Citrus Sinensis ID: 046830

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-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------52
MMMEEERLEEDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQYIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENFE
cccccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHHHHHcHHHHHHHHcccEEEccccccccccEEEEcEEEEcccEEEcccccccccccHHHHHccccccccEEEEEEEEEEEccccccccccEEEccccccccccHHHHHHccccccccccEEEEcccEEEEEEEEcccccEEEEEEEcccccccEEEEEEEEcccccccccEEEEEEEccccccccccccEEEEEcccccccccHHHHHHHcccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHcccccccccccccccccccEEEcccccHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHcEEEccccccHHHHHHHHHHcccccc
cccccccccccccccccHHHHHHHHHHHHHHccHHHHHHccHHHHHHHHHHHHHHccccEEEcccccccccEEEEEEEEEEccccEEcccccccccccHHHHHHcccccccEEEEEEEEEEcccEEEccEEEEEEccEEEcccccHHHHHHccccccccccEEEEEccHHEEEEEHHccccEEEEEEccccccEEEEEEEEEEcccccccccEEEEEEEccccccccccccEEEEEcccccccccEEEEEEHcccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHcccccccccHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEEEEccHHHHHccHHEEccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHccccccHHHccccccccEcccccccccccHHHHHHHHHHEEccccccHHHHHHHHHccccccc
mmmeeerleedeeeetTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDesadieirpesqhnpgqqsdfaeiylskpmmtesdGETATLFLKAARLRNltysaplyvDVTKRVikkghdgeevpIMLRSSYCTLYQNSQKALTelgecpydeggyfiiNGSEKVLIAQEKMSTnhvyvfkkrqpnkYAYVAEVCsmaesqnrppstifvpmlsrtsakggssgqyihatlpyirteIPIIILFRalgftadeDILEHICYDFQDTQMMELLRPSLEEAFFIQNQqyigkrgatvgVTREKMIKYAKEILQkemlphvgtgdfcetkkaYYFGHIIHRLLLCALgrraeddrdhygnkrldlagpllgGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITgglkyslatgnwgqgnaagtrAGVSQVLNCLTYASTFTYYLSWklakprqlhnsqwgmmcpaetpegqacglVKNLALMVYITIGSAAYPILEFLEewgtenfe
mmmeeerleedeeeettqeEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRpesqhnpgqqsDFAEIYLSKPMMTESDGETATLFLKAARLRNltysaplyvdvTKRVikkghdgeevpIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQyigkrgatvgvTREKMIKYAKEilqkemlphVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGnkrldlagpllgGLFRTLFRKLTGDVRSYVQKCvdngkdvnlQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENFE
MMMeeerleedeeeettqeeAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQYIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENFE
********************AWAVISAYFEEKGLVRQQLDSF**************************************************TATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSM***********FV*************GQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQYIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWG*****
***************TTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMA*********IFVP**********SSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQYIG***************YAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENF*
*******************EAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQYIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENFE
********EEDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQYIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTE***
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xxxxxxxxxxxxxxxxxxxxxWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQYIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENFE
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 ?
Query518 2.2.26 [Sep-21-2011]
Q42877 1191 DNA-directed RNA polymera N/A no 0.982 0.427 0.858 0.0
P38420 1188 DNA-directed RNA polymera yes no 0.994 0.433 0.838 0.0
Q54J75 1170 DNA-directed RNA polymera yes no 0.984 0.435 0.595 0.0
Q8CFI7 1174 DNA-directed RNA polymera yes no 0.992 0.437 0.6 0.0
P30876 1174 DNA-directed RNA polymera yes no 0.992 0.437 0.6 0.0
P08266 1176 DNA-directed RNA polymera yes no 0.971 0.427 0.604 1e-179
Q02061 1210 DNA-directed RNA polymera yes no 0.969 0.414 0.546 1e-172
Q10578 1193 DNA-directed RNA polymera yes no 0.994 0.431 0.570 1e-171
A5DHT2 1236 DNA-directed RNA polymera N/A no 0.976 0.409 0.518 1e-159
Q8SR75 1141 DNA-directed RNA polymera yes no 0.955 0.433 0.514 1e-157
>sp|Q42877|RPB2_SOLLC DNA-directed RNA polymerase II subunit RPB2 OS=Solanum lycopersicum GN=RPB2 PE=2 SV=1 Back     alignment and function desciption
 Score =  947 bits (2447), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 467/544 (85%), Positives = 484/544 (88%), Gaps = 35/544 (6%)

Query: 10  EDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHN 69
           +D+EEE TQE+AWAVISAYFEEKGLVRQQLDSFDEF QNTMQEIVDESADIEIRPESQHN
Sbjct: 14  DDDEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHN 73

Query: 70  PGQQSDFAE---------IYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRV 120
           PG QSDFAE         IYLSKPMMTESDGETATLF KAARLRNLTYSAPLYVDVTKRV
Sbjct: 74  PGHQSDFAETIYKINFGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRV 133

Query: 121 IKKGHDGEEV--------------PIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIIN 166
           IKKGHDGEEV              PIMLRSSYCTLYQNS+K LTELGECP D+GGYFIIN
Sbjct: 134 IKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPLDQGGYFIIN 193

Query: 167 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKG 226
           GSEKVLIAQEKMSTNHVYVFKKRQPNKYA+VAEV SMA++QNRPPST+FV MLSRTSAKG
Sbjct: 194 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAFVAEVRSMADTQNRPPSTMFVRMLSRTSAKG 253

Query: 227 GSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAF 286
           GSSGQYI ATLPYIRTEIPIII+FRALGF AD+DILEHICYDF DTQMMELLRPSLEEAF
Sbjct: 254 GSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFNDTQMMELLRPSLEEAF 313

Query: 287 FIQNQQ----YIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHII 342
            IQNQQ    YIGKRGATVGVTREK IKYAKEILQKEMLPHVG G++CETKKAYYFG+II
Sbjct: 314 VIQNQQVALDYIGKRGATVGVTREKRIKYAKEILQKEMLPHVGVGEYCETKKAYYFGYII 373

Query: 343 HRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDV 402
           HRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFR LFRKLT DVR YVQKCVDNGKDV
Sbjct: 374 HRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDV 433

Query: 403 NLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSW----- 457
           NLQFAIKAKTIT GLKYSLATGNWGQ NAAGTRAGVSQVLN LTYAST ++         
Sbjct: 434 NLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIG 493

Query: 458 ---KLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGT 514
              KLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT+GSAAYPILEFLEEWGT
Sbjct: 494 REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGT 553

Query: 515 ENFE 518
           ENFE
Sbjct: 554 ENFE 557
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template.
Solanum lycopersicum (taxid: 4081)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6
>sp|P38420|RPB2_ARATH DNA-directed RNA polymerase II subunit RPB2 OS=Arabidopsis thaliana GN=RPB135 PE=2 SV=2 Back     alignment and function description
>sp|Q54J75|RPB2_DICDI DNA-directed RNA polymerase II subunit rpb2 OS=Dictyostelium discoideum GN=polr2b PE=3 SV=1 Back     alignment and function description
>sp|Q8CFI7|RPB2_MOUSE DNA-directed RNA polymerase II subunit RPB2 OS=Mus musculus GN=Polr2b PE=2 SV=2 Back     alignment and function description
>sp|P30876|RPB2_HUMAN DNA-directed RNA polymerase II subunit RPB2 OS=Homo sapiens GN=POLR2B PE=1 SV=1 Back     alignment and function description
>sp|P08266|RPB2_DROME DNA-directed RNA polymerase II subunit RPB2 OS=Drosophila melanogaster GN=RpII140 PE=2 SV=2 Back     alignment and function description
>sp|Q02061|RPB2_SCHPO DNA-directed RNA polymerase II subunit RPB2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb2 PE=1 SV=2 Back     alignment and function description
>sp|Q10578|RPB2_CAEEL DNA-directed RNA polymerase II subunit RPB2 OS=Caenorhabditis elegans GN=rpb-2 PE=2 SV=2 Back     alignment and function description
>sp|A5DHT2|RPB2_PICGU DNA-directed RNA polymerase II subunit RPB2 OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=RPB2 PE=3 SV=3 Back     alignment and function description
>sp|Q8SR75|RPB2_ENCCU DNA-directed RNA polymerase II subunit RPB2 OS=Encephalitozoon cuniculi (strain GB-M1) GN=RPB2 PE=3 SV=1 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 ?
Query518
350534526 1191 DNA-directed RNA polymerase II subunit R 0.982 0.427 0.858 0.0
449433841 1199 PREDICTED: DNA-directed RNA polymerase I 0.980 0.423 0.858 0.0
224077110 690 predicted protein [Populus trichocarpa] 0.969 0.727 0.856 0.0
70794966 1191 RNA polymerase II second largest subunit 0.969 0.421 0.867 0.0
255556051 1194 DNA-directed RNA polymerase II subunit, 0.961 0.417 0.870 0.0
297799890 1188 hypothetical protein ARALYDRAFT_492703 [ 0.994 0.433 0.84 0.0
15234572 1188 DNA-directed RNA polymerase II subunit R 0.994 0.433 0.838 0.0
68300812 1195 RNA polymerase II second largest subunit 0.969 0.420 0.864 0.0
356558375 1193 PREDICTED: DNA-directed RNA polymerase I 0.961 0.417 0.861 0.0
356530409 1192 PREDICTED: DNA-directed RNA polymerase I 0.961 0.417 0.863 0.0
>gi|350534526|ref|NP_001233889.1| DNA-directed RNA polymerase II subunit RPB2 [Solanum lycopersicum] gi|11134656|sp|Q42877.1|RPB2_SOLLC RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA polymerase II subunit 2; Short=RNA polymerase II subunit B2; AltName: Full=DNA-directed RNA polymerase II 135 kDa polypeptide gi|1049068|gb|AAC49273.1| RNA polymerase II subunit 2 [Solanum lycopersicum] Back     alignment and taxonomy information
 Score =  947 bits (2447), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 467/544 (85%), Positives = 484/544 (88%), Gaps = 35/544 (6%)

Query: 10  EDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHN 69
           +D+EEE TQE+AWAVISAYFEEKGLVRQQLDSFDEF QNTMQEIVDESADIEIRPESQHN
Sbjct: 14  DDDEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHN 73

Query: 70  PGQQSDFAE---------IYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRV 120
           PG QSDFAE         IYLSKPMMTESDGETATLF KAARLRNLTYSAPLYVDVTKRV
Sbjct: 74  PGHQSDFAETIYKINFGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRV 133

Query: 121 IKKGHDGEEV--------------PIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIIN 166
           IKKGHDGEEV              PIMLRSSYCTLYQNS+K LTELGECP D+GGYFIIN
Sbjct: 134 IKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPLDQGGYFIIN 193

Query: 167 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKG 226
           GSEKVLIAQEKMSTNHVYVFKKRQPNKYA+VAEV SMA++QNRPPST+FV MLSRTSAKG
Sbjct: 194 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAFVAEVRSMADTQNRPPSTMFVRMLSRTSAKG 253

Query: 227 GSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAF 286
           GSSGQYI ATLPYIRTEIPIII+FRALGF AD+DILEHICYDF DTQMMELLRPSLEEAF
Sbjct: 254 GSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFNDTQMMELLRPSLEEAF 313

Query: 287 FIQNQQ----YIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHII 342
            IQNQQ    YIGKRGATVGVTREK IKYAKEILQKEMLPHVG G++CETKKAYYFG+II
Sbjct: 314 VIQNQQVALDYIGKRGATVGVTREKRIKYAKEILQKEMLPHVGVGEYCETKKAYYFGYII 373

Query: 343 HRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDV 402
           HRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFR LFRKLT DVR YVQKCVDNGKDV
Sbjct: 374 HRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDV 433

Query: 403 NLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSW----- 457
           NLQFAIKAKTIT GLKYSLATGNWGQ NAAGTRAGVSQVLN LTYAST ++         
Sbjct: 434 NLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIG 493

Query: 458 ---KLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGT 514
              KLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT+GSAAYPILEFLEEWGT
Sbjct: 494 REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGT 553

Query: 515 ENFE 518
           ENFE
Sbjct: 554 ENFE 557

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449433841|ref|XP_004134705.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like [Cucumis sativus] gi|449479313|ref|XP_004155566.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|224077110|ref|XP_002305136.1| predicted protein [Populus trichocarpa] gi|222848100|gb|EEE85647.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|70794966|gb|AAZ08457.1| RNA polymerase II second largest subunit [Rhododendron macrophyllum] Back     alignment and taxonomy information
>gi|255556051|ref|XP_002519060.1| DNA-directed RNA polymerase II subunit, putative [Ricinus communis] gi|223541723|gb|EEF43271.1| DNA-directed RNA polymerase II subunit, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|297799890|ref|XP_002867829.1| hypothetical protein ARALYDRAFT_492703 [Arabidopsis lyrata subsp. lyrata] gi|297313665|gb|EFH44088.1| hypothetical protein ARALYDRAFT_492703 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|15234572|ref|NP_193902.1| DNA-directed RNA polymerase II subunit RPB2 [Arabidopsis thaliana] gi|21542437|sp|P38420.2|RPB2_ARATH RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA polymerase II subunit 2; Short=RNA polymerase II subunit B2; AltName: Full=DNA-directed RNA polymerase II 135 kDa polypeptide; AltName: Full=Protein EMBRYO DEFECTIVE 1989 gi|4455279|emb|CAB36815.1| DNA-directed RNA polymerase (EC 2.7.7.6) II second largest chain [Arabidopsis thaliana] gi|7268968|emb|CAB81278.1| DNA-directed RNA polymerase (EC 2.7.7.6) II second largest chain [Arabidopsis thaliana] gi|332659093|gb|AEE84493.1| DNA-directed RNA polymerase II subunit RPB2 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|68300812|gb|AAY89347.1| RNA polymerase II second largest subunit [Petunia x hybrida] Back     alignment and taxonomy information
>gi|356558375|ref|XP_003547482.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like [Glycine max] Back     alignment and taxonomy information
>gi|356530409|ref|XP_003533774.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like [Glycine max] 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 ?
Query518
TAIR|locus:2119013 1188 NRPB2 [Arabidopsis thaliana (t 0.855 0.372 0.848 5.8e-208
DICTYBASE|DDB_G0288257 1170 rpb2 "RNA polymerase II core s 0.843 0.373 0.604 1.1e-176
POMBASE|SPAC23G3.01 1210 rpb2 "RNA polymerase II comple 0.747 0.319 0.585 4.5e-152
UNIPROTKB|F1NCB0 1174 POLR2B "DNA-directed RNA polym 0.874 0.385 0.617 3.5e-146
UNIPROTKB|A5PJW8 1174 POLR2B "DNA-directed RNA polym 0.874 0.385 0.615 9.3e-146
UNIPROTKB|E2RNN5 1174 POLR2B "DNA-directed RNA polym 0.874 0.385 0.615 9.3e-146
UNIPROTKB|C9J2Y9 1167 POLR2B "DNA-directed RNA polym 0.874 0.388 0.615 9.3e-146
UNIPROTKB|P30876 1174 POLR2B "DNA-directed RNA polym 0.874 0.385 0.615 9.3e-146
UNIPROTKB|I3LGP4 1167 POLR2B "DNA-directed RNA polym 0.874 0.388 0.615 9.3e-146
MGI|MGI:2388280 1174 Polr2b "polymerase (RNA) II (D 0.874 0.385 0.615 9.3e-146
TAIR|locus:2119013 NRPB2 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 2011 (713.0 bits), Expect = 5.8e-208, P = 5.8e-208
 Identities = 398/469 (84%), Positives = 416/469 (88%)

Query:    76 FAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEV----- 130
             F +IYLSKPMMTESDGETATLF KAARLRNLTYSAPLYVDVTKRVIKKGHDGEEV     
Sbjct:    90 FGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQD 149

Query:   131 ---------PIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTN 181
                      PIMLRSSYCTL+QNS+K LTELGECPYD+GGYFIINGSEKVLIAQEKMSTN
Sbjct:   150 FTKVFIGKVPIMLRSSYCTLFQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTN 209

Query:   182 HVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIR 241
             HVYVFKKRQPNKYAYV EV SMAE+QNRPPST+FV ML+R SAKGGSSGQYI  TLPYIR
Sbjct:   210 HVYVFKKRQPNKYAYVGEVRSMAENQNRPPSTMFVRMLARASAKGGSSGQYIRCTLPYIR 269

Query:   242 TEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQ----QYIGKR 297
             TEIPIII+FRALGF AD+DILEHICYDF DTQMMELLRPSLEEAF IQNQ     YIGKR
Sbjct:   270 TEIPIIIVFRALGFVADKDILEHICYDFADTQMMELLRPSLEEAFVIQNQLVALDYIGKR 329

Query:   298 GATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDD 357
             GATVGVT+EK IKYA++ILQKEMLPHVG G+ CETKKAYYFG+IIHRLLLCALGRR EDD
Sbjct:   330 GATVGVTKEKRIKYARDILQKEMLPHVGIGEHCETKKAYYFGYIIHRLLLCALGRRPEDD 389

Query:   358 RDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGL 417
             RDHYGNKRLDLAGPLLGGLFR LFRKLT DVRSYVQKCVDNGK+VNLQFAIKAKTIT GL
Sbjct:   390 RDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKEVNLQFAIKAKTITSGL 449

Query:   418 KYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYL--------SWKLAKPRQLHNSQ 469
             KYSLATGNWGQ NAAGTRAGVSQVLN LTYAST ++            KLAKPRQLHNSQ
Sbjct:   450 KYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQ 509

Query:   470 WGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENFE 518
             WGMMCPAETPEGQACGLVKNLALMVYIT+GSAAYPILEFLEEWGTENFE
Sbjct:   510 WGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFE 558
GO:0003677 "DNA binding" evidence=IEA;ISS
GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS
GO:0009793 "embryo development ending in seed dormancy" evidence=NAS
GO:0032549 "ribonucleoside binding" evidence=IEA
GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=ISS
GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IPI
GO:0005829 "cytosol" evidence=IDA
GO:0009506 "plasmodesma" evidence=IDA
GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA
GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA
GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA
DICTYBASE|DDB_G0288257 rpb2 "RNA polymerase II core subunit" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
POMBASE|SPAC23G3.01 rpb2 "RNA polymerase II complex subunit Rpb2" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
UNIPROTKB|F1NCB0 POLR2B "DNA-directed RNA polymerase" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|A5PJW8 POLR2B "DNA-directed RNA polymerase" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RNN5 POLR2B "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|C9J2Y9 POLR2B "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|P30876 POLR2B "DNA-directed RNA polymerase II subunit RPB2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|I3LGP4 POLR2B "DNA-directed RNA polymerase" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:2388280 Polr2b "polymerase (RNA) II (DNA directed) polypeptide B" [Mus musculus (taxid:10090)] 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) ?
B0R8D6RPOB2_HALS32, ., 7, ., 7, ., 60.30290.86480.8565yesno
Q58444RPOB2_METJA2, ., 7, ., 7, ., 60.33330.89760.9337yesno
P38420RPB2_ARATH2, ., 7, ., 7, ., 60.83810.99420.4335yesno
P0CX04RPOB2_HALSA2, ., 7, ., 7, ., 60.30290.86480.8565yesno
P41558RPOB2_METVS2, ., 7, ., 7, ., 60.33260.90150.9358yesno
O27123RPOB2_METTH2, ., 7, ., 7, ., 60.32640.91310.9113yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.70.766
4th Layer2.7.7.60.824

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query518
pfam04563394 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta sub 1e-144
PRK08565 1103 PRK08565, PRK08565, DNA-directed RNA polymerase su 1e-138
PRK09606494 PRK09606, PRK09606, DNA-directed RNA polymerase su 1e-122
COG0085 1060 COG0085, RpoB, DNA-directed RNA polymerase, beta s 1e-108
cd00653 866 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun 3e-61
pfam04561185 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, do 6e-54
cd00653 866 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun 8e-53
pfam0456568 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, do 1e-17
TIGR02013 1065 TIGR02013, rpoB, DNA-directed RNA polymerase, beta 5e-12
CHL00207 1077 CHL00207, rpoB, RNA polymerase beta subunit; Provi 2e-09
PRK00405 1112 PRK00405, rpoB, DNA-directed RNA polymerase subuni 2e-08
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 4e-06
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 7e-05
CHL00001 1070 CHL00001, rpoB, RNA polymerase beta subunit 2e-04
PRK00405 1112 PRK00405, rpoB, DNA-directed RNA polymerase subuni 0.001
CHL00001 1070 CHL00001, rpoB, RNA polymerase beta subunit 0.004
>gnl|CDD|191028 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta subunit Back     alignment and domain information 
 Score =  419 bits (1080), Expect = e-144
 Identities = 164/402 (40%), Positives = 211/402 (52%), Gaps = 18/402 (4%)

Query: 33  GLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGE 92
           GLV QQLDSF+ F    +QE +DE   IE   E    P       +I L+KP + ESDG+
Sbjct: 1   GLVEQQLDSFNWFLDEGLQEEIDEFPPIEDEDE---EPEFSLKVGQIKLAKPKIKESDGK 57

Query: 93  TATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEE------VPIMLRSSYCTLYQNSQ 146
           T  ++ + ARLRNLTYS+PLYV     V       +E      +P+MLRS+ C L   S+
Sbjct: 58  TREIYPREARLRNLTYSSPLYVPAELTVNNTEEIEKEKVFIGKIPLMLRSNACILNGASE 117

Query: 147 KALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAES 206
             L +LGECP D GGYFI+NGSEKV+I Q + S N  YVFKK +     Y A + S    
Sbjct: 118 SELVKLGECPLDPGGYFIVNGSEKVIINQIQRSPNIYYVFKKDKNGIRIYSASIISNRGR 177

Query: 207 QNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHIC 266
             R   T    + +R ++        +   L     EI + +L   +     +DI  +  
Sbjct: 178 SLRLEITSKGKIYARINSGAKLIMFVLLLALGLNLVEIILNLLVPEVDLEIQDDIGINDE 237

Query: 267 YDFQDTQMMELLRPSLEEAFFIQNQQ----YIGKRGATVGVTREKMIKYAKEILQKEMLP 322
            D   T      +P LEE F IQ Q     YIG RG+  G  RE+ I  A  IL   +LP
Sbjct: 238 EDEFLTD-----KPELEEQFVIQTQDEALDYIGGRGSAKGFPRERRILGAVGILDLNLLP 292

Query: 323 HVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFR 382
           H+G  +   T KA   G++IHRLLL ALGR   DD DH GNKRL LAG LL   FR L  
Sbjct: 293 HLGVSENTRTLKAQDIGYMIHRLLLLALGRGPLDDIDHLGNKRLRLAGELLQSQFRILLN 352

Query: 383 KLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATG 424
           +L  DVR  +QKC+    D  LQ  + +K IT G++Y L TG
Sbjct: 353 RLERDVRERIQKCLKKKFDFTLQNLVNSKPITSGIRYFLGTG 394

RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain. Length = 394
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional Back     alignment and domain information
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B''; Validated Back     alignment and domain information
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|218151 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, domain 2 Back     alignment and domain information
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|146955 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, domain 3 Back     alignment and domain information
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit Back     alignment and domain information
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional Back     alignment and domain information
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed Back     alignment and domain information
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed Back     alignment and domain information
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 518
PRK09606494 DNA-directed RNA polymerase subunit B''; Validated 100.0
KOG0214 1141 consensus RNA polymerase II, second largest subuni 100.0
PRK08565 1103 DNA-directed RNA polymerase subunit B; Provisional 100.0
KOG0216 1111 consensus RNA polymerase I, second largest subunit 100.0
COG0085 1060 RpoB DNA-directed RNA polymerase, beta subunit/140 100.0
CHL00001 1070 rpoB RNA polymerase beta subunit 100.0
TIGR02013 1065 rpoB DNA-directed RNA polymerase, beta subunit. Th 100.0
PRK00405 1112 rpoB DNA-directed RNA polymerase subunit beta; Rev 100.0
cd00653 866 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po 100.0
CHL00207 1077 rpoB RNA polymerase beta subunit; Provisional 100.0
KOG0215 1153 consensus RNA polymerase III, second largest subun 100.0
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 100.0
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 100.0
PF04563203 RNA_pol_Rpb2_1: RNA polymerase beta subunit; Inter 100.0
PF0456568 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; Int 99.93
PF04561190 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; Int 99.81
KOG0215 1153 consensus RNA polymerase III, second largest subun 97.43
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated Back     alignment and domain information 
Probab=100.00  E-value=6.1e-111  Score=905.45  Aligned_cols=474  Identities=39%  Similarity=0.642  Sum_probs=413.1

Q ss_pred             HHHHHHhhhcccCCcchhHHHHHHHHHHHHhHHHHHHhhcCCeeecCCCCCCCCceEEEEEEEEecCcccCCCCcccccC
Q 046830           18 QEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLF   97 (518)
Q Consensus        18 ~~~~~~~i~~~f~~~~lv~~qi~SFn~Fi~~gl~~i~~~~~pi~~~~~~~~~~~~~i~f~~~~i~~P~~~~~~~~~~~l~   97 (518)
                      +++.|.++++||+.++|++|||+|||+|+++||++++++.+||++..    .....++|.++++++|.+.+.++...+++
T Consensus         2 ~~~~~~~i~~~~~~~~lv~~qi~SFn~Fi~~gl~~ii~~~~~i~~~~----~~~~~l~~~~~~l~~P~~~~~~~~~~~l~   77 (494)
T PRK09606          2 MEDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEI----EDGVYVELGKIRVGKPVVKEADGSEREIY   77 (494)
T ss_pred             chHHHHHHHHHHCCCChHHHHHHHHHHHHHHhHHHHHHhcCCEEEec----CCcEEEEEEEEEECCCcccccCCccccCC
Confidence            35789999999999999999999999999999999999999998642    23457889999999999887766678999


Q ss_pred             HHHHHhcCCCcceeEEEEEEEEEeec-----CcccceeeeeeeecccccCCCCHHHHHHhCCccCCCCceEEEeCceeEE
Q 046830           98 LKAARLRNLTYSAPLYVDVTKRVIKK-----GHDGEEVPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVL  172 (518)
Q Consensus        98 P~ecR~r~~TYs~~l~v~v~~~~~~~-----~~~~~~iPIMv~S~~C~L~~~~~~e~i~~gE~p~d~GGYFIING~ErVi  172 (518)
                      |+|||++++||+|+++|++.+...+.     ....|+|||||+|++|||++++++|++..||||.|+||||||||+||||
T Consensus        78 P~eaR~r~~TYs~~l~v~i~~~~~~~~~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d~GGyFIING~ErVi  157 (494)
T PRK09606         78 PMEARLRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVL  157 (494)
T ss_pred             HHHHHhcCCCccceEEEEEEEEECCCceEEeeEEeccCCeEeccCcccCCCCCHHHHHhcCCCcCCCCCeEEECCCeEEE
Confidence            99999999999999999999864321     1345789999999999999999999999999999999999999999999


Q ss_pred             EEeeecccCceEEEeecCCCceeEEEEEEeecCCCCCCCceEEEEEEecCCCCCCCCCceEEEEeccccccchhhhHHHh
Q 046830          173 IAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRA  252 (518)
Q Consensus       173 i~q~~~s~n~~~~~~~~~~~~~~~~~~i~s~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~IPl~illrA  252 (518)
                      ++|++++||+|++++++..+...|.++++|.+++|   .....+++..         ++.+++++++.+.+||+++||||
T Consensus       158 ~~q~~~~~n~~~~~~~~~~~~~~~~~~i~s~~~~~---~~~~~l~~~~---------~g~i~~~~~~~~~~iPi~~llkA  225 (494)
T PRK09606        158 MTLEDLAPNKILVEKDERYGDRIEVAKVFSQRRGY---RALVTVERNR---------DGLLEVSFPSVPGSIPFVILMRA  225 (494)
T ss_pred             EEEEeccCCeeEEEeccCCCccceEEEEEcccccc---eeeEEEEEec---------CCeEEEEEcCccccccHHHHHHH
Confidence            99999999999998765444446899999999876   2334577764         47799999976679999999999


Q ss_pred             cCCCCHHHHHHHhhhcCCcHHHHHHhhhhHHHHhcccccc----eeeecCccccccchhhHHHHHHHHHhccCCCCCCCC
Q 046830          253 LGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQ----YIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGD  328 (518)
Q Consensus       253 Lg~~sd~eI~~~i~~~~~~~~~~~~L~~~~~~~~~~~~~~----~ig~~~~~~~~~~~~~~~~~~~il~~~~l~hl~~~~  328 (518)
                      ||.+||+||++.+..   +..+.+++..++++.. ..+++    |||++++... .+....+.++++|++++|||+|.+.
T Consensus       226 Lg~~sd~eI~~~i~~---~~~~~~~l~~~~~~~~-~~t~~~al~~ig~~~~~~~-~~~~~~~~~~~~l~~~~l~hig~~~  300 (494)
T PRK09606        226 LGLETDEEIVEAVSD---DPEIVKFMLENLEEAE-VDTQEEALEYIGKRVAPGQ-TKEYRIKRAEYVIDRYLLPHLGVEP  300 (494)
T ss_pred             cCCCCHHHHHHHhCC---cHHHHHHHHHHHHhcc-cCCHHHHHHHHHHhcCCCC-CcchHHHHHHHHHHHhhhcccCCCc
Confidence            999999999999943   3445555555665542 33443    9999987633 3455668899999999999999765


Q ss_pred             cchhhHhhHHHHHHHHHHHhhcCCCCCCCCCcccceEEccccchhHHHHHHHHHHHHHHHHHHHHhhhcCCCCCcHHHhh
Q 046830          329 FCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAI  408 (518)
Q Consensus       329 ~~~~~K~~~L~~mi~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~~~f~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~i  408 (518)
                      .+..+|+++|++|++||+.++.|.+.+||+|||+||||+++|+||+.+||.+|+++++.++..+.+...+++.+++..++
T Consensus       301 ~~~~~K~~~L~~m~~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~~~fr~~l~~~~~~~k~~l~~~~~~~~~~~~~~~~  380 (494)
T PRK09606        301 EVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAV  380 (494)
T ss_pred             chhhHHHHHHHHHHHHHHHHhcCCCCCCCcccccCceeeccchhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHhc
Confidence            45568999999999999999999999999999999999999999999999999999999998887765555567888899


Q ss_pred             hhcchhHHHHHHhccCCCCCCCCCCccccceeeccccCccccccccc--------CCCCCCccccCCCCcccccccCCCC
Q 046830          409 KAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYL--------SWKLAKPRQLHNSQWGMMCPAETPE  480 (518)
Q Consensus       409 ~~~~it~~i~~~f~TGnw~~~~~~~~~sG~sq~ldr~N~l~~lSh~R--------~gk~t~vR~lhps~~G~iCPveTPE  480 (518)
                      +++.||++|++|||||||+++     ++|+||+|||+||+|+|||+|        .++.++||+||||||||+|||||||
T Consensus       381 ~~~~It~~l~~~~~TGnw~~~-----~~glSq~ldr~N~la~lSh~Rrv~s~~~r~~~~~~vR~lhps~~G~iCPveTPE  455 (494)
T PRK09606        381 RSDVLTERLEHAMATGNWVGG-----RTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPE  455 (494)
T ss_pred             CchhhhHHHHHHhhcccccCC-----CceEEEEccCCCHHHHhhHHHhccCCccccCccccccccCcccceecccCcCCC
Confidence            988999999999999999975     589999999999999999999        2356799999999999999999999


Q ss_pred             CccccccccccceEEEecCCChhhHHHHHHHcCCccc
Q 046830          481 GQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENF  517 (518)
Q Consensus       481 G~~cGLi~~La~~a~is~~~~~~~i~~~l~~~g~~~~  517 (518)
                      |+|||||+|||++|+|+++.+.+.|.++|.++||+++
T Consensus       456 G~~cGLv~~La~~a~V~~~~~~~~i~~~l~~lg~~~~  492 (494)
T PRK09606        456 GPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPE  492 (494)
T ss_pred             CCcccHHHhhhceEEEeCCCChHHHHHHHHHCcCeeC
Confidence            9999999999999999999888889999999999986

>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription] Back     alignment and domain information
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional Back     alignment and domain information
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription] Back     alignment and domain information
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>CHL00001 rpoB RNA polymerase beta subunit Back     alignment and domain information
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit Back     alignment and domain information
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed Back     alignment and domain information
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit Back     alignment and domain information
>CHL00207 rpoB RNA polymerase beta subunit; Provisional Back     alignment and domain information
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription] Back     alignment and domain information
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>PF04563 RNA_pol_Rpb2_1: RNA polymerase beta subunit; InterPro: IPR007644 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>PF04565 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; InterPro: IPR007645 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>PF04561 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; InterPro: IPR007642 RNA polymerases catalyse the DNA-dependent polymerisation of RNA Back     alignment and domain information
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription] 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 ?
Query518
3h0g_B 1210 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 1e-170
1i3q_B 1224 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 1e-154
2pmz_B 1124 Archaeal Rna Polymerase From Sulfolobus Solfataricu 1e-86
2waq_B 1131 The Complete Structure Of The Archaeal 13-Subunit D 1e-86
1i6v_C 1118 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 2e-08
1hqm_C 1119 Crystal Structure Of Thermus Aquaticus Core Rna Pol 2e-08
1l9u_C 1118 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 2e-08
1ynj_C 1119 Taq Rna Polymerase-Sorangicin Complex Length = 1119 2e-08
1iw7_C 1119 Crystal Structure Of The Rna Polymerase Holoenzyme 1e-07
3lu0_C 1342 Molecular Model Of Escherichia Coli Core Rna Polyme 2e-05
3iyd_C 1342 Three-Dimensional Em Structure Of An Intact Activat 2e-05
>pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1210 Back     alignment and structure 
Iteration: 1

 Score =  596 bits (1536), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 295/539 (54%), Positives = 378/539 (70%), Gaps = 45/539 (8%)
Query: 22  WAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQ-------QS 74
           W VIS++FEE  L RQQL SFDEF QNTMQEIVD+ + + +   +QH   Q       + 
Sbjct: 18  WTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEI 77
Query: 75  DFAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGE------ 128
           +F +IYLS+P MTE+DG T T+F + ARLRNLTYS+PLYVD+ K+V+             
Sbjct: 78  NFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEE 137
Query: 129 ----------------EVPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVL 172
                           ++PIMLRS++C L   S   L +L ECPYD+GGYFIINGSEKV+
Sbjct: 138 WLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVI 197
Query: 173 IAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQY 232
           IAQE+ + N V VFKK  P+  AYVAE+ S  E  +R  S++ + +++R +    +SGQ 
Sbjct: 198 IAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTE---NSGQT 254
Query: 233 IHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQ 292
           I ATLPYIR++IPI+I+FRALG   D DILEHICYD  D QM+E+++P +EEAF IQ++ 
Sbjct: 255 IRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVIQDKD 314
Query: 293 ----YIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLC 348
               YIGKRG+T GVTREK ++YA +ILQKE+LPH+ T +  ET+KA++ G++IHR+LLC
Sbjct: 315 IALDYIGKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLC 374
Query: 349 ALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAI 408
           AL RR  DDRDH+G KRLDLAGPLL  LFR LFRK+T DV  Y+QKCV+  ++ NL  A+
Sbjct: 375 ALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNREFNLTLAV 434
Query: 409 KAKTITGGLKYSLATGNWG-QGNAAGTRAGVSQVLNCLTYASTFTYY--------LSWKL 459
           K+  IT GL+YSLATGNWG Q  +   R GVSQVLN  T+AST ++            KL
Sbjct: 435 KSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNTPIGRDGKL 494
Query: 460 AKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENFE 518
           AKPRQLHN+ WGM+CPAETPEGQACGLVKNL+LM Y+++GS + PI+EFLEEWG E  E
Sbjct: 495 AKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLE 553
>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1224 Back     alignment and structure
>pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 1124 Back     alignment and structure
>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 1131 Back     alignment and structure
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1118 Back     alignment and structure
>pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase- Includes Complete Structure With Side-Chains (Except For Disordered Regions)-Further Refined From Original Deposition-Contains Additional Sequence Information Length = 1119 Back     alignment and structure
>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1118 Back     alignment and structure
>pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex Length = 1119 Back     alignment and structure
>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1119 Back     alignment and structure
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1342 Back     alignment and structure
>pdb|3IYD|C Chain C, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1342 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 ?
Query518
3h0g_B 1210 DNA-directed RNA polymerase II subunit RPB2; trans 0.0
1twf_B 1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 0.0
4ayb_B 1131 DNA-directed RNA polymerase; transferase, multi-su 0.0
2a6h_C 1119 DNA-directed RNA polymerase beta chain; RNA polyme 7e-13
2a6h_C 1119 DNA-directed RNA polymerase beta chain; RNA polyme 8e-04
3lu0_C 1342 DNA-directed RNA polymerase subunit beta; E. coli 7e-09
3lu0_C 1342 DNA-directed RNA polymerase subunit beta; E. coli 4e-08
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 9e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-05
3mlq_A188 DNA-directed RNA polymerase subunit beta; tudor, t 2e-05
3lvg_D190 LCB, clathrin light chain B; SELF assembly, coated 8e-04
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1210 Back     alignment and structure
 Score =  730 bits (1887), Expect = 0.0
 Identities = 299/552 (54%), Positives = 380/552 (68%), Gaps = 45/552 (8%)

Query: 9   EEDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQH 68
           +    E  TQE+ W VIS++FEE  L RQQL SFDEF QNTMQEIVD+ + + +   +QH
Sbjct: 5   DYQYNETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQH 64

Query: 69  NPGQQSD-------FAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVI 121
              Q          F +IYLS+P MTE+DG T T+F + ARLRNLTYS+PLYVD+ K+V+
Sbjct: 65  TGAQGDVTRRYEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVM 124

Query: 122 KKGHDGEE----------------------VPIMLRSSYCTLYQNSQKALTELGECPYDE 159
                                         +PIMLRS++C L   S   L +L ECPYD+
Sbjct: 125 VAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQ 184

Query: 160 GGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPML 219
           GGYFIINGSEKV+IAQE+ + N V VFKK  P+  AYVAE+ S  E  +R  S++ + ++
Sbjct: 185 GGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLM 244

Query: 220 SRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLR 279
           +R      +SGQ I ATLPYIR++IPI+I+FRALG   D DILEHICYD  D QM+E+++
Sbjct: 245 AR---NTENSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMK 301

Query: 280 PSLEEAFFIQNQ----QYIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKA 335
           P +EEAF IQ++     YIGKRG+T GVTREK ++YA +ILQKE+LPH+ T +  ET+KA
Sbjct: 302 PCIEEAFVIQDKDIALDYIGKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKA 361

Query: 336 YYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKC 395
           ++ G++IHR+LLCAL RR  DDRDH+G KRLDLAGPLL  LFR LFRK+T DV  Y+QKC
Sbjct: 362 FFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKC 421

Query: 396 VDNGKDVNLQFAIKAKTITGGLKYSLATGNWG-QGNAAGTRAGVSQVLNCLTYASTFTYY 454
           V+  ++ NL  A+K+  IT GL+YSLATGNWG Q  +   R GVSQVLN  T+AST ++ 
Sbjct: 422 VETNREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHL 481

Query: 455 L--------SWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPIL 506
                      KLAKPRQLHN+ WGM+CPAETPEGQACGLVKNL+LM Y+++GS + PI+
Sbjct: 482 RRTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPII 541

Query: 507 EFLEEWGTENFE 518
           EFLEEWG E  E
Sbjct: 542 EFLEEWGLETLE 553
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ... Length = 1224 Back     alignment and structure
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B Length = 1131 Back     alignment and structure
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Length = 1119 Back     alignment and structure
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Length = 1119 Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 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
>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
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus} Length = 188 Back     alignment and structure
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query518
3h0g_B 1210 DNA-directed RNA polymerase II subunit RPB2; trans 100.0
1twf_B 1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 100.0
4ayb_B 1131 DNA-directed RNA polymerase; transferase, multi-su 100.0
2a6h_C 1119 DNA-directed RNA polymerase beta chain; RNA polyme 100.0
3lu0_C 1342 DNA-directed RNA polymerase subunit beta; E. coli 100.0
3mlq_A188 DNA-directed RNA polymerase subunit beta; tudor, t 99.96
3lti_A296 DNA-directed RNA polymerase subunit beta; BBM2, nu 98.41
3mlq_A188 DNA-directed RNA polymerase subunit beta; tudor, t 97.82
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
Probab=100.00  E-value=1.9e-117  Score=1020.27  Aligned_cols=502  Identities=59%  Similarity=0.987  Sum_probs=447.2

Q ss_pred             cchhHHHHHHhhhcccCCcchhHHHHHHHHHHHHhHHHHHHhhcCCeeecCCCCC-------CCCceEEEEEEEEecCcc
Q 046830           14 EETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQH-------NPGQQSDFAEIYLSKPMM   86 (518)
Q Consensus        14 ~~~~~~~~~~~i~~~f~~~~lv~~qi~SFn~Fi~~gl~~i~~~~~pi~~~~~~~~-------~~~~~i~f~~~~i~~P~~   86 (518)
                      +++++++.|.++++||+.++||+|||+|||+|+++||++++++.++|+++.+.++       ...+.++|++++|++|.+
T Consensus        10 ~~~~~ed~w~li~aff~~~gLV~qHIdSFN~FI~~~Lq~IV~~~~~I~~~~~~~~~~~~~~~~~~~~l~f~~i~v~kP~~   89 (1210)
T 3h0g_B           10 ETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQIYLSRPTM   89 (1210)
T ss_dssp             CCCCHHHHHHHHHHHHHHTCTTCSSSSSSSSSTTTTHHHHSSTTCCCC-------------------CEEEEEECCCCCC
T ss_pred             ccCCHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhHHHHHhccCcEEecCccCcccccccCCceEEEEEEEEEEcCCce
Confidence            4588999999999999999999999999999999999999999999987653221       234678999999999999


Q ss_pred             cCCCCcccccCHHHHHhcCCCcceeEEEEEEEEEeec----------------------CcccceeeeeeeecccccCCC
Q 046830           87 TESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKK----------------------GHDGEEVPIMLRSSYCTLYQN  144 (518)
Q Consensus        87 ~~~~~~~~~l~P~ecR~r~~TYs~~l~v~v~~~~~~~----------------------~~~~~~iPIMv~S~~C~L~~~  144 (518)
                      .+.++..++|||+|||+|++||+|||+|+|++.+.+.                      ....|+|||||||++|||+++
T Consensus        90 ~e~d~~~~~l~P~EcRlR~lTYsapl~Vdi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IG~iPIMlrS~~C~L~g~  169 (1210)
T 3h0g_B           90 TEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGV  169 (1210)
T ss_dssp             BCTTSCBCCCCTTTTTTTCCCCEEEEEEEEEC---------------------CCSSCCCEEEEEEECCSSSTTSSSSSC
T ss_pred             ecCCCcccccCHHHHHhcCCccceeEEEEEEEEEcCccccccccccccccccccccccceEEEecCCEEeCCCcccCCCC
Confidence            9988889999999999999999999999999876531                      124578999999999999999


Q ss_pred             CHHHHHHhCCccCCCCceEEEeCceeEEEEeeecccCceEEEeecCCCceeEEEEEEeecCCCCCCCceEEEEEEecCCC
Q 046830          145 SQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSA  224 (518)
Q Consensus       145 ~~~e~i~~gE~p~d~GGYFIING~ErVii~q~~~s~n~~~~~~~~~~~~~~~~~~i~s~~~~~~~~~~~~~l~~~~~~~~  224 (518)
                      +++|++.+||||+|+||||||||+|||||+|+++|+|+|+++++++++++.|.|+|||++++.++.++.+++++..+.+.
T Consensus       170 s~~eL~~~gEcp~D~GGYFIING~EKVII~qerla~N~~iv~~~~~~~~~~~~a~irS~~~~~~~~~s~~~v~~~~~~~~  249 (1210)
T 3h0g_B          170 SDSELYDLNECPYDQGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTE  249 (1210)
T ss_dssp             CHHHHHHTTCCTTCCCCCBCGGGSCBCCCBCBCCCCSCCCCCCCCCSSSCCCCCCCCCCCCSSSCCCCCCCCCCCCCCTT
T ss_pred             CHHHHHhcCCCCCCCCCEEEEeCEEEEEEechhhccceEEEEeecCCCCceEEEEEEEEecCCccceeEEEEEEEecccc
Confidence            99999999999999999999999999999999999999999988888888999999999998765555556666542111


Q ss_pred             CCCCCCceEEEEeccccccchhhhHHHhcCCCCHHHHHHHhhhcCCcHHHHHHhhhhHHHHhcccccc----eeeecCcc
Q 046830          225 KGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQ----YIGKRGAT  300 (518)
Q Consensus       225 ~~~~~~~~i~~~~~~~~~~IPl~illrALg~~sd~eI~~~i~~~~~~~~~~~~L~~~~~~~~~~~~~~----~ig~~~~~  300 (518)
                         ..++.+.+++++++.+||++++|||||.+||+||++.|+++..|..+.++|+.+++++..+++++    |||++++.
T Consensus       250 ---~~~~~i~~~~~~~~~~IPi~ivlkALg~~sD~EI~~~I~~~~~d~~~~~~l~~slee~~~i~tq~~aL~yIG~r~~~  326 (1210)
T 3h0g_B          250 ---NSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVIQDKDIALDYIGKRGST  326 (1210)
T ss_dssp             ---SCSCCCCCCCTTSCSCCCSHHHHTTTTCCSTTHHHHHHCCSSCCHHHHHTHHHHHHTTSSCCSSHHHHHTTCCCSSS
T ss_pred             ---CCCceEEEEEeccccCCcHHHHHHHcCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHhhhcCCHHHHHHHHHHhccc
Confidence               12578899999999999999999999999999999999988888899999999999987667764    99999986


Q ss_pred             ccccchhhHHHHHHHHHhccCCCCCCCCcchhhHhhHHHHHHHHHHHhhcCCCCCCCCCcccceEEccccchhHHHHHHH
Q 046830          301 VGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTL  380 (518)
Q Consensus       301 ~~~~~~~~~~~~~~il~~~~l~hl~~~~~~~~~K~~~L~~mi~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~~~f~~~  380 (518)
                      ....+++++++|+++|++++|||++....++.+|+.||+||++||+.++.|.+.+||+|||+||||+++|+||+.+||+.
T Consensus       327 ~~~~~~~~~~~a~~iL~~~lLpHl~~~~~~~~~Ka~fL~~MvrkLl~~~~G~~~~Dd~D~~~nkrl~l~G~Ll~~lfr~~  406 (1210)
T 3h0g_B          327 TGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRML  406 (1210)
T ss_dssp             CCCCHHHHHHHHHHHHTTTSSCSSCCSSSCCSSHHHHHHHHHHHHHHHHTTSSCCCCTTCSSSCCBCCHHHHHHHHHHHH
T ss_pred             cCCCchhHHHHHHHHHHhhEEeCcCCCccchhHHHHHHHHHHHHHHHHhCCCCCCCCCccccCeEEecHHHHHHHHHHHH
Confidence            55567788899999999999999998877777999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhcCCCCCcHHHhhhhcchhHHHHHHhccCCCCCCCC-CCccccceeeccccCccccccccc----
Q 046830          381 FRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNA-AGTRAGVSQVLNCLTYASTFTYYL----  455 (518)
Q Consensus       381 l~~~~~~~~~~l~~~~~~~~~~~~~~~i~~~~it~~i~~~f~TGnw~~~~~-~~~~sG~sq~ldr~N~l~~lSh~R----  455 (518)
                      |+++++.+++.+++.+++++.+++..++++..||++|++|||||||+..+. .++++|+||+|+|+||+|+|||||    
T Consensus       407 ~~~~~~~i~~~l~k~~~~~~~~~~~~~i~~~~It~~l~~~laTGNW~~~kk~~~~~sGvsqvl~R~n~~s~lShlRrv~~  486 (1210)
T 3h0g_B          407 FRKMTRDVYKYMQKCVETNREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNT  486 (1210)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCSCCCTTSSCSTTTSHHHHHHHSSSCSSTTSSCCSCCCCSCCBCCCSSHHHHHHHTTBBCC
T ss_pred             HHHHHHHHHHHHHHHhhcCCccCHHHhcchhhhHHHHHHHhhcCCcccccccccCcCCEEEEcccCCHHHHHHHHHhccC
Confidence            999999999999998877778888888898899999999999999997664 468999999999999999999999    


Q ss_pred             ----CCCCCCccccCCCCcccccccCCCCCccccccccccceEEEecCCChhhHHHHHHHcCCcccC
Q 046830          456 ----SWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENFE  518 (518)
Q Consensus       456 ----~gk~t~vR~lhps~~G~iCPveTPEG~~cGLi~~La~~a~is~~~~~~~i~~~l~~~g~~~~~  518 (518)
                          +||+++||+||||||||+||+|||||++|||+||||++|.||++++..+|.++|.++||++++
T Consensus       487 p~~~~~K~~~~R~Lhpt~WG~iCP~eTPEG~~cGLvknLal~~~Isvg~~~~pI~~~l~~~gme~le  553 (1210)
T 3h0g_B          487 PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLE  553 (1210)
T ss_dssp             SCCSSCCSSSSSSCCGGGTTTCCCSCCCSSSSTTTSCBCCSSCCBCCCCCSSHHHHHHHSSSCCCCS
T ss_pred             chhhccccccccccChhhheeeccccCCCCCcccccccccceeeeECCCCcHHHHHHHHHhCCcchh
Confidence                689999999999999999999999999999999999999999999999999999999998763
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ... Back     alignment and structure
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B Back     alignment and structure
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Back     alignment and structure
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus} Back     alignment and structure
>3lti_A DNA-directed RNA polymerase subunit beta; BBM2, nucleotidyltransferase, transcription, transferase; HET: MLY MSE; 1.60A {Escherichia coli} PDB: 3e7h_A Back     alignment and structure
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus} 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 518
d1twfb_ 1207 e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces c 1e-144
d1smyc_ 1119 e.29.1.1 (C:) RNA-polymerase beta {Thermus thermop 1e-66
>d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1207 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta
domain: RBP2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  442 bits (1137), Expect = e-144
 Identities = 279/553 (50%), Positives = 370/553 (66%), Gaps = 48/553 (8%)

Query: 10  EDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHN 69
           EDE    T E++WAVISA+F EKGLV QQLDSF++F   T+Q+I+ E + + +   +QH 
Sbjct: 2   EDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHT 61

Query: 70  PGQQSD-------FAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIK 122
               +        F +IY++KPM+ ESDG T  L+ + ARLRNLTYS+ L+VDV KR  +
Sbjct: 62  TESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYE 121

Query: 123 KGHDGE------------------------EVPIMLRSSYCTLYQNSQKALTELGECPYD 158
                                          +PIMLRS  C L + ++  L +L ECP+D
Sbjct: 122 AIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFD 181

Query: 159 EGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPM 218
            GGYFIINGSEKVLIAQE+ + N V VFKK  P+  ++VAE+ S  E  +R  ST+ V +
Sbjct: 182 MGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKL 241

Query: 219 LSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELL 278
                 + GSS + I ATLPYI+ +IPI+I+FRALG   D +ILEHICYD  D QM+E+L
Sbjct: 242 YG----REGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEML 297

Query: 279 RPSLEEAFFIQNQQ----YIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKK 334
           +P +E+ F IQ+++    +IG+RG  +G+ +EK I+YAK+ILQKE LPH+   +  E++K
Sbjct: 298 KPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRK 357

Query: 335 AYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQK 394
           A++ G++I+RLLLCAL R+ +DDRDH+G KRLDLAGPLL  LF+TLF+KLT D+  Y+Q+
Sbjct: 358 AFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQR 417

Query: 395 CVDNGKDVNLQFAIKAKTITGGLKYSLATGNWG-QGNAAGTRAGVSQVLNCLTYASTFT- 452
            V+   D N++ AI AKTIT GLKY+LATGNWG Q  A  +RAGVSQVLN  TY+ST + 
Sbjct: 418 TVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSH 477

Query: 453 -------YYLSWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPI 505
                       KLAKPRQLHN+ WG++CPAETPEGQACGLVKNL+LM  I++G+   PI
Sbjct: 478 LRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPI 537

Query: 506 LEFLEEWGTENFE 518
           + FL EWG E  E
Sbjct: 538 ITFLSEWGMEPLE 550
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Length = 1119 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 ?
Query518
d1twfb_ 1207 RBP2 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1smyc_ 1119 RNA-polymerase beta {Thermus thermophilus [TaxId: 100.0
>d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta
domain: RBP2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.2e-104  Score=932.98  Aligned_cols=504  Identities=55%  Similarity=0.912  Sum_probs=428.7

Q ss_pred             cccccchhHHHHHHhhhcccCCcchhHHHHHHHHHHHHhHHHHHHhhcCCeeecCCCC-------CCCCceEEEEEEEEe
Q 046830           10 EDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQ-------HNPGQQSDFAEIYLS   82 (518)
Q Consensus        10 ~~~~~~~~~~~~~~~i~~~f~~~~lv~~qi~SFn~Fi~~gl~~i~~~~~pi~~~~~~~-------~~~~~~i~f~~~~i~   82 (518)
                      ||.++.++++|.|++|++||+.++|++|||+|||+||++||++++++.+||.+.....       ....+.++|++++|+
T Consensus         2 ~~~~~~~~~~d~w~~i~~~f~~~~Lv~~qidSFn~Fi~~gi~~Ii~~~~pi~~~~~~~~~~~~~~~~~~~~l~f~~i~i~   81 (1207)
T d1twfb_           2 EDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVT   81 (1207)
T ss_dssp             CCTTCCCCTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHTHHHHHHHTTCBCC------------------CCEECCCEEE
T ss_pred             CccCCCCCHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHCHHHHHHhcCCeEeeccccccccccCCCceEEEEEEEEEEc
Confidence            4668899999999999999999999999999999999999999999999997643221       122466889999999


Q ss_pred             cCcccCCCCcccccCHHHHHhcCCCcceeEEEEEEEEEeec------------------------Ccccceeeeeeeecc
Q 046830           83 KPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKK------------------------GHDGEEVPIMLRSSY  138 (518)
Q Consensus        83 ~P~~~~~~~~~~~l~P~ecR~r~~TYs~~l~v~v~~~~~~~------------------------~~~~~~iPIMv~S~~  138 (518)
                      +|.+.+.++..++|||+|||+|++||+|+|+|+|.+.+...                        +...|+|||||+|++
T Consensus        82 kP~~~e~~g~~~~l~P~EcR~r~lTYs~~l~v~i~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~v~iG~IPIMv~S~~  161 (1207)
T d1twfb_          82 KPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKN  161 (1207)
T ss_dssp             EEEECCSSSCCEECCHHHHHHTTCCCEEEEECCEECCCCC-------------------------CCEEEEEECCTTSTT
T ss_pred             CCeEEcCCCcccccCHHHHHhcCCccceEEEEEEEEEEEecccccccccceeecccccccceeeeeEEEEECCEEeCCCc
Confidence            99999988888999999999999999999999998654211                        123578999999999


Q ss_pred             cccCCCCHHHHHHhCCccCCCCceEEEeCceeEEEEeeecccCceEEEeecCCCceeEEEEEEeecCCCCCCCceEEEEE
Q 046830          139 CTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPM  218 (518)
Q Consensus       139 C~L~~~~~~e~i~~gE~p~d~GGYFIING~ErVii~q~~~s~n~~~~~~~~~~~~~~~~~~i~s~~~~~~~~~~~~~l~~  218 (518)
                      |||+++++++++..||||+|+||||||||+|||||+|++.++|+++++++++++++.|+|+|||+++++....+++.+++
T Consensus       162 C~L~~~~~~~l~~~gEc~~D~GGYFIING~EKVIi~Q~r~~~n~~~v~~~~~~~~~~~~~~irS~~~~~~~~~~~~~~~~  241 (1207)
T d1twfb_         162 CYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKL  241 (1207)
T ss_dssp             SGGGTCCHHHHHHTTCCTTCCCCSEEETTEEEEECEEEEECSSCCEEEECCTTSSEEEEEEEECCCSSSCCCCCEEEEEE
T ss_pred             ccCCCcCHHHHHHcCCCCCCCCcEEEECCEEEEEEEEEecCCCeEEEEEcCCCCceEEEEEEEEEeCCCCceeEEEEEEE
Confidence            99999999999999999999999999999999999999999999999998888899999999999988766666666666


Q ss_pred             EecCCCCCCCCCceEEEEeccccccchhhhHHHhcCCCCHHHHHHHhhhcCCcHHHHHHhhhhHHHHhcccccc----ee
Q 046830          219 LSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQ----YI  294 (518)
Q Consensus       219 ~~~~~~~~~~~~~~i~~~~~~~~~~IPl~illrALg~~sd~eI~~~i~~~~~~~~~~~~L~~~~~~~~~~~~~~----~i  294 (518)
                      .....    .....+.+.+++++.+||+++||||||..+|+||++.++++..+..+.+.|+.+.+++....+++    ||
T Consensus       242 ~~~~~----~~~~~i~~~~~~~~~~IPl~illrALG~~sD~eI~~~i~~~~~~~~~~~~l~~~~~~~~~~~t~e~al~yi  317 (1207)
T d1twfb_         242 YGREG----SSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFI  317 (1207)
T ss_dssp             ESCSS----CSSCCEEEECTTCSSCEEHHHHHHHTTCCSHHHHHHHHCCCTTCHHHHHHHHHHHHHTTTCCSHHHHHHHH
T ss_pred             EEcCC----ccceEEEEEeehhcccchHHHHHHHhCCcchhhhhhhcccCchhhHHHHHHHHHHhhccchhhHHHHHHHH
Confidence            54221    12356889999889999999999999999999999999988777777788888888776666554    99


Q ss_pred             eecCccccccchhhHHHHHHHHHhccCCCCCCCCcchhhHhhHHHHHHHHHHHhhcCCCCCCCCCcccceEEccccchhH
Q 046830          295 GKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLG  374 (518)
Q Consensus       295 g~~~~~~~~~~~~~~~~~~~il~~~~l~hl~~~~~~~~~K~~~L~~mi~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~  374 (518)
                      |++++.......+..+.++++|.+++|||++........|+.+|++|++||+.+..|.+.+||+|||+||||+++|+||+
T Consensus       318 g~~~~~~~~~~~~~~~~~~~iL~~~llpHl~~~~~~~~~K~~~L~~mi~kll~~~~g~~~~dd~D~~~nkrv~~~G~Ll~  397 (1207)
T d1twfb_         318 GRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLA  397 (1207)
T ss_dssp             HHTTSCTTSCHHHHHHHHHHHHHHTSSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEEEECHHHHHH
T ss_pred             HhhccccCCCccchHHHHHHHHHhhhccccccccchhhhHHHHHHHHHHHHHHhhhcccCCcchhhhccchhhhHHHHHH
Confidence            99877655566677899999999999999997766677899999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhcCCCCCcHHHhhhhcchhHHHHHHhccCCCCCCCC-CCccccceeeccccCccccccc
Q 046830          375 GLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNA-AGTRAGVSQVLNCLTYASTFTY  453 (518)
Q Consensus       375 ~~f~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~i~~~~it~~i~~~f~TGnw~~~~~-~~~~sG~sq~ldr~N~l~~lSh  453 (518)
                      .+||..|+++.+.+++.+.+...+.+.+++...+++..||++|++||+||||+.... ..+++|+||+|||+||++++||
T Consensus       398 ~~fr~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~it~~i~~~~~TGn~~~~~~~~~~~~G~sq~l~r~n~l~~lSh  477 (1207)
T d1twfb_         398 QLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSH  477 (1207)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCCC--------CCCCTHHHHHHHHHHHHHCCCC---------CCCEEECCCSSHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhhccccccccccChhhhhccCcHHHHHHHHHhcCcccccccccccccchhhhhhhcCHHHHHHh
Confidence            999999999999999999887666666777778888899999999999999998764 4679999999999999999999


Q ss_pred             cc--------CCCCCCccccCCCCcccccccCCCCCccccccccccceEEEecCCChhhHHHHHHHcCCccc
Q 046830          454 YL--------SWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENF  517 (518)
Q Consensus       454 ~R--------~gk~t~vR~lhps~~G~iCPveTPEG~~cGLi~~La~~a~is~~~~~~~i~~~l~~~g~~~~  517 (518)
                      +|        .+++++||+||||||||+||||||||+||||++|||++|.|+.+.+...+.++|.++|+.++
T Consensus       478 ~Rrv~~~~~~~~k~~~~R~Lhps~~G~iCPveTPEG~~~GLv~~La~~a~i~~~~~~~~~~~~l~~~g~~~~  549 (1207)
T d1twfb_         478 LRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPL  549 (1207)
T ss_dssp             HTEEECCC------CCTTSCCGGGTTTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCHHHHHHHHHTTCEEG
T ss_pred             hhcccCCcccccccchhhhcchhhccceeeeeCCCCCcccceeccceeeeeccccccceeeEEeeccCcccc
Confidence            99        57889999999999999999999999999999999999999999888999999999998653
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure