
>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens} Length = 656 Back     alignment and structure
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Length = 269 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query309
4bbr_M345 Transcription initiation factor IIB; RNA polymeras 100.0
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 100.0
1c9b_A207 General transcription factor IIB; protein-DNA comp 100.0
1ais_B200 TFB TFIIB, protein (transcription initiation facto 100.0
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 99.94
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 99.91
2ivx_A257 Cyclin-T2; transcription regulation, cell division 99.91
3rgf_B285 Cyclin-C; protein kinase complex, transferase,tran 99.9
2b9r_A269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 99.9
2cch_B260 Cyclin A2, cyclin-A; complex(transferase/cell divi 99.89
2w96_A271 G1/S-specific cyclin-D1; serine/threonine-protein 99.88
2pk2_A358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 99.87
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 99.85
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 99.84
1jkw_A323 Cyclin H; cell cycle, cell division, nuclear prote 99.83
1w98_B283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 99.8
3g33_B306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 99.78
3k1f_M197 Transcription initiation factor IIB; RNA polymeras 99.77
1dl6_A58 Transcription factor II B (TFIIB); zinc ribbon, ge 99.73
1pft_A50 TFIIB, PFTFIIBN; N-terminal domain, transcription 99.67
1f5q_B252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 99.51
1ais_B200 TFB TFIIB, protein (transcription initiation facto 99.44
4bbr_M 345 Transcription initiation factor IIB; RNA polymeras 99.32
1c9b_A207 General transcription factor IIB; protein-DNA comp 99.23
3k7a_M 345 Transcription initiation factor IIB; RNA polymeras 99.06
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 98.34
3h4c_A260 Transcription factor TFIIB-like; cyclin, transcrip 97.86
2ivx_A 257 Cyclin-T2; transcription regulation, cell division 97.81
2i53_A 258 Cyclin K; cell cycle, transcription, cyclin BOX, C 97.8
1jkw_A 323 Cyclin H; cell cycle, cell division, nuclear prote 97.79
3rgf_B 285 Cyclin-C; protein kinase complex, transferase,tran 97.72
2b9r_A 269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 97.48
3m03_A95 ORC6, origin recognition complex subunit 6; helix 97.47
2pk2_A 358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 97.43
3m03_A95 ORC6, origin recognition complex subunit 6; helix 97.35
2w96_A 271 G1/S-specific cyclin-D1; serine/threonine-protein 97.33
2cch_B 260 Cyclin A2, cyclin-A; complex(transferase/cell divi 97.28
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 97.11
1w98_B 283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 97.0
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 96.76
1qxf_A66 GR2, 30S ribosomal protein S27E; structural genomi 96.76
3j20_W63 30S ribosomal protein S27E; archaea, archaeal, KIN 96.6
2jny_A67 Uncharacterized BCR; structure, CGR1, NESG, struct 96.39
2js4_A70 UPF0434 protein BB2007; NESG, northeast structural 96.38
2xzm_681 RPS27E; ribosome, translation; 3.93A {Tetrahymena 96.33
2pk7_A69 Uncharacterized protein; NESG, PLR1, putative tetr 96.32
3u5c_b82 RP61, YS20, 40S ribosomal protein S27-A; translati 96.32
2jr6_A68 UPF0434 protein NMA0874; solution, structural geno 96.26
3g33_B 306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 96.25
1vq8_Z83 50S ribosomal protein L37AE; ribosome 50S, protein 96.22
2hf1_A68 Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A 96.17
2r7g_A347 PP110, retinoblastoma-associated protein, P105-RB, 96.13
4ell_A411 Retinoblastoma-associated protein; cyclin fold, tu 96.13
3iz6_X86 40S ribosomal protein S27 (S27E); eukaryotic ribos 96.12
2akl_A138 PHNA-like protein PA0128; two domains, Zn binding 95.85
3j20_Y50 30S ribosomal protein S27AE; archaea, archaeal, KI 95.8
4elj_A656 Retinoblastoma-associated protein; cyclin fold, tu 95.73
2qdj_A304 Retinoblastoma-associated protein; cyclin fold, cy 95.47
2r7g_A347 PP110, retinoblastoma-associated protein, P105-RB, 94.81
2k4x_A55 30S ribosomal protein S27AE; metal-binding, ribonu 93.84
1f5q_B252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 93.04
4elj_A 656 Retinoblastoma-associated protein; cyclin fold, tu 92.99
3j21_i83 50S ribosomal protein L37AE; archaea, archaeal, KI 92.86
3jyw_972 60S ribosomal protein L43; eukaryotic ribosome, RA 92.8
2kpi_A56 Uncharacterized protein SCO3027; zinc finger, PSI- 92.77
2pmi_B293 PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de 92.72
3cc2_Z116 50S ribosomal protein L37AE, 50S ribosomal protein 92.64
2jt1_A77 PEFI protein; solution structure, winged helix-tur 92.59
3iz5_m92 60S ribosomal protein L43 (L37AE); eukaryotic ribo 92.41
2lnb_A80 Z-DNA-binding protein 1; structural genomics, nort 92.3
1ffk_W73 Ribosomal protein L37AE; ribosome assembly, RNA-RN 92.14
3izc_m92 60S ribosomal protein RPL43 (L37AE); eukaryotic ri 91.93
2qdj_A 304 Retinoblastoma-associated protein; cyclin fold, cy 91.87
2k5r_A97 Uncharacterized protein XF2673; solution structure 91.37
3h4c_A 260 Transcription factor TFIIB-like; cyclin, transcrip 91.35
4ell_A411 Retinoblastoma-associated protein; cyclin fold, tu 91.19
4a17_Y103 RPL37A, 60S ribosomal protein L32; eukaryotic ribo 90.31
2w7n_A101 TRFB transcriptional repressor protein; INCP, plas 89.93
2pmi_B 293 PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de 89.5
1qyp_A57 RNA polymerase II; transcription, RPB9, Zn ribbon, 88.74
3j21_g51 50S ribosomal protein L40E; archaea, archaeal, KIN 88.66
1twf_L70 ABC10-alpha, DNA-directed RNA polymerases I, II, a 88.51
2p7v_B68 Sigma-70, RNA polymerase sigma factor RPOD; RSD, r 88.2
1nui_A255 DNA primase/helicase; zinc-biding domain, toprim f 88.16
1jhg_A101 Trp operon repressor; complex (regulatory protein- 87.97
1uxc_A65 FRUR (1-57), fructose repressor; DNA-binding prote 87.56
2heo_A67 Z-DNA binding protein 1; protein DLM1-Z-DNA comple 86.87
1k81_A36 EIF-2-beta, probable translation initiation factor 86.64
1xn7_A78 Hypothetical protein YHGG; alpha+beta, GFT structu 86.38
1tc3_C51 Protein (TC3 transposase); DNA binding, helix-turn 86.23
2apo_B60 Ribosome biogenesis protein NOP10; protein-protein 86.18
1qbj_A81 Protein (double-stranded RNA specific adenosine D 86.02
2o8x_A70 Probable RNA polymerase sigma-C factor; promoter r 85.9
1j1v_A94 Chromosomal replication initiator protein DNAA, 5' 85.85
4ham_A134 LMO2241 protein; structural genomics, PSI-biology, 85.71
2jpc_A61 SSRB; DNA binding protein, structural genomics, PS 85.29
1je8_A82 Nitrate/nitrite response regulator protein NARL; p 85.19
1wii_A85 Hypothetical UPF0222 protein MGC4549; domain of un 85.04
1qgp_A77 Protein (double stranded RNA adenosine deaminase); 84.41
3neu_A125 LIN1836 protein; structural genomics, PSI-2, prote 84.25
1fse_A74 GERE; helix-turn-helix DNA-binding protein transcr 83.81
1ku3_A73 Sigma factor SIGA; helix-turn-helix, transcription 83.69
1t6s_A162 Conserved hypothetical protein; A winged helix-tur 83.48
2htj_A81 P fimbrial regulatory protein KS71A; winged helix- 83.24
3ulq_B90 Transcriptional regulatory protein COMA; tetratric 83.17
3tqn_A113 Transcriptional regulator, GNTR family; regulatory 83.11
3i4p_A162 Transcriptional regulator, ASNC family; PSI, struc 83.11
1tty_A87 Sigma-A, RNA polymerase sigma factor RPOD; helix-t 83.07
2y75_A129 HTH-type transcriptional regulator CYMR; DNA bindi 82.85
3hug_A92 RNA polymerase sigma factor; ECF sigma factor, zin 82.66
6rxn_A46 Rubredoxin; electron transfer(iron-sulfur protein) 82.51
2x48_A55 CAG38821; archeal virus, viral protein; 2.60A {Sul 82.49
2b0l_A102 GTP-sensing transcriptional pleiotropic repressor; 82.13
2kv1_A124 Methionine-R-sulfoxide reductase B1; MSRB1, SELR, 81.85
3lwf_A159 LIN1550 protein, putative transcriptional regulato 81.77
1x3u_A79 Transcriptional regulatory protein FIXJ; helix-tur 81.75
1gh9_A71 8.3 kDa protein (gene MTH1184); beta+alpha complex 81.74
1dxg_A36 Desulforedoxin; non-heme iron protein, rubredoxin 81.51
2w48_A 315 Sorbitol operon regulator; SORC, activator, repres 81.46
2k02_A87 Ferrous iron transport protein C; FEOC, iron-sulfu 81.4
4ich_A 311 Transcriptional regulator; structural genomics, PS 81.33
1tfi_A50 Transcriptional elongation factor SII; transcripti 81.26
3by6_A126 Predicted transcriptional regulator; structural ge 81.16
3e6c_C250 CPRK, cyclic nucleotide-binding protein; CPRK, hal 81.03
2l8n_A67 Transcriptional repressor CYTR; bacterial gene rep 81.03
2ek5_A129 Predicted transcriptional regulators; helix-turn-h 80.85
3iwf_A107 Transcription regulator RPIR family; transcription 80.76
3c57_A95 Two component transcriptional regulatory protein; 80.74
2heo_A67 Z-DNA binding protein 1; protein DLM1-Z-DNA comple 80.65
3h0g_I113 DNA-directed RNA polymerases I, II, and III subuni 80.64
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M Back     alignment and structure
Probab=100.00  E-value=4.1e-76  Score=540.90  Aligned_cols=304  Identities=35%  Similarity=0.605  Sum_probs=173.7

Q ss_pred             cccCCCCCC--CCeeeeCCCCceecCCCCccccCcccccCCCcccccCCC-CCCCCCCCCCCCCCcccCCCCceeeccCC
Q psy6534           5 KVCCYEHPD--APLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEK-SGVDPSRVGGPENPLLNGSDLSTMIGPGR   81 (309)
Q Consensus         5 ~~~Cp~C~~--~~~v~D~~~G~~vC~~CG~V~~e~~id~~~ewr~f~~~~-~~~~~sr~g~~~~~~~~~~~l~t~i~~~~   81 (309)
                      ...||+||+  +++++|+++|++||++||+|++|++||+|||||+|++++ ++.|++|+|+|.|+++||.+|+|.|+++.
T Consensus        21 ~~~Cp~C~~~~~~lv~D~~~G~~vC~~CGlVl~e~~iD~g~EWR~f~~d~~~~~d~sRvG~~~~~~~~~~glsT~I~~~~  100 (345)
T 4bbr_M           21 VLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEASNPLLDGNNLSTRIGKGE  100 (345)
T ss_dssp             -CCCSSCCCSSCCEEEEGGGTEEEETTTCBEEESCCBCHHHHHTTTSCSCSSSCCSSCCEEEECHHHHCSCCCCEEECCS
T ss_pred             CCcCCCCCCCCCceeEECCCCcEEeCCCCCCccCcccccCccccCCCcccccCCCcCCCCCCCCccccCCCcceeecCCC
Confidence            458999996  689999999999999999999999999999999999765 46899999999999999999999999764


Q ss_pred             CCCCCCCCCcccccccccCChhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHH
Q psy6534          82 GDASFDGFGMSKYQNRRTMNSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIAC  161 (309)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~ac  161 (309)
                      ++.........+||++..++++|++|.+|++.|.++|++|+||+.+.++|..+|+++++.++++||+.+.++|||||+||
T Consensus       101 ~~~~~~~~~L~r~q~r~~~~~~er~L~~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~a~~~~~~rGrs~e~vaAAclYiAC  180 (345)
T 4bbr_M          101 TTDMRFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGC  180 (345)
T ss_dssp             SCCHHHHHHHHHHHHHTCCCCSSSSTTHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCTTTTTCCHHHHHHHHHHHHH
T ss_pred             CcchhhHHHHHHHHHhhhcChHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHH
Confidence            32101011234688887788999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCCCccHHHHHHHhcccHHHHHHHHHHHHHHhccc------------CCCCChHHHHHHHHhhCCCCHHHHHHHHHHH
Q psy6534         162 RQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETS------------VDLITTGDFMSRFCSNLSLPNMVQKAATHIA  229 (309)
Q Consensus       162 R~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~------------~~~~~p~~~i~~~~~~L~l~~~~~~~a~~i~  229 (309)
                      |++++|+|++||++++++++++|+++|+.|.+.|++.            +++++|.+||.|||++|+|++++.+.|++|+
T Consensus       181 R~~~~prtl~eI~~~~~v~~keigr~~k~l~~~L~l~~~~~~~~~~~~~~~~~~p~~~i~Rf~s~L~l~~~v~~~A~~i~  260 (345)
T 4bbr_M          181 RRAEVARTFKEIQSLIHVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAEYTA  260 (345)
T ss_dssp             HHTCCBCCHHHHHHHHTCCTTHHHHHHHHHHHCC----------------------------------------------
T ss_pred             HhcCCCccHHHHHHHhCCCHHHHHHHHHHHHHHhCccccccccccccccCCCCCHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            9999999999999999999999999999999999864            6788999999999999999999999999999


Q ss_pred             HHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCcCC--CCCCCCCC
Q psy6534         230 RKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVF--HTPIHELP  307 (309)
Q Consensus       230 ~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~~~~~~~--~~~~~~~~  307 (309)
                      +.+.+.|+..||+|.+|||||||+|++++|.+++++||++++||+++||+++|+||++++.+|+|++|..  ..+++.||
T Consensus       261 ~~~~~~~i~~GR~P~~IAAAaIylAa~l~g~~~t~~eIa~v~~Vse~TIr~rykel~~~~~~l~~~~~~~~~~~~~~~l~  340 (345)
T 4bbr_M          261 KKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSGYKILYEHRDKLVDPQLIANGVVSLDNLP  340 (345)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHhcccccCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcCHHHhhcccCchhhCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999833  57899999


Q ss_pred             C
Q psy6534         308 Q  308 (309)
Q Consensus       308 ~  308 (309)
                      +
T Consensus       341 ~  341 (345)
T 4bbr_M          341 G  341 (345)
T ss_dssp             -
T ss_pred             C
Confidence            6
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae} Back     alignment and structure
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A* Back     alignment and structure
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Back     alignment and structure
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Back     alignment and structure
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B* Back     alignment and structure
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens} Back     alignment and structure
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Back     alignment and structure
>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ... Back     alignment and structure
>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A Back     alignment and structure
>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C Back     alignment and structure
>1g3n_C V-cyclin; cyclin-dependent kinase, INK4 inhibitor, viral cyclin, cell cycle, signaling protein; 2.90A {Human herpesvirus 8} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A Back     alignment and structure
>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A Back     alignment and structure
>1w98_B Cyclin E, G1/S-specific cyclin E1; cell cycle, transferase; HET: TPO; 2.15A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens} Back     alignment and structure
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Back     alignment and structure
>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A Back     alignment and structure
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1 Back     alignment and structure
>1f5q_B Gamma herpesvirus cyclin; herpesviral cyclin, cyclin dependent kinase. protein/protein complex, transferase; 2.50A {Murid herpesvirus 4} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Back     alignment and structure
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M Back     alignment and structure
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A* Back     alignment and structure
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae} Back     alignment and structure
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Back     alignment and structure
>3h4c_A Transcription factor TFIIB-like; cyclin, transcription factor TFIIB repeat; 2.30A {Trypanosoma brucei brucei} Back     alignment and structure
>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B* Back     alignment and structure
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A Back     alignment and structure
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens} Back     alignment and structure
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Back     alignment and structure
>3m03_A ORC6, origin recognition complex subunit 6; helix turn helix, DNA binding protein, origin recognition CO DNA replication; HET: MES; 2.50A {Homo sapiens} Back     alignment and structure
>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C Back     alignment and structure
>3m03_A ORC6, origin recognition complex subunit 6; helix turn helix, DNA binding protein, origin recognition CO DNA replication; HET: MES; 2.50A {Homo sapiens} Back     alignment and structure
>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A Back     alignment and structure
>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ... Back     alignment and structure
>1g3n_C V-cyclin; cyclin-dependent kinase, INK4 inhibitor, viral cyclin, cell cycle, signaling protein; 2.90A {Human herpesvirus 8} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>1w98_B Cyclin E, G1/S-specific cyclin E1; cell cycle, transferase; HET: TPO; 2.15A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A Back     alignment and structure
>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4 Back     alignment and structure
>3j20_W 30S ribosomal protein S27E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1 Back     alignment and structure
>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50} Back     alignment and structure
>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6 Back     alignment and structure
>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1 Back     alignment and structure
>3u5c_b RP61, YS20, 40S ribosomal protein S27-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_X 3u5g_b Back     alignment and structure
>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis} Back     alignment and structure
>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens} Back     alignment and structure
>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ... Back     alignment and structure
>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1 Back     alignment and structure
>2r7g_A PP110, retinoblastoma-associated protein, P105-RB, RB; retinoblastoma protein, E2F displacement, transcription repressor; 1.67A {Homo sapiens} SCOP: a.74.1.3 a.74.1.3 PDB: 1n4m_A 3pom_A 1gh6_B 1gux_A 1o9k_A 1ad6_A 1gux_B 1o9k_B Back     alignment and structure
>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor, cell cycle; 1.98A {Homo sapiens} Back     alignment and structure
>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Back     alignment and structure
>2akl_A PHNA-like protein PA0128; two domains, Zn binding protein, beta-strand protein, structural genomics, PSI; NMR {Pseudomonas aeruginosa PAO1} SCOP: b.34.11.2 g.41.3.5 Back     alignment and structure
>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens} Back     alignment and structure
>2qdj_A Retinoblastoma-associated protein; cyclin fold, cyclin wedge, antitumor protein; 2.00A {Homo sapiens} Back     alignment and structure
>2r7g_A PP110, retinoblastoma-associated protein, P105-RB, RB; retinoblastoma protein, E2F displacement, transcription repressor; 1.67A {Homo sapiens} SCOP: a.74.1.3 a.74.1.3 PDB: 1n4m_A 3pom_A 1gh6_B 1gux_A 1o9k_A 1ad6_A 1gux_B 1o9k_B Back     alignment and structure
>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8 Back     alignment and structure
>1f5q_B Gamma herpesvirus cyclin; herpesviral cyclin, cyclin dependent kinase. protein/protein complex, transferase; 2.50A {Murid herpesvirus 4} SCOP: a.74.1.1 a.74.1.1 Back     alignment and structure
>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens} Back     alignment and structure
>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} Back     alignment and structure
>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor} Back     alignment and structure
>2pmi_B PHO85 cyclin PHO80, aminoglycoside anti; cyclin-dependent kinase, signaling protein,transfera cycle complex; HET: MES AGS; 2.90A {Saccharomyces cerevisiae} PDB: 2pk9_B* Back     alignment and structure
>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, ribosoma protein, RNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z* 3i56_Z* 3cpw_Y* 4adx_Z Back     alignment and structure
>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2} Back     alignment and structure
>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens} Back     alignment and structure
>1ffk_W Ribosomal protein L37AE; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1jj2_Y 1k73_1* 1k8a_1* 1k9m_1* 1kc8_1* 1kd1_1* 1kqs_Y* 1m1k_1* 1m90_1* 1n8r_1* 1nji_1* 1q7y_1* 1q81_1* 1q82_1* 1q86_1* 1qvf_Y 1qvg_Y 1w2b_Y 3cxc_Y* Back     alignment and structure
>2qdj_A Retinoblastoma-associated protein; cyclin fold, cyclin wedge, antitumor protein; 2.00A {Homo sapiens} Back     alignment and structure
>2k5r_A Uncharacterized protein XF2673; solution structure, structural genomics, PSI-2, protein structure initiative; NMR {Xylella fastidiosa TEMECULA1} Back     alignment and structure
>3h4c_A Transcription factor TFIIB-like; cyclin, transcription factor TFIIB repeat; 2.30A {Trypanosoma brucei brucei} Back     alignment and structure
>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor, cell cycle; 1.98A {Homo sapiens} Back     alignment and structure
>4a17_Y RPL37A, 60S ribosomal protein L32; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_Y 4a1c_Y 4a1e_Y Back     alignment and structure
>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli} Back     alignment and structure
>2pmi_B PHO85 cyclin PHO80, aminoglycoside anti; cyclin-dependent kinase, signaling protein,transfera cycle complex; HET: MES AGS; 2.90A {Saccharomyces cerevisiae} PDB: 2pk9_B* Back     alignment and structure
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1 Back     alignment and structure
>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ... Back     alignment and structure
>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2 Back     alignment and structure
>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2 Back     alignment and structure
>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A* Back     alignment and structure
>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A Back     alignment and structure
>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A Back     alignment and structure
>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1 Back     alignment and structure
>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62 Back     alignment and structure
>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2 Back     alignment and structure
>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A Back     alignment and structure
>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A Back     alignment and structure
>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis} Back     alignment and structure
>1j1v_A Chromosomal replication initiator protein DNAA, 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3'; protein-DNA complex; 2.10A {Escherichia coli} SCOP: a.4.12.2 Back     alignment and structure
>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes} Back     alignment and structure
>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium} Back     alignment and structure
>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A Back     alignment and structure
>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4 Back     alignment and structure
>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19 Back     alignment and structure
>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua} Back     alignment and structure
>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2 Back     alignment and structure
>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A* Back     alignment and structure
>1t6s_A Conserved hypothetical protein; A winged helix-turn-helix, structural genomics, BSGC structu by NIH, protein structure initiative, PSI; 1.95A {Chlorobium tepidum tls} SCOP: a.4.5.60 a.4.5.60 Back     alignment and structure
>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73 Back     alignment and structure
>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A Back     alignment and structure
>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii} Back     alignment and structure
>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str} Back     alignment and structure
>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2 Back     alignment and structure
>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis} Back     alignment and structure
>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis} Back     alignment and structure
>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1 Back     alignment and structure
>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid} Back     alignment and structure
>2b0l_A GTP-sensing transcriptional pleiotropic repressor; CODY, DNA-binding, nucleotide-binding, transcript regulation, winged HTH motif.; 2.90A {Bacillus subtilis} SCOP: a.4.5.66 Back     alignment and structure
>2kv1_A Methionine-R-sulfoxide reductase B1; MSRB1, SELR, metal-binding, nucleus, oxidoreductase, seleniu; NMR {Mus musculus} Back     alignment and structure
>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua} Back     alignment and structure
>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti} Back     alignment and structure
>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1 Back     alignment and structure
>1dxg_A Desulforedoxin; non-heme iron protein, rubredoxin type metal center, electron transport; 1.80A {Desulfovibrio gigas} SCOP: g.41.5.2 PDB: 1dcd_A 1dhg_A 1cfw_A 2lk5_A 2lk6_A Back     alignment and structure
>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae} Back     alignment and structure
>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp} Back     alignment and structure
>4ich_A Transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, transcription RE; 1.95A {Saccharomonospora viridis} Back     alignment and structure
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1 Back     alignment and structure
>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni} Back     alignment and structure
>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration; HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP: a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A* 3e5q_A 2h6b_A* 2h6c_A Back     alignment and structure
>2l8n_A Transcriptional repressor CYTR; bacterial gene repressor, helix turn helix binding domain, L family, transcription regulation, binding protein; NMR {Escherichia coli} PDB: 2lcv_A Back     alignment and structure
>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A Back     alignment and structure
>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis} Back     alignment and structure
>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A Back     alignment and structure
>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A Back     alignment and structure
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 309
d1vola2109 a.74.1.2 (A:208-316) Transcription factor IIB (TFI 5e-39
d1vola2109 a.74.1.2 (A:208-316) Transcription factor IIB (TFI 6e-23
d1vola195 a.74.1.2 (A:113-207) Transcription factor IIB (TFI 4e-29
d1vola195 a.74.1.2 (A:113-207) Transcription factor IIB (TFI 9e-19
d1aisb198 a.74.1.2 (B:1108-1205) Transcription factor IIB (T 1e-27
d1aisb198 a.74.1.2 (B:1108-1205) Transcription factor IIB (T 7e-21
d1aisb295 a.74.1.2 (B:1206-1300) Transcription factor IIB (T 6e-26
d1aisb295 a.74.1.2 (B:1206-1300) Transcription factor IIB (T 8e-23
d1dl6a_58 g.41.3.1 (A:) Transcription initiation factor TFII 2e-19
d1pfta_50 g.41.3.1 (A:) Transcription initiation factor TFII 2e-13
d1f5qb1141 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesviru 1e-06
d2ivxa1143 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) 3e-05
d2r7ga2142 a.74.1.3 (A:644-785) Retinoblastoma tumor suppress 6e-05
d2i53a1144 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) 7e-05
d1jkwa1151 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo s 9e-05
d1bu2a1127 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saim 2e-04
d1g3nc1132 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma 2e-04
d2cchb1128 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [T 5e-04
d1w98b2140 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human 0.001
>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Length = 109 Back     information, alignment and structure

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  131 bits (330), Expect = 5e-39
 Identities = 89/109 (81%), Positives = 98/109 (89%)

Query: 201 LITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSD 260
           LITTGDFMSRFCSNL LP  VQ AATHIARKAVELD+VPGRSPISVAAAAIYMASQAS++
Sbjct: 1   LITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAE 60

Query: 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPIHELPQL 309
           KR+QKEIGDIAGVA+VTIRQSY+L+YP A  LFP DF F TP+ +LPQL
Sbjct: 61  KRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPVDKLPQL 109
>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Length = 109 Back     information, alignment and structure
>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Length = 95 Back     information, alignment and structure
>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Length = 95 Back     information, alignment and structure
>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 98 Back     information, alignment and structure
>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 98 Back     information, alignment and structure
>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 95 Back     information, alignment and structure
>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 95 Back     information, alignment and structure
>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 58 Back     information, alignment and structure
>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 50 Back     information, alignment and structure
>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Length = 141 Back     information, alignment and structure
>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Length = 143 Back     information, alignment and structure
>d2r7ga2 a.74.1.3 (A:644-785) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]} Length = 142 Back     information, alignment and structure
>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Length = 144 Back     information, alignment and structure
>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Length = 151 Back     information, alignment and structure
>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} Length = 127 Back     information, alignment and structure
>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]} Length = 132 Back     information, alignment and structure
>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Length = 128 Back     information, alignment and structure
>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]} Length = 140 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query309
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 99.94
d1aisb295 Transcription factor IIB (TFIIB), core domain {Arc 99.88
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 99.87
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 99.86
d1pfta_50 Transcription initiation factor TFIIB, N-terminal 99.8
d1dl6a_58 Transcription initiation factor TFIIB, N-terminal 99.8
d1aisb295 Transcription factor IIB (TFIIB), core domain {Arc 99.79
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 99.76
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 99.75
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 99.74
d2ivxa1143 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 98.94
d2i53a1144 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 98.91
d1jkwa1151 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 98.73
d2ivxa2113 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 98.35
d1bu2a1127 Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} 98.34
d1g3nc1132 Viral cyclin {Kaposi's sarcoma-associated herpesvi 98.31
d2cchb1128 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 98.31
d1w98b2140 G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax 98.18
d2i53a2110 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 98.13
d1f5qb1141 Viral cyclin {Murine herpesvirus 68 [TaxId: 33708] 98.1
d2cchb2124 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 97.53
d2i53a1144 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 97.52
d2ivxa1143 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 97.51
d1jkwa1151 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 97.29
d1qxfa_58 Ribosomal protein S27e {Archaeon Archaeoglobus ful 96.86
d2r7ga2142 Retinoblastoma tumor suppressor domains {Human (Ho 96.83
d2ivxa2113 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 96.63
d2akla238 Hypothetical protein PA0128, N-terminal domain {Ps 96.3
d2cchb1128 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 95.92
d1bu2a1127 Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} 95.78
d2jnya159 Uncharacterized protein Cgl1405/cg1592 {Corynebact 95.73
d1f5qb1141 Viral cyclin {Murine herpesvirus 68 [TaxId: 33708] 95.71
d2i53a2110 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 95.71
d2pk7a159 Uncharacterized protein PFL1779 {Pseudomonas fluor 95.58
d2hf1a159 Hypothetical protein CV3345 {Chromobacterium viola 95.29
d1g3nc1132 Viral cyclin {Kaposi's sarcoma-associated herpesvi 95.1
d2r7ga2142 Retinoblastoma tumor suppressor domains {Human (Ho 94.96
d1jkwa2126 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 94.57
d1w98b2140 G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax 94.33
d1nuia254 Zinc-binding domain of primase-helicase {Bacteriop 94.01
d1vd4a_62 Transcription initiation factor TFIIE-alpha {Human 93.19
d1i1ga160 LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]} 93.17
d2cfxa163 Transcriptional regulator LrpC {Bacillus subtilis 92.96
d1hw1a174 Fatty acid responsive transcription factor FadR, N 92.35
d1vqoz173 Ribosomal protein L37ae {Archaeon Haloarcula maris 92.16
d1jkwa2126 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 92.13
d2cyya160 Putative transcriptional regulator PH1519 {Archaeo 92.05
d2k4xa155 Ribosomal protein S27ae {Thermoplasma acidophilum 92.01
d1biaa163 Biotin repressor, N-terminal domain {Escherichia c 92.0
d3e5ua180 Chlorophenol reduction protein CprK {Desulfitobact 91.99
d2hsga157 Glucose-resistance amylase regulator CcpA, N-termi 91.83
d1neea237 Zinc-binding domain of translation initiation fact 91.76
d1j5ya165 Putative transcriptional regulator TM1602, N-termi 91.75
d2gaua181 Transcriptional regulator PG0396, C-terminal domai 91.69
d1efaa159 Lac repressor (LacR), N-terminal domain {Escherich 91.44
d1jj2y_73 Ribosomal protein L37ae {Archaeon Haloarcula maris 91.44
d2cg4a163 Regulatory protein AsnC {Escherichia coli [TaxId: 91.02
d1i5za169 Catabolite gene activator protein (CAP), C-termina 91.02
d1k81a_36 Zinc-binding domain of translation initiation fact 90.5
d2hs5a169 Putative transcriptional regulator RHA1_ro03477 {R 90.1
d1uxda_59 Fructose repressor (FruR), N-terminal domain {Esch 89.87
d1qpza157 Purine repressor (PurR), N-terminal domain {Escher 89.72
d3bwga178 Transcriptional regulator YydK {Bacillus subtilis 89.71
d1bl0a154 MarA {Escherichia coli [TaxId: 562]} 89.06
d2ev0a161 Manganese transport regulator MntR {Bacillus subti 88.55
d1pfva335 Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch 88.51
d1ft9a180 CO-sensing protein CooA, C-terminal domain {Rhodos 88.23
d1zyba173 Probable transcription regulator BT4300, C-termina 87.93
d1z05a171 Transcriptional regulator VC2007 N-terminal domain 87.75
d2isya163 Iron-dependent regulator IdeR {Mycobacterium tuber 87.42
d1l3la165 Quorum-sensing transcription factor TraR, C-termin 86.88
d1d5ya154 Rob transcription factor, N-terminal domain {Esche 86.74
d1rqga335 Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro 86.68
d1fsea_67 Germination protein GerE {Bacillus subtilis [TaxId 86.65
d2o3fa183 Putative transcriptional regulator YbbH {Bacillus 86.58
d2cchb2124 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 85.32
d1ku9a_151 DNA-binding protein Mj223 {Archaeon Methanococcus 84.61
d1rp3a271 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 84.6
d1y0ja139 Erythroid transcription factor GATA-1 {Mouse (Mus 84.44
d2j9ub147 Vacuolar protein-sorting-associated protein 36, VP 83.94
d1yioa170 Response regulatory protein StyR, C-terminal domai 83.89
d1jhfa171 LexA repressor, N-terminal DNA-binding domain {Esc 83.65
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 83.29
d3e5ua180 Chlorophenol reduction protein CprK {Desulfitobact 83.25
d2zcwa182 Transcriptional regulator TTHA1359, C-terminal dom 83.1
d1a04a167 Nitrate/nitrite response regulator (NarL) {Escheri 82.83
d2bgca1100 Listeriolysin regulatory protein PrfA, C-terminal 82.4
d1z0xa168 Transcriptional regulator EF0787 {Enterococcus fae 82.39
d1efaa159 Lac repressor (LacR), N-terminal domain {Escherich 82.09
d2vuti142 Erythroid transcription factor GATA-1 {Emericella 81.69
d2hoea162 N-acetylglucosamine kinase {Thermotoga maritima [T 81.56
d2ak3a237 Microbial and mitochondrial ADK, insert "zinc fing 81.43
d1twfi272 RBP9 subunit of RNA polymerase II {Baker's yeast ( 81.33
d1or7a168 SigmaE factor (RpoE) {Escherichia coli [TaxId: 562 81.18
d1zina235 Microbial and mitochondrial ADK, insert "zinc fing 81.14
d1s3ga235 Microbial and mitochondrial ADK, insert "zinc fing 81.01
d1z6ra170 Mlc protein N-terminal domain {Escherichia coli [T 80.8
d1ku9a_151 DNA-binding protein Mj223 {Archaeon Methanococcus 80.65
d1qypa_57 RBP9 subunit of RNA polymerase II {Archaeon Thermo 80.57
d2j015159 Ribosomal protein L32p {Thermus thermophilus [TaxI 80.29
d1dcqa2122 Pyk2-associated protein beta ARF-GAP domain {Mouse 80.1
d2ct7a173 Ring finger protein 31 {Human (Homo sapiens) [TaxI 80.05
d1akya238 Microbial and mitochondrial ADK, insert "zinc fing 80.03
>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=1.2e-26  Score=176.53  Aligned_cols=108  Identities=81%  Similarity=1.219  Sum_probs=105.1

Q ss_pred             CChHHHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHH
Q psy6534         202 ITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQS  281 (309)
Q Consensus       202 ~~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~  281 (309)
                      ++|.+||+|||++|+|++.+.+.|.++++.+.+.++..||+|.++||||||+||+.+|.+++++|||+++||++.||+++
T Consensus         2 i~~~d~i~Rf~s~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~iaAa~iY~a~r~~~~~~t~~eIa~~~~vs~~tI~k~   81 (109)
T d1vola2           2 ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQS   81 (109)
T ss_dssp             CCGGGTHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHHHTSSSCCCHHHHHHHHTCCHHHHHHH
T ss_pred             CCHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHH
Confidence            67999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcccCCCCcCCCCCCCCCCCC
Q psy6534         282 YKLMYPHASKLFPQDFVFHTPIHELPQL  309 (309)
Q Consensus       282 ~kei~~~~~~l~~~~~~~~~~~~~~~~~  309 (309)
                      ||+|.+++.+|+|.+|....++++||++
T Consensus        82 yk~l~~~~~~lip~~~~~~~~~~~lP~~  109 (109)
T d1vola2          82 YRLIYPRAPDLFPTDFKFDTPVDKLPQL  109 (109)
T ss_dssp             HHHHGGGHHHHSCSSCCCSSCGGGSCC-
T ss_pred             HHHHHHHHHHhCChhhcccCCHHHcCCC
Confidence            9999999999999999999999999986
>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Back     information, alignment and structure
>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Back     information, alignment and structure
>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Back     information, alignment and structure
>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Back     information, alignment and structure
>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ivxa2 a.74.1.1 (A:150-262) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} Back     information, alignment and structure
>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]} Back     information, alignment and structure
>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2i53a2 a.74.1.1 (A:158-267) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Back     information, alignment and structure
>d2cchb2 a.74.1.1 (B:309-432) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d2r7ga2 a.74.1.3 (A:644-785) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ivxa2 a.74.1.1 (A:150-262) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} Back     information, alignment and structure
>d2jnya1 b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg1592 {Corynebacterium glutamicum [TaxId: 1718]} Back     information, alignment and structure
>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Back     information, alignment and structure
>d2i53a2 a.74.1.1 (A:158-267) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2pk7a1 b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pseudomonas fluorescens [TaxId: 294]} Back     information, alignment and structure
>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]} Back     information, alignment and structure
>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]} Back     information, alignment and structure
>d2r7ga2 a.74.1.3 (A:644-785) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jkwa2 a.74.1.1 (A:162-287) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1nuia2 g.41.3.2 (A:10-63) Zinc-binding domain of primase-helicase {Bacteriophage T7 [TaxId: 10760]} Back     information, alignment and structure
>d1vd4a_ g.41.3.1 (A:) Transcription initiation factor TFIIE-alpha {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vqoz1 g.41.8.1 (Z:10-82) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure
>d1jkwa2 a.74.1.1 (A:162-287) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]} Back     information, alignment and structure
>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]} Back     information, alignment and structure
>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]} Back     information, alignment and structure
>d1neea2 g.59.1.1 (A:99-135) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]} Back     information, alignment and structure
>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1jj2y_ g.41.8.1 (Y:) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure
>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1k81a_ g.59.1.1 (A:) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]} Back     information, alignment and structure
>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1pfva3 g.41.1.1 (A:141-175) Methionyl-tRNA synthetase (MetRS), Zn-domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]} Back     information, alignment and structure
>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]} Back     information, alignment and structure
>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]} Back     information, alignment and structure
>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1rqga3 g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyrococcus abyssi [TaxId: 29292]} Back     information, alignment and structure
>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d2cchb2 a.74.1.1 (B:309-432) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1y0ja1 g.39.1.1 (A:200-238) Erythroid transcription factor GATA-1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2j9ub1 g.41.11.1 (B:115-161) Vacuolar protein-sorting-associated protein 36, VPS36 {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure
>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]} Back     information, alignment and structure
>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} Back     information, alignment and structure
>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]} Back     information, alignment and structure
>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]} Back     information, alignment and structure
>d1z0xa1 a.4.1.9 (A:4-71) Transcriptional regulator EF0787 {Enterococcus faecalis [TaxId: 1351]} Back     information, alignment and structure
>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2vuti1 g.39.1.1 (I:671-712) Erythroid transcription factor GATA-1 {Emericella nidulans [TaxId: 162425]} Back     information, alignment and structure
>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2ak3a2 g.41.2.1 (A:125-161) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]} Back     information, alignment and structure
>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1zina2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1s3ga2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus globisporus [TaxId: 1459]} Back     information, alignment and structure
>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]} Back     information, alignment and structure
>d2j0151 g.41.8.5 (5:2-60) Ribosomal protein L32p {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1dcqa2 g.45.1.1 (A:247-368) Pyk2-associated protein beta ARF-GAP domain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1akya2 g.41.2.1 (A:131-168) Microbial and mitochondrial ADK, insert "zinc finger" domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure