Citrus Sinensis ID: 014847

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-------
MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRPEDSLVMNQASLECGVFRSESYKAEVDNKDIQVKSRPSDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLSGVSMAAV
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccHHHHHcccccccccccEEEEEEEEccccccccccccccccccccEEEccccEEEEEEcccccEEEEEEcccccEEEEEEEEEEcccccEEEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccEEEEccccccccccccccccccccEEEEEEEEEEcHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccccHHHHHccccccccccccccccEEEEEccHHHHHHHHHHHHccccEEEEEEEEcccccccc
ccEEHEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEEEccccHHHEEEEcHHHHHccccEEEEEEEcccHHccccHHcccccccccccEEEccccEEEEccccccccccEEcccccccEEEEEEEEEcccccEEEEEEEEccccccccccccccHccccccccEEEEEEEccccccccccccccccEEEEccccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHccccccccEEEEccccccccEEEEEEEcHHHHHHHHHHHHHHHHHcccccEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEcccEEEccccccccEEEEEcHHHHHHHHHHHHHHHHHcccEEEEcccEEEEEc
msfllglscgiipshlQTMTMQGWVLYqsqkhspqaigfpttnpnirVDTLLQQlfypqrplfWILIsdclgrpedslvMNQASlecgvfrsesykaevdnkdiqvksrpsddmlnfgkiqsksgdiVIGKYAEIGADHSIKLKHTERGLVLKVLLssnddgknfAVVSIRQSVNMVHSaclgdkfssmhgqkgvlgfLEQTPAQLLEAALGKgacdglmsyatpfatstggviteQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSedkvkfrntgsfqpltgrpvadrkrfggiefgemKCDCLIahgasgnlherlkcknVANVIQRVvggpycricnsaddiikanvpYGAKLLSQELSFSMGitlkfdtqlsgvsmaav
MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRPEDSLVMNQASLECGVFrsesykaevdnkdiqvksrpsddmlnfgkiqsksgdiVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTgsfqpltgrpvadrKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLkfdtqlsgvsmaav
MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRPEDSLVMNQASLECGVFRSESYKAEVDNKDIQVKSRPSDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLSGVSMAAV
**FLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRPEDSLVMNQASLECGVFRS************************FGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQ*********
*SFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRPEDSLVMNQASLECGVFRSESYKAEVD**********SDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQL********
MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRPEDSLVMNQASLECGVFRSESYKAEVDNKDIQVKSRPSDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQL********
*SFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRPEDSLVMNQASLECGVFRSESYKAEVDNKDIQVKSRPSDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLSGVSMAAV
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRPEDSLVMNQASLECGVFRSESYKAEVDNKDIQVKSRPSDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLSGVSMAAV
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 ?
Query417 2.2.26 [Sep-21-2011]
Q9LK401172 DNA-directed RNA polymera yes no 0.901 0.320 0.494 1e-114
Q9LV321119 DNA-directed RNA polymera no no 0.901 0.336 0.495 1e-114
A5DHT21236 DNA-directed RNA polymera N/A no 0.918 0.309 0.303 6e-42
P384201188 DNA-directed RNA polymera no no 0.904 0.317 0.313 3e-40
Q428771191 DNA-directed RNA polymera N/A no 0.899 0.314 0.306 7e-40
P085181224 DNA-directed RNA polymera yes no 0.908 0.309 0.290 2e-38
Q6FLD51223 DNA-directed RNA polymera yes no 0.908 0.309 0.290 3e-38
Q753Q41222 DNA-directed RNA polymera yes no 0.908 0.310 0.290 6e-38
Q54J751170 DNA-directed RNA polymera yes no 0.896 0.319 0.294 8e-37
Q020611210 DNA-directed RNA polymera yes no 0.904 0.311 0.290 1e-36
>sp|Q9LK40|RPD2A_ARATH DNA-directed RNA polymerase D subunit 2a OS=Arabidopsis thaliana GN=NRPD2a PE=1 SV=1 Back     alignment and function desciption
 Score =  412 bits (1059), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 253/512 (49%), Positives = 298/512 (58%), Gaps = 136/512 (26%)

Query: 1    MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQR 60
            +SFLLG+SC ++P           VLYQSQKH  QAIGF +TNPNIR DTL QQLFYPQ+
Sbjct: 693  LSFLLGVSCAVVP--FANHDHGRRVLYQSQKHCQQAIGFSSTNPNIRCDTLSQQLFYPQK 750

Query: 61   PLFWILISDCLGRP--------------------EDSLVMNQASLECGVFRSE---SYKA 97
            PLF  L S+CL +                     EDS+VMN+ASLE G+FRSE   SYKA
Sbjct: 751  PLFKTLASECLKKEVLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRSYKA 810

Query: 98   EVDNKDIQVKSRPSDDMLNFGKIQSK--------------------SGDIVIGKYAEIGA 137
            EVD KD + K +  D+++ FGK  SK                    +GDIVIG+  E GA
Sbjct: 811  EVDAKDSE-KRKKMDELVQFGKTHSKIGKVDSLEDDGFPFIGANMSTGDIVIGRCTESGA 869

Query: 138  DHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG 197
            DHSIKLKHTERG+V KV+LSSND+GKNFA VS+RQ    V S CLGDKFSSMHGQKGVLG
Sbjct: 870  DHSIKLKHTERGIVQKVVLSSNDEGKNFAAVSLRQ----VRSPCLGDKFSSMHGQKGVLG 925

Query: 198  FLE--------------------------QTPAQLLEAALGKG------------ACDGL 219
            +LE                          QTP QLLEAAL KG            A   L
Sbjct: 926  YLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALSKGIACPIQKEGSSAAYTKL 985

Query: 220  MSYATPFATSTGGVITEQ-HQSFVSQLLN--CIGARNSGITFIFKHYFLFCLFECPMDWI 276
              +ATPF+T     ITEQ H++  S+  N      R+                       
Sbjct: 986  TRHATPFSTPGVTEITEQLHRAGFSRWGNERVYNGRSGE--------------------- 1024

Query: 277  AFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKC 336
                ++RS+IF   TFYQ+ +HMSEDKVKFRNTG   PLT +PVADRKRFGGI+FGEM+ 
Sbjct: 1025 ----MMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMER 1080

Query: 337  DCLIAHGASGNLHERL-------------KCKNVANVIQRV------VGGPYCRICNSAD 377
            DCLIAHGAS NLHERL             KCK  ANVI+R       + GPYCR+C S+D
Sbjct: 1081 DCLIAHGASANLHERLFTLSDSSQMHICRKCKTYANVIERTPSSGRKIRGPYCRVCVSSD 1140

Query: 378  DIIKANVPYGAKLLSQELSFSMGITLKFDTQL 409
             +++  VPYGAKLL QEL FSMGITL FDT+L
Sbjct: 1141 HVVRVYVPYGAKLLCQEL-FSMGITLNFDTKL 1171
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity). Second largest component of RNA polymerase IVa (Pol IV) and IVb (Pol V) which mediate short-interfering RNAs (siRNA) accumulation and subsequent RNA-directed DNA methylation-dependent (RdDM) transcriptional gene silencing (TGS) of endogenous repeated sequences, including transposable elements. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Also required for full erasure of methylation when the RNA trigger is withdrawn. Required for intercellular RNA interference (RNAi) leading to systemic post-transcriptional gene silencing. Involved in the maintenance of post-transcriptional RNA silencing. During interphase, mediates siRNA-independent heterochromatin association and methylation into chromocenters and condensation and cytosine methylation at pericentromeric major repeats. Required for complete maintenance of the 35S promoter homology-dependent TGS in transgenic plants.
Arabidopsis thaliana (taxid: 3702)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6
>sp|Q9LV32|RPD2B_ARATH DNA-directed RNA polymerase D subunit 2b OS=Arabidopsis thaliana GN=NRPD2b PE=2 SV=1 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|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|Q42877|RPB2_SOLLC DNA-directed RNA polymerase II subunit RPB2 OS=Solanum lycopersicum GN=RPB2 PE=2 SV=1 Back     alignment and function description
>sp|P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB2 PE=1 SV=2 Back     alignment and function description
>sp|Q6FLD5|RPB2_CANGA DNA-directed RNA polymerase II subunit RPB2 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=RPB2 PE=3 SV=1 Back     alignment and function description
>sp|Q753Q4|RPB2_ASHGO DNA-directed RNA polymerase II subunit RPB2 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=RPB2 PE=3 SV=1 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|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

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 ?
Query417
255548744 1203 DNA-directed RNA polymerase subunit, put 0.904 0.313 0.544 1e-128
224141967 1160 predicted protein [Populus trichocarpa] 0.906 0.325 0.551 1e-128
225430474 1198 PREDICTED: DNA-directed RNA polymerase D 0.908 0.316 0.521 1e-123
449455519 1197 PREDICTED: DNA-directed RNA polymerase D 0.911 0.317 0.528 1e-123
296082132 1220 unnamed protein product [Vitis vinifera] 0.906 0.309 0.533 1e-122
357466021 1237 DNA-directed RNA polymerase subunit beta 0.904 0.304 0.526 1e-122
67515338 1019 RNA polymerase IV second largest subunit 0.911 0.372 0.510 1e-121
356518213 1205 PREDICTED: DNA-directed RNA polymerase D 0.904 0.312 0.520 1e-120
356509878 1205 PREDICTED: DNA-directed RNA polymerase D 0.904 0.312 0.521 1e-120
67515342 821 RNA polymerase IV second largest subunit 0.908 0.461 0.5 1e-116
>gi|255548744|ref|XP_002515428.1| DNA-directed RNA polymerase subunit, putative [Ricinus communis] gi|223545372|gb|EEF46877.1| DNA-directed RNA polymerase subunit, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  465 bits (1197), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 280/514 (54%), Positives = 312/514 (60%), Gaps = 137/514 (26%)

Query: 1    MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQR 60
            MSFLLGLSCGIIP           VLYQ+QKHS QAIGFPTTNPNIRVDTL  QL+YPQR
Sbjct: 721  MSFLLGLSCGIIP--FANHDHARRVLYQAQKHSQQAIGFPTTNPNIRVDTLSHQLYYPQR 778

Query: 61   PLFWILISDCLGRP---------------------------------EDSLVMNQASLEC 87
            PLF  + SDCLG+P                                 EDSLVMN+ASLE 
Sbjct: 779  PLFRTVTSDCLGKPGDTRGHNGIVPKPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLER 838

Query: 88   GVFRSE---SYKAEVDNKDIQVKSRPSDDMLNFGKIQSK--------------------S 124
            G+FRSE   SYKA+VDNK++  K R  DD +NFGKI SK                    S
Sbjct: 839  GMFRSEHIRSYKADVDNKELLDKRRKYDDNVNFGKIPSKIGRVDSLDDDGFPFIGANLQS 898

Query: 125  GDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGD 184
            GDIVIG+ AE G DHSIKLKHTERG+V KV+LSSND+GKNFAVVS+RQ    V S CLGD
Sbjct: 899  GDIVIGRCAESGPDHSIKLKHTERGMVQKVVLSSNDEGKNFAVVSLRQ----VRSPCLGD 954

Query: 185  KFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACD 217
            KFSSMHGQKGVLGFLE                          QTP QLLEAALGKG AC 
Sbjct: 955  KFSSMHGQKGVLGFLESQENFPFTRQGIVPDIVINPHSFPSRQTPGQLLEAALGKGIACG 1014

Query: 218  GLMSYATPFATSTGGVITEQ-HQSFVSQLLN--CIGARNSGITFIFKHYFLFCLFECPMD 274
            G M YATPF+T +   IT Q H++  S+  N      R                      
Sbjct: 1015 GSMKYATPFSTLSVEAITNQLHRAGFSRWGNERVYNGRTGE------------------- 1055

Query: 275  WIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEM 334
                  +VRSLIF   TFYQ+ IHM+EDKVKFRNTG   PLT +PVADRKRFGGI+FGEM
Sbjct: 1056 ------MVRSLIFMGPTFYQRLIHMAEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEM 1109

Query: 335  KCDCLIAHGASGNLHERL-------------KCKNVANVIQRVV------GGPYCRICNS 375
            + DCLIAHGAS NLHERL             KCKNVANVIQR V       GPYCR+C S
Sbjct: 1110 ERDCLIAHGASANLHERLFTLSDSSQMHICQKCKNVANVIQRAVPGGRKIRGPYCRVCES 1169

Query: 376  ADDIIKANVPYGAKLLSQELSFSMGITLKFDTQL 409
             D+I+K NVPYGAKLL QEL FSMGI+LKF+T+L
Sbjct: 1170 VDEIVKVNVPYGAKLLCQEL-FSMGISLKFETRL 1202

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224141967|ref|XP_002324332.1| predicted protein [Populus trichocarpa] gi|222865766|gb|EEF02897.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225430474|ref|XP_002283296.1| PREDICTED: DNA-directed RNA polymerase D subunit 2a-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|449455519|ref|XP_004145500.1| PREDICTED: DNA-directed RNA polymerase D subunit 2a-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|296082132|emb|CBI21137.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|357466021|ref|XP_003603295.1| DNA-directed RNA polymerase subunit beta [Medicago truncatula] gi|355492343|gb|AES73546.1| DNA-directed RNA polymerase subunit beta [Medicago truncatula] Back     alignment and taxonomy information
>gi|67515338|gb|AAY68198.1| RNA polymerase IV second largest subunit [Rhododendron macrophyllum] Back     alignment and taxonomy information
>gi|356518213|ref|XP_003527775.1| PREDICTED: DNA-directed RNA polymerase D subunit 2a-like [Glycine max] Back     alignment and taxonomy information
>gi|356509878|ref|XP_003523670.1| PREDICTED: DNA-directed RNA polymerase D subunit 2a-like [Glycine max] Back     alignment and taxonomy information
>gi|67515342|gb|AAY68200.1| RNA polymerase IV second largest subunit [Antirrhinum majus] 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 ?
Query417
TAIR|locus:20952331172 NRPD2A "nuclear RNA polymerase 0.206 0.073 0.688 1.4e-75
CGD|CAL00041451234 orf19.3349 [Candida albicans ( 0.302 0.102 0.394 4.1e-31
UNIPROTKB|Q5A8Y51234 RPB140 "DNA-directed RNA polym 0.302 0.102 0.394 4.1e-31
SGD|S0000056771224 RPB2 "RNA polymerase II second 0.297 0.101 0.405 1.3e-30
GENEDB_PFALCIPARUM|PFB0715w1340 PFB0715w "DNA-directed RNA pol 0.287 0.089 0.383 2.2e-30
UNIPROTKB|O962361340 PFB0715w "DNA-directed RNA pol 0.287 0.089 0.383 2.2e-30
ASPGD|ASPL00000397701252 AN9120 [Emericella nidulans (t 0.306 0.102 0.415 5.2e-30
TAIR|locus:21190131188 NRPB2 [Arabidopsis thaliana (t 0.297 0.104 0.394 1.2e-29
DICTYBASE|DDB_G02882571170 rpb2 "RNA polymerase II core s 0.292 0.104 0.392 1.4e-25
POMBASE|SPAC23G3.011210 rpb2 "RNA polymerase II comple 0.292 0.100 0.392 1.6e-24
TAIR|locus:2095233 NRPD2A "nuclear RNA polymerase D2A" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 300 (110.7 bits), Expect = 1.4e-75, Sum P(4) = 1.4e-75
 Identities = 62/90 (68%), Positives = 70/90 (77%)

Query:   112 DDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIR 171
             DD   F      +GDIVIG+  E GADHSIKLKHTERG+V KV+LSSND+GKNFA VS+R
Sbjct:   844 DDGFPFIGANMSTGDIVIGRCTESGADHSIKLKHTERGIVQKVVLSSNDEGKNFAAVSLR 903

Query:   172 QSVNMVHSACLGDKFSSMHGQKGVLGFLEQ 201
             Q    V S CLGDKFSSMHGQKGVLG+LE+
Sbjct:   904 Q----VRSPCLGDKFSSMHGQKGVLGYLEE 929
GO:0003677 "DNA binding" evidence=IEA;ISS
GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM;IDA
GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS
GO:0032549 "ribonucleoside binding" evidence=IEA
GO:0031047 "gene silencing by RNA" evidence=IMP
GO:0000418 "DNA-directed RNA polymerase IV complex" evidence=IDA;IPI
GO:0005720 "nuclear heterochromatin" evidence=IDA
GO:0006306 "DNA methylation" evidence=IMP;IDA
GO:0030422 "production of siRNA involved in RNA interference" evidence=IGI;IMP
GO:0000419 "DNA-directed RNA polymerase V complex" evidence=IDA;IPI
GO:0030880 "RNA polymerase complex" evidence=IPI
GO:0035194 "posttranscriptional gene silencing by RNA" evidence=IMP
GO:0005515 "protein binding" evidence=IPI
GO:0050776 "regulation of immune response" evidence=IMP
GO:0050832 "defense response to fungus" evidence=IMP
CGD|CAL0004145 orf19.3349 [Candida albicans (taxid:5476)] Back     alignment and assigned GO terms
UNIPROTKB|Q5A8Y5 RPB140 "DNA-directed RNA polymerase" [Candida albicans SC5314 (taxid:237561)] Back     alignment and assigned GO terms
SGD|S000005677 RPB2 "RNA polymerase II second largest subunit B150" [Saccharomyces cerevisiae (taxid:4932)] Back     alignment and assigned GO terms
GENEDB_PFALCIPARUM|PFB0715w PFB0715w "DNA-directed RNA polymerase II second largest subunit, putative" [Plasmodium falciparum (taxid:5833)] Back     alignment and assigned GO terms
UNIPROTKB|O96236 PFB0715w "DNA-directed RNA polymerase" [Plasmodium falciparum 3D7 (taxid:36329)] Back     alignment and assigned GO terms
ASPGD|ASPL0000039770 AN9120 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
TAIR|locus:2119013 NRPB2 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
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

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.70.691
4th Layer2.7.7.6LOW CONFIDENCE prediction!

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 ?
Query417
cd00653866 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun 9e-83
TIGR03670599 TIGR03670, rpoB_arch, DNA-directed RNA polymerase 1e-54
PRK085651103 PRK08565, PRK08565, DNA-directed RNA polymerase su 5e-50
COG00851060 COG0085, RpoB, DNA-directed RNA polymerase, beta s 3e-49
PRK07225605 PRK07225, PRK07225, DNA-directed RNA polymerase su 4e-47
pfam00562373 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, do 6e-47
pfam0456078 pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, do 2e-15
CHL002071077 CHL00207, rpoB, RNA polymerase beta subunit; Provi 2e-11
TIGR020131065 TIGR02013, rpoB, DNA-directed RNA polymerase, beta 2e-09
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 8e-07
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 2e-06
PRK004051112 PRK00405, rpoB, DNA-directed RNA polymerase subuni 4e-05
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit Back     alignment and domain information 
 Score =  270 bits (693), Expect = 9e-83
 Identities = 151/507 (29%), Positives = 202/507 (39%), Gaps = 145/507 (28%)

Query: 2   SFLLGLSCGIIP--SHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQ 59
           S +L ++  +IP   H Q        LYQS     QA+G P  N   R+DT L  L YPQ
Sbjct: 403 SQILSVAASLIPFPEHNQ----SPRNLYQSNMQK-QAVGTPALNQQYRMDTKLYLLLYPQ 457

Query: 60  RPLFWILISDCLGRP--------------------EDSLVMNQASLECGVFRS---ESYK 96
           +PL    I + +                       ED++++N++S++ G FRS   + Y+
Sbjct: 458 KPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYE 517

Query: 97  AEVDNK----------DIQVKSRPSDDMLNF-GKI----QSKSGDIVIGKYAEIGA---- 137
            E+             DI   S      L+  G I    + + GDI++GK    G     
Sbjct: 518 IELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETEST 577

Query: 138 -----------DHSIKLKHTERGLVLKVLLSS---NDDGKNFAVVSIRQSVNMVHSACLG 183
                      D S+K    E+G+V  V + S   ND G     V IRQ         +G
Sbjct: 578 PIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQ----KRKPQIG 633

Query: 184 DKFSSMHGQKGVLG---------FLEQ-----------------TPAQLLEAALGK-GAC 216
           DKF+S HGQKGV+          F E                  T  QLLE+ LGK GA 
Sbjct: 634 DKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGAL 693

Query: 217 DGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARN----SGITFIFKHYFLFCLFECP 272
            G    ATPF  +    I+E         LN  G        G T            E P
Sbjct: 694 LGKFGDATPFDGAEEEDISE---LLGEAGLNYYG--KEVLYDGRTGE--------PLEAP 740

Query: 273 MDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFG 332
                        IF    +YQ+  HM +DK+  R+TG +  LT +P+  R R GG  FG
Sbjct: 741 -------------IFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFG 787

Query: 333 EMKCDCLIAHGASGNLHERL-------------KCKNVANVIQRVVGGPYCRICNSADDI 379
           EM+ D LIAHGA+  L ERL             KC  + +          CR+C    +I
Sbjct: 788 EMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN-------LCRLCKKGTNI 840

Query: 380 IKANVPYGAKLLSQELSFSMGITLKFD 406
            K  +PY  KLL QEL  SM I  +  
Sbjct: 841 SKVGIPYAFKLLFQELQ-SMNIDPRLK 866

RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation. Length = 866
>gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B Back     alignment and domain information
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional 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|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B'; Validated Back     alignment and domain information
>gnl|CDD|215994 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6 Back     alignment and domain information
>gnl|CDD|146952 pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, domain 7 Back     alignment and domain information
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional Back     alignment and domain information
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit 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|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 417
PRK07225605 DNA-directed RNA polymerase subunit B'; Validated 100.0
TIGR03670599 rpoB_arch DNA-directed RNA polymerase subunit B. T 100.0
PRK085651103 DNA-directed RNA polymerase subunit B; Provisional 100.0
cd00653866 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po 100.0
KOG02161111 consensus RNA polymerase I, second largest subunit 100.0
KOG02151153 consensus RNA polymerase III, second largest subun 100.0
COG00851060 RpoB DNA-directed RNA polymerase, beta subunit/140 100.0
TIGR020131065 rpoB DNA-directed RNA polymerase, beta subunit. Th 100.0
PRK004051112 rpoB DNA-directed RNA polymerase subunit beta; Rev 100.0
CHL000011070 rpoB RNA polymerase beta subunit 100.0
CHL002071077 rpoB RNA polymerase beta subunit; Provisional 100.0
KOG02141141 consensus RNA polymerase II, second largest subuni 100.0
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 100.0
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 100.0
PF00562386 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; Int 100.0
PF0456081 RNA_pol_Rpb2_7: RNA polymerase Rpb2, domain 7; Int 99.92
COG0085 1060 RpoB DNA-directed RNA polymerase, beta subunit/140 96.24
KOG02141141 consensus RNA polymerase II, second largest subuni 96.23
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated Back     alignment and domain information 
Probab=100.00  E-value=3.7e-121  Score=973.01  Aligned_cols=377  Identities=31%  Similarity=0.489  Sum_probs=347.7

Q ss_pred             CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeeccccccCCC------
Q 014847            1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRP------   74 (417)
Q Consensus         1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~lg~n------   74 (417)
                      |+++||++||+|||+||  ||||||||||| |+|||||++++|+..|+|++.|.|+|||+|||+|+.++.++++      
T Consensus       129 p~~ilgv~AslIPF~~h--NQSPRn~yq~~-M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~  205 (605)
T PRK07225        129 PSLILGIGAGMIPYPEH--NASPRITMGAG-MIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQ  205 (605)
T ss_pred             CcceeEEEeeccCCCCC--Cccchhhhhhh-hhhcccCccccceeeecCCcccEEeeCCcceEEccchHhhCCCccCCCe
Confidence            78999999999999999  99999999999 8999999999999999999999999999999999998865443      


Q ss_pred             --------------CCeEEEecceecccceeeEEEEEEEec--------ccccC---------------CCCCCCccccc
Q 014847           75 --------------EDSLVMNQASLECGVFRSESYKAEVDN--------KDIQV---------------KSRPSDDMLNF  117 (417)
Q Consensus        75 --------------EDAiIiNKssidRG~f~s~~Yk~e~~~--------~~~~~---------------~~~~~~g~~~~  117 (417)
                                    ||||||||+|+|||||||++|+++...        .+.++               +.+|.||++.+
T Consensus       206 N~iVAvmsy~GYn~EDAiIiNkssidRGlf~s~~~k~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~  285 (605)
T PRK07225        206 NFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNP  285 (605)
T ss_pred             eEEEEEECcCCCChhHeeeeehhhhhcCceEEEEEEEEEEEeeecCCCcceEEecCCchhccccChHHhhcCCCCCCccC
Confidence                          999999999999999999988765421        11111               23678999999


Q ss_pred             cccccccCCeEEEEeccC---------------CceeEEEecCCCceeEEEEEEEeCCCCCeEEEEEEeecccccccccc
Q 014847          118 GKIQSKSGDIVIGKYAEI---------------GADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACL  182 (417)
Q Consensus       118 g~~~v~~GDiligk~~~~---------------~~d~s~~~k~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~~~~~R~p~i  182 (417)
                      |. .|++|||||||++|.               .+|+|++++++|+|+||+|.++.++++.+.|||++|+    .|+|+|
T Consensus       286 G~-~v~~gdiligk~sp~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~ir~----~R~p~i  360 (605)
T PRK07225        286 ET-EVKEGDVLIGKTSPPRFLEEPDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRD----LRIPEL  360 (605)
T ss_pred             CC-EECCCCEEEEEecCCCCccchhhhcccccCcceeeEEecCCCcEEEEEEEEEecCCCCEEEEEEEEE----EEeccc
Confidence            96 899999999998862               3789999999999999999999988888999999999    999999


Q ss_pred             ccccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHH
Q 014847          183 GDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVIT  235 (417)
Q Consensus       183 GDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~  235 (417)
                      |||||||||||||||+||                          ||||||+|+++||+ ++.|.+.|+|||...+.+++.
T Consensus       361 GDKfssRHGQKGvvs~i~~~eDMPft~~G~~PDiIiNPhg~PSRMTiGql~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~  440 (605)
T PRK07225        361 GDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLR  440 (605)
T ss_pred             cchhhhcccCceeEEeEeccccCCcCCCCCcccEEECcccccccCcHHHHHHHHHHHHHHhcCceEeecCCCCchHHHHH
Confidence            999999999999999999                          99999999999999 789999999999999999999


Q ss_pred             HHHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCC
Q 014847          236 EQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQP  314 (417)
Q Consensus       236 ~~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~  314 (417)
                      +.|.+ ||+++|+         |.||||              +||++|+++||+|++|||||+|||+||+|+|++||++.
T Consensus       441 ~~L~~~g~~~~G~---------e~my~G--------------~TG~~~~~~if~G~~yYqrL~HmV~DK~haR~~Gp~~~  497 (605)
T PRK07225        441 EALEKLGFEHTGK---------EVMYDG--------------ITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQV  497 (605)
T ss_pred             HHHHHhCcCCCCe---------EEEEcC--------------CCCCEecccEEEeehheeechhhhcchhhhccCCCCcc
Confidence            99999 9999888         999999              99999999999999999999999999999999999999


Q ss_pred             cccCCcccccCCCceeeeeccchhhhhcchhhhhhhhh----------ccccccccccc--ccCCeeecccCCCCccccc
Q 014847          315 LTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL----------KCKNVANVIQR--VVGGPYCRICNSADDIIKA  382 (417)
Q Consensus       315 lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL----------~c~~~~~~~~~--~~~~~~c~~c~~~~~~~~~  382 (417)
                      |||||++||+|+|||||||||||||+|||||++|+|||          .|..|+.+...  .....+|+.|.++..+.++
T Consensus       498 lTrQP~~GR~r~GG~RfGEMErd~lia~Gas~~L~Erl~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v  577 (605)
T PRK07225        498 LTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPV  577 (605)
T ss_pred             cccCCccccccCCCeeeeeeehhhhhhhhhHHHHHHHHhccCcceeEEeecCcCcceehhcccCceeecccCCCCceeec
Confidence            99999999999999999999999999999999999999          77777766532  2235679999998899999


Q ss_pred             cChHhHHHHHHHHHhhcCCeEEEEecc
Q 014847          383 NVPYGAKLLSQELSFSMGITLKFDTQL  409 (417)
Q Consensus       383 ~ipy~~k~l~~EL~~sm~i~~~l~~~~  409 (417)
                      .+|||||||+||| +||||+++|.+++
T Consensus       578 ~iPya~kll~~EL-~sm~i~~~l~~~~  603 (605)
T PRK07225        578 EMSYAFKLLLDEL-KSLGIAPRLELED  603 (605)
T ss_pred             cCChhHHHHHHHH-HHCCceeEEEecc
Confidence            9999999999999 9999999999874

>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B Back     alignment and domain information
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional Back     alignment and domain information
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit Back     alignment and domain information
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription] Back     alignment and domain information
>KOG0215 consensus RNA polymerase III, 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
>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
>CHL00001 rpoB RNA polymerase beta subunit Back     alignment and domain information
>CHL00207 rpoB RNA polymerase beta subunit; Provisional Back     alignment and domain information
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription] Back     alignment and domain information
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PF04560 RNA_pol_Rpb2_7: RNA polymerase Rpb2, domain 7; InterPro: IPR007641 RNA polymerases catalyse the DNA-dependent polymerisation of RNA Back     alignment and domain information
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>KOG0214 consensus RNA polymerase II, 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 ?
Query417
1i3q_B1224 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 1e-39
3h0g_B1210 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 1e-37
2waq_B1131 The Complete Structure Of The Archaeal 13-Subunit D 8e-32
2pmz_B1124 Archaeal Rna Polymerase From Sulfolobus Solfataricu 4e-30
1iw7_C1119 Crystal Structure Of The Rna Polymerase Holoenzyme 2e-08
1ynj_C1119 Taq Rna Polymerase-Sorangicin Complex Length = 1119 5e-08
1hqm_C1119 Crystal Structure Of Thermus Aquaticus Core Rna Pol 5e-08
1l9u_C1118 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 5e-08
1i6v_C1118 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 5e-08
3lu0_C1342 Molecular Model Of Escherichia Coli Core Rna Polyme 2e-06
3iyd_C1342 Three-Dimensional Em Structure Of An Intact Activat 2e-06
>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1224 Back     alignment and structure 
Iteration: 1

 Score =  160 bits (405), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 147/506 (29%), Positives = 218/506 (43%), Gaps = 127/506 (25%)
Query: 2    SFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRP 61
            S +LG++  IIP      + +    YQS     QA+G   TN N+R+DT+   L+YPQ+P
Sbjct: 746  SMILGVAASIIPFPDHNQSPRN--TYQSAM-GKQAMGVFLTNYNVRMDTMANILYYPQKP 802
Query: 62   LFWILISDCLG--------------------RPEDSLVMNQASLECGVFRSESYKAEVDN 101
            L      + L                       EDS++MNQ+S++ G+FRS  +++ +D 
Sbjct: 803  LGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQ 862
Query: 102  KD------IQVKSRP----------------SDDMLNFGKIQSKSGDIVIGKYAEIGADH 139
            +        +   +P                 DD L    ++    D++IGK   I  D 
Sbjct: 863  EKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDE 922
Query: 140  ---------------SIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGD 184
                           S  L+ TE G+V +VL+++N DG  F  V +R +        +GD
Sbjct: 923  EELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTT----KIPQIGD 978
Query: 185  KFSSMHGQKGVLGFL---EQTP-----------------------AQLLEAALGK-GACD 217
            KF+S HGQKG +G     E  P                       A L+E  L K  A  
Sbjct: 979  KFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALS 1038
Query: 218  GLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIA 277
            G    A+PF   T           +S+LL   G ++ G   ++  +    L         
Sbjct: 1039 GNEGDASPFTDIT--------VEGISKLLREHGYQSRGFEVMYNGHTGKKLM-------- 1082
Query: 278  FICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCD 337
                  + IF   T+YQ+  HM +DK+  R  G  Q LT +PV  R R GG+ FGEM+ D
Sbjct: 1083 ------AQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERD 1136
Query: 338  CLIAHGASGNLHERLKCKNVA------------NVIQRVVGGPY-CRICNSADDIIKANV 384
            C+IAHGA+  L ERL   + A             VI ++    + C+ C++  DI + ++
Sbjct: 1137 CMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHI 1196
Query: 385  PYGAKLLSQELSFSMGITLKFDTQLS 410
            PY AKLL QEL  +M IT +  T  S
Sbjct: 1197 PYAAKLLFQEL-MAMNITPRLYTDRS 1221
>pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1210 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|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 1124 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|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex Length = 1119 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|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1118 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 ?
Query417
1twf_B1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 6e-80
4ayb_B1131 DNA-directed RNA polymerase; transferase, multi-su 2e-79
3h0g_B1210 DNA-directed RNA polymerase II subunit RPB2; trans 3e-78
2a6h_C1119 DNA-directed RNA polymerase beta chain; RNA polyme 6e-07
>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
 Score =  267 bits (683), Expect = 6e-80
 Identities = 140/510 (27%), Positives = 201/510 (39%), Gaps = 143/510 (28%)

Query: 4    LLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLF 63
            +LG++  IIP        Q            QA+G   TN N+R+DT+   L+YPQ+PL 
Sbjct: 748  ILGVAASIIPFPDHN---QSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLG 804

Query: 64   WILISDCLGRPE--------------------DSLVMNQASLECGVFRSE---SYKAEVD 100
                 + L   E                    DS++MNQ+S++ G+FRS    SY  +  
Sbjct: 805  TTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEK 864

Query: 101  NKDIQVKSR---PSDDMLNFGKIQS----------------KSGDIVIGKYAEIGA---- 137
               + +      P        K  +                   D++IGK   I      
Sbjct: 865  KYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEE 924

Query: 138  -----------DHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKF 186
                       D S  L+ TE G+V +VL+++N DG  F  V +R          +GDKF
Sbjct: 925  LGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRT----TKIPQIGDKF 980

Query: 187  SSMHGQKGVLGFL--------------------------EQTPAQLLEAALGK-GACDGL 219
            +S HGQKG +G                              T A L+E  L K  A  G 
Sbjct: 981  ASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGN 1040

Query: 220  MSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFEC-------- 271
               A+PF      +  E     +S+LL   G ++ G             FE         
Sbjct: 1041 EGDASPF----TDITVEG----ISKLLREHGYQSRG-------------FEVMYNGHTGK 1079

Query: 272  PMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEF 331
             +          + IF   T+YQ+  HM +DK+  R  G  Q LT +PV  R R GG+ F
Sbjct: 1080 KL---------MAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRF 1130

Query: 332  GEMKCDCLIAHGASGNLHERL-------------KCKNVANVIQRVVGGPYCRICNSADD 378
            GEM+ DC+IAHGA+  L ERL              C  +  + +       C+ C++  D
Sbjct: 1131 GEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKID 1190

Query: 379  IIKANVPYGAKLLSQELSFSMGITLKFDTQ 408
            I + ++PY AKLL QEL  +M IT +  T 
Sbjct: 1191 IYQIHIPYAAKLLFQEL-MAMNITPRLYTD 1219
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query417
1twf_B1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 100.0
3h0g_B1210 DNA-directed RNA polymerase II subunit RPB2; trans 100.0
4ayb_B1131 DNA-directed RNA polymerase; transferase, multi-su 100.0
2a6h_C1119 DNA-directed RNA polymerase beta chain; RNA polyme 100.0
3lu0_C1342 DNA-directed RNA polymerase subunit beta; E. coli 100.0
3qqc_A 436 DNA-directed RNA polymerase subunit B, DNA-direct 98.53
3tbi_B228 DNA-directed RNA polymerase subunit beta; transcri 98.34
>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
Probab=100.00  E-value=8.1e-118  Score=1008.68  Aligned_cols=378  Identities=37%  Similarity=0.522  Sum_probs=329.5

Q ss_pred             CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeecccccc---------
Q 014847            1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCL---------   71 (417)
Q Consensus         1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~l---------   71 (417)
                      |++||||+||+||||||  ||||||||||| |+|||||++.+|+..|+|+..|.|+|||+|||+|..++.+         
T Consensus       745 Ps~ILgV~ASlIPF~dH--NqSpRn~yqs~-M~kQA~g~~~~n~~~r~dt~~~~l~ypQkPlV~t~~~~~~~~~elp~G~  821 (1224)
T 1twf_B          745 PSMILGVAASIIPFPDH--NQSPRNTYQSA-MGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQ  821 (1224)
T ss_dssp             GGGGSCTTGGGSSSGGG--SCHHHHHHHHH-HGGGBCBCSCTTTTTCCCSEEEEESSCBCCSEECTTHHHHTTTTSCCCE
T ss_pred             CccccceeecccCCccc--cccchhhhccc-ccccccccccceeeeecccccceeecCcCCeEEcccccccccccCCCCe
Confidence            89999999999999999  99999999999 8999999999999999999999999999999999877743         


Q ss_pred             ----------CCC-CCeEEEecceecccceeeEEEEEEEec--------ccccCC---------------CCCCCccccc
Q 014847           72 ----------GRP-EDSLVMNQASLECGVFRSESYKAEVDN--------KDIQVK---------------SRPSDDMLNF  117 (417)
Q Consensus        72 ----------g~n-EDAiIiNKssidRG~f~s~~Yk~e~~~--------~~~~~~---------------~~~~~g~~~~  117 (417)
                                |+| ||||||||+|+|||+|||++|+++...        .+.+++               .+|.||++.+
T Consensus       822 N~iVAvm~y~GYN~EDAiIin~~sv~rg~~~s~~~~~y~~~~~~~~~~~~e~~~~P~~~~~~~~~~~~~~~LD~dGiv~~  901 (1224)
T 1twf_B          822 NAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAP  901 (1224)
T ss_dssp             EEEEEECBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECCCCSCTTCCCEESCCCCSSSCBCCSSCGGGCCTTSBCCT
T ss_pred             eEEEEEecccCcccchhhhhhhhHHhcCCeeEEEEEEEEEEeeeCCCCceeEecCCChhhccCccHHHHhhcccCCccCC
Confidence                      444 999999999999999999988776532        111221               2578899999


Q ss_pred             cccccccCCeEEEEeccCC---------------ceeEEEecCCCceeEEEEEEEeCCCCCeEEEEEEeecccccccccc
Q 014847          118 GKIQSKSGDIVIGKYAEIG---------------ADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACL  182 (417)
Q Consensus       118 g~~~v~~GDiligk~~~~~---------------~d~s~~~k~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~~~~~R~p~i  182 (417)
                      |. .|++|||||||++|++               +|+|++++++|.|+||+|.++++++|.+.|||++|+    .|.|+|
T Consensus       902 G~-~V~~gDilvgK~~p~~~~~~~~~~~~~~~~~rd~s~~~~~~e~g~Vd~V~~~~~~~g~~~vkV~ir~----~R~p~i  976 (1224)
T 1twf_B          902 GV-RVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRT----TKIPQI  976 (1224)
T ss_dssp             TC-EECTTCEEECEECCCC-------------CCBBCCEECCTTCCEEEEEEEEEECSSSCEEEEEEEEE----EECCCT
T ss_pred             cc-EecCCCEEEEEecCCCccccccccccccCccceeEEEeeCCCCeEEEEEEEEecCCCCEEEEEEEEe----cCCCCc
Confidence            96 8999999999999842               789999999999999999999999999999999999    999999


Q ss_pred             ccccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHH
Q 014847          183 GDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVIT  235 (417)
Q Consensus       183 GDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~  235 (417)
                      |||||||||||||||+||                          ||||||+|+++||+ ++.|...|+|||++.++++|.
T Consensus       977 GDKfasRHGqKGvis~i~p~eDMPf~~dG~~pDiIiNPhg~PSRMtiGqllE~~lgka~~~~G~~~datpF~~~~~~~i~ 1056 (1224)
T 1twf_B          977 GDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGIS 1056 (1224)
T ss_dssp             TCEEECTTSCEEEEEEEECTTTSCEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSSSCCHHHHH
T ss_pred             hhhhhhhccCcceeeeecccccCCcCCCCCCccEEeCCCcCccccccchhHHHHhhHHHHhcCceeecCCCCCccHHHHH
Confidence            999999999999999999                          99999999999999 789999999999999999999


Q ss_pred             HHHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCC
Q 014847          236 EQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQP  314 (417)
Q Consensus       236 ~~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~  314 (417)
                      +.|++ ||+++|+         |.||||              +||++|+++||+|++|||||+|||+||+|||++|||+.
T Consensus      1057 ~~L~~~g~~~~G~---------e~ly~G--------------~TG~~~~~~i~vG~~YyqkL~HmV~DKihaRs~GP~~~ 1113 (1224)
T 1twf_B         1057 KLLREHGYQSRGF---------EVMYNG--------------HTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQV 1113 (1224)
T ss_dssp             HHHHTTTSCTTSE---------ECEECT--------------TTCCBCSSCEEEEEEEEEEBSSCGGGTCEEECCCC---
T ss_pred             HHHHHcCCCCCCC---------EEeecC--------------CCCCCccceEEEehhHhhcchhhcccCceEEeeCCCcc
Confidence            99999 9988777         999999              99999999999999999999999999999999999999


Q ss_pred             cccCCcccccCCCceeeeeccchhhhhcchhhhhhhhhc----------ccccccccc---cccCCeeecccCCCCcccc
Q 014847          315 LTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLK----------CKNVANVIQ---RVVGGPYCRICNSADDIIK  381 (417)
Q Consensus       315 lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL~----------c~~~~~~~~---~~~~~~~c~~c~~~~~~~~  381 (417)
                      |||||++||+|+|||||||||||||+|||||++|+|||+          |..|+.+.+   ...+.++|+.|.++.++..
T Consensus      1114 lT~QP~~Gr~r~GG~RfGEMErd~L~a~Gaa~~L~ErL~~~SD~~~~~vC~~cG~~~~~~~~~~~~~~c~~c~~~~~i~~ 1193 (1224)
T 1twf_B         1114 LTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQ 1193 (1224)
T ss_dssp             -------------CCCCCHHHHHHHHHHTCHHHHHHHHCCSSCCCEEEEESSSCSSCCEEETTTTEEEBTTTTBSSSEEE
T ss_pred             cccCCCcccccCCceecchhhhhhHHhccHHHHHHHHHhcCCccceeEeeccCCCeeeecccccCceECCcCCCCCcccc
Confidence            999999999999999999999999999999999999993          444444411   1223467999998889999


Q ss_pred             ccChHhHHHHHHHHHhhcCCeEEEEeccC
Q 014847          382 ANVPYGAKLLSQELSFSMGITLKFDTQLS  410 (417)
Q Consensus       382 ~~ipy~~k~l~~EL~~sm~i~~~l~~~~~  410 (417)
                      +.+|||||||+||| +||||++++.+++.
T Consensus      1194 ~~iPysfklL~~EL-~sm~i~~~l~~~~~ 1221 (1224)
T 1twf_B         1194 IHIPYAAKLLFQEL-MAMNITPRLYTDRS 1221 (1224)
T ss_dssp             EECCHHHHHHHHHH-HHTTBCCEEESCSS
T ss_pred             ccCCHhHHHHHHHH-HHCCCeeEEEeccc
Confidence            99999999999999 99999999998853
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} 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
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus} Back     alignment and structure
>3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory protein, transcription; 3.00A {Escherichia coli} 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 417
d1twfb_1207 e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces c 2e-55
d1smyc_1119 e.29.1.1 (C:) RNA-polymerase beta {Thermus thermop 1e-39
>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 =  195 bits (497), Expect = 2e-55
 Identities = 141/504 (27%), Positives = 205/504 (40%), Gaps = 127/504 (25%)

Query: 2    SFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRP 61
            S +LG++  IIP        Q            QA+G   TN N+R+DT+   L+YPQ+P
Sbjct: 729  SMILGVAASIIPF---PDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKP 785

Query: 62   LFWILISDCLGRP--------------------EDSLVMNQASLECGVFRS---ESYKAE 98
            L      + L                       EDS++MNQ+S++ G+FRS    SY  +
Sbjct: 786  LGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQ 845

Query: 99   VDNKDIQVKSRPS-------------------DDMLNFGKIQSKSGDIVIGKYAEIGADH 139
                 + +                        DD L    ++    D++IGK   I  D 
Sbjct: 846  EKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDE 905

Query: 140  ---------------SIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGD 184
                           S  L+ TE G+V +VL+++N DG  F  V +R          +GD
Sbjct: 906  EELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRT----TKIPQIGD 961

Query: 185  KFSSMHGQKGVLG---------FLEQ-----------------TPAQLLEAALGK-GACD 217
            KF+S HGQKG +G         F  +                 T A L+E  L K  A  
Sbjct: 962  KFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALS 1021

Query: 218  GLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIA 277
            G    A+PF      +  E     +S+LL   G ++ G   ++                 
Sbjct: 1022 GNEGDASPF----TDITVEG----ISKLLREHGYQSRGFEVMY----------NGHTGKK 1063

Query: 278  FICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCD 337
                  + IF   T+YQ+  HM +DK+  R  G  Q LT +PV  R R GG+ FGEM+ D
Sbjct: 1064 L----MAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERD 1119

Query: 338  CLIAHGASGNLHERL-------------KCKNVANVIQRVVGGPYCRICNSADDIIKANV 384
            C+IAHGA+  L ERL              C  +  + +       C+ C++  DI + ++
Sbjct: 1120 CMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHI 1179

Query: 385  PYGAKLLSQELSFSMGITLKFDTQ 408
            PY AKLL QEL  +M IT +  T 
Sbjct: 1180 PYAAKLLFQELM-AMNITPRLYTD 1202
>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 ?
Query417
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=6.4e-112  Score=963.62  Aligned_cols=378  Identities=36%  Similarity=0.516  Sum_probs=330.7

Q ss_pred             CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeeccccccCC-------
Q 014847            1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGR-------   73 (417)
Q Consensus         1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~lg~-------   73 (417)
                      |++|||++|++|||+||  ||||||+|||| |+|||||++.+|+..|+|++.|.|+|||+|||+|+.++.+++       
T Consensus       728 p~~ilg~~as~iPf~~h--NqSpRn~yq~q-m~KQa~G~~~~~~~~r~D~~~~~l~~pQ~Plv~t~~~~~~~~~e~p~G~  804 (1207)
T d1twfb_         728 PSMILGVAASIIPFPDH--NQSPRNTYQSA-MGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQ  804 (1207)
T ss_dssp             GGGGSCTTGGGSSSGGG--SCHHHHHHHHH-HGGGBCBCSCTTTTTCCCSEEEEESSCBCCSEECTTHHHHTTTTSCCCE
T ss_pred             cceEEeeecceEEeccc--ccccceeeccc-CCcccCCccccccceeccccceeEecCCCceeeccchhhhhhhcccchh
Confidence            78999999999999999  99999999999 899999999999999999999999999999999988774443       


Q ss_pred             ------------C-CCeEEEecceecccceeeEEEEEEEecc--------cccC---------------CCCCCCccccc
Q 014847           74 ------------P-EDSLVMNQASLECGVFRSESYKAEVDNK--------DIQV---------------KSRPSDDMLNF  117 (417)
Q Consensus        74 ------------n-EDAiIiNKssidRG~f~s~~Yk~e~~~~--------~~~~---------------~~~~~~g~~~~  117 (417)
                                  | ||||||||+|+|||||||++|+++....        +.+.               ..++++|++.+
T Consensus       805 N~iVAvmsy~GYN~EDAiIiNk~si~rG~f~s~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~  884 (1207)
T d1twfb_         805 NAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAP  884 (1207)
T ss_dssp             EEEEEECBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECCCCSCTTCCCEESCCCCSSSCBCCSSCGGGCCTTSBCCT
T ss_pred             ceEEEEEeccCcccccccccchhhhhhcccceeeeEEEEEEeccccccccccccccccccccccchhhhhcccccccccc
Confidence                        3 9999999999999999999988765320        1110               12678899999


Q ss_pred             cccccccCCeEEEEeccCC---------------ceeEEEecCCCceeEEEEEEEeCCCCCeEEEEEEeecccccccccc
Q 014847          118 GKIQSKSGDIVIGKYAEIG---------------ADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACL  182 (417)
Q Consensus       118 g~~~v~~GDiligk~~~~~---------------~d~s~~~k~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~~~~~R~p~i  182 (417)
                      |. .+++||+|+||++|..               +|+|++++.++.|+||+|.++.+.++.+.++|++|+    .|+|+|
T Consensus       885 G~-~v~~gdilvgk~~p~~~~~~~~~~~~~~~~~~~~s~~~~~~~~g~V~~v~~~~~~~~~~~~kv~i~~----~R~p~i  959 (1207)
T d1twfb_         885 GV-RVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRT----TKIPQI  959 (1207)
T ss_dssp             TC-EECTTCEEECEECCCC-------------CCBBCCEECCTTCCEEEEEEEEEECSSSCEEEEEEEEE----EECCCT
T ss_pred             cc-cccCCceeeeeeeccCCchhhhhhccccccccceeEEccCCCCeEEEEEEEeecccccceeeEEEEE----Eeccch
Confidence            96 7999999999998642               689999999999999999999999999999999999    999999


Q ss_pred             ccccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHH
Q 014847          183 GDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVIT  235 (417)
Q Consensus       183 GDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~  235 (417)
                      |||||||||||||||+||                          ||||||+|+++||+ |+.|.+.|+|||++.+.+++.
T Consensus       960 GDKfasRhGqKGv~s~i~p~eDMPf~~dG~~pDiI~NP~g~PSRMtiGql~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~ 1039 (1207)
T d1twfb_         960 GDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGIS 1039 (1207)
T ss_dssp             TCEEECTTSCEEEEEEEECTTTSCEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSSSCCHHHHH
T ss_pred             hhhhhhccCCcceeeeeechhhCCcCCCCCCccEEECCCcCcccCcHHHHHHHHHHHHHHhcCCccccCCCCCccHHHHH
Confidence            999999999999999999                          99999999999999 889999999999999999999


Q ss_pred             HHHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCC
Q 014847          236 EQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQP  314 (417)
Q Consensus       236 ~~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~  314 (417)
                      +.|.+ ||+++|+         |.||||              +||++|+++||+|++|||||+|||+||+|||++||++.
T Consensus      1040 ~~L~~~g~~~~G~---------e~ly~G--------------~tG~~~~~~i~~G~~yy~rL~HmV~DK~~~Rs~Gp~~~ 1096 (1207)
T d1twfb_        1040 KLLREHGYQSRGF---------EVMYNG--------------HTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQV 1096 (1207)
T ss_dssp             HHHHTTTSCTTSE---------ECEECT--------------TTCCBCSSCEEEEEEEEEEBSSCGGGTCEEECCCC---
T ss_pred             HHHHHcCCCCCCC---------EEEECC--------------CCCCCccceEEEehhHhhhhhhhhccccEeeccCCCCc
Confidence            99999 9999888         999999              99999999999999999999999999999999999999


Q ss_pred             cccCCcccccCCCceeeeeccchhhhhcchhhhhhhhh----------cccccccccc--c-ccCCeeecccCCCCcccc
Q 014847          315 LTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL----------KCKNVANVIQ--R-VVGGPYCRICNSADDIIK  381 (417)
Q Consensus       315 lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL----------~c~~~~~~~~--~-~~~~~~c~~c~~~~~~~~  381 (417)
                      |||||++||+++|||||||||||||+|||||++|+|||          .|..|+.+..  + ....++|+.|.++.++.+
T Consensus      1097 lT~QP~~Gr~~~GG~R~GEME~dal~a~Gaa~~L~e~l~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~c~~c~~~~~i~~ 1176 (1207)
T d1twfb_        1097 LTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQ 1176 (1207)
T ss_dssp             -------------CCCCCHHHHHHHHHHTCHHHHHHHHCCSSCCCEEEEESSSCSSCCEEETTTTEEEBTTTTBSSSEEE
T ss_pred             cccCCCCccccCCCcceehHHHHHHHHHhHHHHHHHHhhccCCccceeccccCCceEEEecccccceeecCCCCCCCccc
Confidence            99999999999999999999999999999999999999          4555554432  2 234578999999999999


Q ss_pred             ccChHhHHHHHHHHHhhcCCeEEEEeccC
Q 014847          382 ANVPYGAKLLSQELSFSMGITLKFDTQLS  410 (417)
Q Consensus       382 ~~ipy~~k~l~~EL~~sm~i~~~l~~~~~  410 (417)
                      +.+|||||||++|| +||||+++|.+++.
T Consensus      1177 ~~iPy~fk~l~~EL-~sm~i~~~l~~~~~ 1204 (1207)
T d1twfb_        1177 IHIPYAAKLLFQEL-MAMNITPRLYTDRS 1204 (1207)
T ss_dssp             EECCHHHHHHHHHH-HHTTBCCEEESCSS
T ss_pred             cCCCHHHHHHHHHH-HHCCCceEEEecCc
Confidence            99999999999999 99999999998764
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure