Citrus Sinensis ID: 019610

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-------34
MNQASLECGVFRSESYKAEVDNKDIQVKSRPSDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLSGVSMAAV
ccccccccccccEEEEEEEEccccccccccccccccccccEEEccccEEEEEEcccccEEEEEccccccEEEEEEEEEEccccccEEEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccEEEEcccccccccccccccccccccEEEEEEEEEEEEHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHcHHHHHHHHHccccHHHHHHHcccccccccccccccEEEEEcHHHHHHHHHHHHHHcccEEEEEEEEcccccccc
ccHHHHHccccEEEEEEEccccccccHHHHccccccEcccEEEccccEEEEEEcccccccEEEcccccccEEEEEEEEEcccccEEEEEEEEEEEEEEEccccccccccccccccEEEEEEEccccccccccccccccEEEccccccccccHHHHHHHHHHHHHHHcccccccccHHHHHHHccccccccEEEEccccccccccccEEEcHHHHHHHHHHHHccHHccccccEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccEEEEEcccEEEEccccccccccccccHHHHHHHHHHHHHHHccccEEEEccccEEEEEc
mnqaslecgvfrsesykaevdnkdiqvksrpsddmlnfgkiqsksgdiVIGKYAEIGADHSIKLKHTERGLVLKVLLssnddgknfAVVSIRQSVNMVHSaclgdkfssmhgqkgvlgfLEQTPAQLLEAALGKgacdglmsyatpfatstggviteQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSedkvkfrntgsfqpltgrpvadrkrfggiefgemKCDCLIahgasgnlherlkcknVANVIQRVvggpycricnsaddiikanvpYGAKLLSQELSFSMGitlkfdtqlsgvsmaav
mnqaslecgvfrsesykaevdnkdiqvksrpsddmlnfgkiqsksgdiVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTgsfqpltgrpvadrKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLkfdtqlsgvsmaav
MNQASLECGVFRSESYKAEVDNKDIQVKSRPSDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLSGVSMAAV
****************************************IQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQ*********
MNQASLECGVFRSESYKAEVD***********DDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLS*******
MNQASLECGVFRSESYKAEVDNKDIQVKSRPSDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQL********
****SLECGVFRSESYKAEVDNKDIQVKSRPSDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLSGVSMAAV
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MNQASLECGVFRSESYKAEVDNKDIQVKSRPSDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLSGVSMAAV
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 ?
Query338 2.2.26 [Sep-21-2011]
Q9LK401172 DNA-directed RNA polymera yes no 0.884 0.255 0.498 7e-90
Q9LV321119 DNA-directed RNA polymera no no 0.884 0.267 0.497 3e-89
A5DHT21236 DNA-directed RNA polymera N/A no 0.911 0.249 0.310 4e-34
P384201188 DNA-directed RNA polymera no no 0.884 0.251 0.312 2e-32
Q428771191 DNA-directed RNA polymera N/A no 0.887 0.251 0.311 6e-32
Q6FLD51223 DNA-directed RNA polymera yes no 0.899 0.248 0.291 5e-30
P085181224 DNA-directed RNA polymera yes no 0.899 0.248 0.291 6e-30
Q753Q41222 DNA-directed RNA polymera yes no 0.899 0.248 0.294 2e-29
Q020611210 DNA-directed RNA polymera yes no 0.893 0.249 0.298 2e-29
O27124603 DNA-directed RNA polymera yes no 0.852 0.477 0.292 4e-28
>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 =  330 bits (847), Expect = 7e-90,   Method: Compositional matrix adjust.
 Identities = 206/413 (49%), Positives = 242/413 (58%), Gaps = 114/413 (27%)

Query: 1    MNQASLECGVFRSE---SYKAEVDNKDIQVKSRPSDDMLNFGKIQSK------------- 44
            MN+ASLE G+FRSE   SYKAEVD KD + K +  D+++ FGK  SK             
Sbjct: 790  MNKASLERGMFRSEQIRSYKAEVDAKDSE-KRKKMDELVQFGKTHSKIGKVDSLEDDGFP 848

Query: 45   -------SGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNM 97
                   +GDIVIG+  E GADHSIKLKHTERG+V KV+LSSND+GKNFA VS+RQ    
Sbjct: 849  FIGANMSTGDIVIGRCTESGADHSIKLKHTERGIVQKVVLSSNDEGKNFAAVSLRQ---- 904

Query: 98   VHSACLGDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAA 131
            V S CLGDKFSSMHGQKGVLG+LE                          QTP QLLEAA
Sbjct: 905  VRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAA 964

Query: 132  LGKG-ACD-----------GLMSYATPFATSTGGVITEQ-HQSFVSQLLN--CIGARNSG 176
            L KG AC             L  +ATPF+T     ITEQ H++  S+  N      R+  
Sbjct: 965  LSKGIACPIQKEGSSAAYTKLTRHATPFSTPGVTEITEQLHRAGFSRWGNERVYNGRSGE 1024

Query: 177  ITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPL 236
                                     ++RS+IF   TFYQ+ +HMSEDKVKFRNTG   PL
Sbjct: 1025 -------------------------MMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPL 1059

Query: 237  TGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KCKNVANVIQ 283
            T +PVADRKRFGGI+FGEM+ DCLIAHGAS NLHERL             KCK  ANVI+
Sbjct: 1060 TRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSSQMHICRKCKTYANVIE 1119

Query: 284  RV------VGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQL 330
            R       + GPYCR+C S+D +++  VPYGAKLL QEL FSMGITL FDT+L
Sbjct: 1120 RTPSSGRKIRGPYCRVCVSSDHVVRVYVPYGAKLLCQEL-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|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|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|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|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|O27124|RPOB1_METTH DNA-directed RNA polymerase subunit B' OS=Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) GN=rpoB1 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 ?
Query338
224141967 1160 predicted protein [Populus trichocarpa] 0.890 0.259 0.548 1e-99
255548744 1203 DNA-directed RNA polymerase subunit, put 0.887 0.249 0.552 2e-99
449455519 1197 PREDICTED: DNA-directed RNA polymerase D 0.896 0.253 0.551 3e-99
67515338 1019 RNA polymerase IV second largest subunit 0.896 0.297 0.521 7e-95
225430474 1198 PREDICTED: DNA-directed RNA polymerase D 0.893 0.252 0.522 1e-94
357466021 1237 DNA-directed RNA polymerase subunit beta 0.887 0.242 0.534 1e-94
296082132 1220 unnamed protein product [Vitis vinifera] 0.893 0.247 0.522 1e-94
356518213 1205 PREDICTED: DNA-directed RNA polymerase D 0.887 0.248 0.534 1e-94
356509878 1205 PREDICTED: DNA-directed RNA polymerase D 0.887 0.248 0.532 8e-94
67515342 821 RNA polymerase IV second largest subunit 0.896 0.369 0.518 3e-93
>gi|224141967|ref|XP_002324332.1| predicted protein [Populus trichocarpa] gi|222865766|gb|EEF02897.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  369 bits (947), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 221/403 (54%), Positives = 252/403 (62%), Gaps = 102/403 (25%)

Query: 1    MNQASLECGVFRSE---SYKAEVDNKDIQVKSRPSDDMLNFGKIQSK------------- 44
            MN+ASLE G+FRSE   SYKAEVDNK++  K R S+D + FGKIQSK             
Sbjct: 788  MNRASLERGMFRSEHIRSYKAEVDNKELTDKRRKSEDSITFGKIQSKIGRVDSLDDDGFP 847

Query: 45   -------SGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNM 97
                   SGDIVIGK AE GADHS+KLKHTERG+V KV+LSSND+GKNFAVVS+RQ    
Sbjct: 848  FIGANMQSGDIVIGKCAESGADHSVKLKHTERGMVQKVVLSSNDEGKNFAVVSLRQ---- 903

Query: 98   VHSACLGDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAA 131
            V S CLGDKFSSMHGQKGVLGFLE                          QTP QLLEAA
Sbjct: 904  VRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGVVPDIVINPHAFPSRQTPGQLLEAA 963

Query: 132  LGKG-ACDGLMSYATPFAT-STGGVITEQHQSFVSQLLN--CIGARNSGITFIFKHYFLF 187
            LGKG AC G   YATPF+T S   +I + H++  S+  N      R              
Sbjct: 964  LGKGIACGGSKRYATPFSTLSVDDIIDQLHRAKFSRWGNERVYNGRTGE----------- 1012

Query: 188  CLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRF 247
                          +VRSLIF   TFYQ+ +HM+EDKVKFRNTG   PLT +PVADRKRF
Sbjct: 1013 --------------MVRSLIFMGPTFYQRLVHMAEDKVKFRNTGPVHPLTRQPVADRKRF 1058

Query: 248  GGIEFGEMKCDCLIAHGASGNLHERL-------------KCKNVANVIQRVVG------G 288
            GGI+FGEM+ DCLIAHGAS NLHERL             KCKNVANVIQR V       G
Sbjct: 1059 GGIKFGEMERDCLIAHGASANLHERLFTLSDSSEMHICQKCKNVANVIQRGVPGGRKIRG 1118

Query: 289  PYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLS 331
            PYCR+C S DD++K +VPYGAKLL QEL FSMGI+LKFDT++S
Sbjct: 1119 PYCRVCESVDDLVKVSVPYGAKLLCQEL-FSMGISLKFDTRVS 1160

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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
>gi|449455519|ref|XP_004145500.1| PREDICTED: DNA-directed RNA polymerase D subunit 2a-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|67515338|gb|AAY68198.1| RNA polymerase IV second largest subunit [Rhododendron macrophyllum] 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|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|296082132|emb|CBI21137.3| unnamed protein product [Vitis vinifera] 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 ?
Query338
TAIR|locus:20952331172 NRPD2A "nuclear RNA polymerase 0.254 0.073 0.688 3.6e-59
ASPGD|ASPL00000397701252 AN9120 [Emericella nidulans (t 0.378 0.102 0.415 7.4e-26
TAIR|locus:21190131188 NRPB2 [Arabidopsis thaliana (t 0.366 0.104 0.394 1.4e-25
CGD|CAL00041451234 orf19.3349 [Candida albicans ( 0.372 0.102 0.394 7.1e-25
UNIPROTKB|Q5A8Y51234 RPB140 "DNA-directed RNA polym 0.372 0.102 0.394 7.1e-25
SGD|S0000056771224 RPB2 "RNA polymerase II second 0.366 0.101 0.405 9.1e-24
GENEDB_PFALCIPARUM|PFB0715w1340 PFB0715w "DNA-directed RNA pol 0.355 0.089 0.383 1.1e-22
UNIPROTKB|O962361340 PFB0715w "DNA-directed RNA pol 0.355 0.089 0.383 1.1e-22
GENEDB_PFALCIPARUM|PFL0330c1450 PFL0330c "DNA-directed RNA pol 0.736 0.171 0.334 1.4e-20
UNIPROTKB|Q8I5X91450 PFL0330c "DNA-directed RNA pol 0.736 0.171 0.334 1.4e-20
TAIR|locus:2095233 NRPD2A "nuclear RNA polymerase D2A" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 300 (110.7 bits), Expect = 3.6e-59, Sum P(3) = 3.6e-59
 Identities = 62/90 (68%), Positives = 70/90 (77%)

Query:    33 DDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIR 92
             DD   F      +GDIVIG+  E GADHSIKLKHTERG+V KV+LSSND+GKNFA VS+R
Sbjct:   844 DDGFPFIGANMSTGDIVIGRCTESGADHSIKLKHTERGIVQKVVLSSNDEGKNFAAVSLR 903

Query:    93 QSVNMVHSACLGDKFSSMHGQKGVLGFLEQ 122
             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
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
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
GENEDB_PFALCIPARUM|PFL0330c PFL0330c "DNA-directed RNA polymerase III subunit, putative" [Plasmodium falciparum (taxid:5833)] Back     alignment and assigned GO terms
UNIPROTKB|Q8I5X9 PFL0330c "DNA-directed RNA polymerase" [Plasmodium falciparum 3D7 (taxid:36329)] 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

Your Input:
estExt_Genewise1_v1.C_LG_XVIII1865
hypothetical protein (1161 aa)
(Populus trichocarpa)
Predicted Functional Partners:
gw1.I.2689.1
hypothetical protein (1334 aa)
• ••• • 0.829
estExt_fgenesh4_pg.C_1570036
hypothetical protein (206 aa)
•   ••• 0.606
gw1.IX.2304.1
hypothetical protein (321 aa)
  • ••• 0.600
eugene3.00060510
hypothetical protein (1168 aa)
• ••  • 0.597
grail3.0014029901
hypothetical protein (52 aa)
    ••• 0.537
eugene3.00012667
hypothetical protein (390 aa)
  • • • 0.506
NRPD903
RNA polymerase IV subunit (924 aa)
  •   • 0.499
eugene3.00081703
SubName- Full=Putative uncharacterized protein; (536 aa)
  •     0.466
estExt_Genewise1_v1.C_LG_X5038
hypothetical protein (536 aa)
  •     0.465
grail3.2024000101
hypothetical protein (140 aa)
  •     0.456

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query338
cd00653866 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun 6e-66
COG00851060 COG0085, RpoB, DNA-directed RNA polymerase, beta s 5e-41
TIGR03670599 TIGR03670, rpoB_arch, DNA-directed RNA polymerase 1e-40
PRK085651103 PRK08565, PRK08565, DNA-directed RNA polymerase su 2e-39
PRK07225605 PRK07225, PRK07225, DNA-directed RNA polymerase su 2e-34
pfam00562373 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, do 3e-31
pfam0456078 pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, do 2e-15
CHL002071077 CHL00207, rpoB, RNA polymerase beta subunit; Provi 1e-11
TIGR020131065 TIGR02013, rpoB, DNA-directed RNA polymerase, beta 2e-09
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 6e-07
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 2e-06
PRK004051112 PRK00405, rpoB, DNA-directed RNA polymerase subuni 3e-05
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit Back     alignment and domain information 
 Score =  222 bits (568), Expect = 6e-66
 Identities = 123/407 (30%), Positives = 162/407 (39%), Gaps = 118/407 (28%)

Query: 1   MNQASLECGVFRS---ESYKAEVDNK----------DIQVKSRPSDDMLNF-GKI----Q 42
           +N++S++ G FRS   + Y+ E+             DI   S      L+  G I    +
Sbjct: 498 INKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGAR 557

Query: 43  SKSGDIVIGKYAEIGA---------------DHSIKLKHTERGLVLKVLLSS---NDDGK 84
            + GDI++GK    G                D S+K    E+G+V  V + S   ND G 
Sbjct: 558 VEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGN 617

Query: 85  NFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FLEQ------------- 122
               V IRQ         +GDKF+S HGQKGV+          F E              
Sbjct: 618 KLVKVYIRQ----KRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGF 673

Query: 123 ----TPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARN--- 174
               T  QLLE+ LGK GA  G    ATPF  +    I+E         LN  G      
Sbjct: 674 PSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISE---LLGEAGLNYYG--KEVL 728

Query: 175 -SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSF 233
             G T            E P             IF    +YQ+  HM +DK+  R+TG +
Sbjct: 729 YDGRTGE--------PLEAP-------------IFVGPVYYQRLKHMVDDKIHARSTGPY 767

Query: 234 QPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KCKNVAN 280
             LT +P+  R R GG  FGEM+ D LIAHGA+  L ERL             KC  + +
Sbjct: 768 SLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILS 827

Query: 281 VIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFD 327
                     CR+C    +I K  +PY  KLL QEL  SM I  +  
Sbjct: 828 AN-------LCRLCKKGTNISKVGIPYAFKLLFQELQ-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|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>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|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 338
PRK07225605 DNA-directed RNA polymerase subunit B'; Validated 100.0
TIGR03670599 rpoB_arch DNA-directed RNA polymerase subunit B. T 100.0
COG00851060 RpoB DNA-directed RNA polymerase, beta subunit/140 100.0
PRK085651103 DNA-directed RNA polymerase subunit B; Provisional 100.0
cd00653866 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po 100.0
CHL002071077 rpoB RNA polymerase beta subunit; Provisional 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
KOG02161111 consensus RNA polymerase I, second largest subunit 100.0
KOG02151153 consensus RNA polymerase III, second largest subun 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 99.93
KOG02141141 consensus RNA polymerase II, second largest subuni 95.53
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated Back     alignment and domain information 
Probab=100.00  E-value=3.7e-92  Score=729.66  Aligned_cols=301  Identities=32%  Similarity=0.486  Sum_probs=275.6

Q ss_pred             CcccccccccceeeeEEEEEeec--------ccccc---------------CCCCCCcccccccccCCCCeEEEEeccC-
Q 019610            1 MNQASLECGVFRSESYKAEVDNK--------DIQVK---------------SRPSDDMLNFGKIQSKSGDIVIGKYAEI-   56 (338)
Q Consensus         1 iNKsSidRG~f~s~~Ykte~~~~--------~~~~~---------------~~~~~~~~~~g~~~v~~gDvligk~~~~-   56 (338)
                      |||||||||||||++|+++....        +.++.               .+|+||++.+|. .|++|||||||++|. 
T Consensus       225 iNkssidRGlf~s~~~k~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~-~v~~gdiligk~sp~~  303 (605)
T PRK07225        225 MNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNPET-EVKEGDVLIGKTSPPR  303 (605)
T ss_pred             eehhhhhcCceEEEEEEEEEEEeeecCCCcceEEecCCchhccccChHHhhcCCCCCCccCCC-EECCCCEEEEEecCCC
Confidence            79999999999999988865311        11221               256788999888 789999999998762 


Q ss_pred             --------------CceeEEEecCCCceeEEEEEEEeCCCCCeeEEEEEeeccccccccccccccccccCCcceeeeec-
Q 019610           57 --------------GADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE-  121 (338)
Q Consensus        57 --------------~~d~s~~~~~~e~g~Vd~V~~~~~~~g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~i~-  121 (338)
                                    .+|+|++++++|+|+||+|.++.+++|...++|++|+    .|+|+||||||||||||||||+|| 
T Consensus       304 ~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~ir~----~R~p~iGDKfssRHGQKGvvs~i~~  379 (605)
T PRK07225        304 FLEEPDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRD----LRIPELGDKFASRHGQKGVIGLIVP  379 (605)
T ss_pred             CccchhhhcccccCcceeeEEecCCCcEEEEEEEEEecCCCCEEEEEEEEE----EEeccccchhhhcccCceeEEeEec
Confidence                          4789999999999999999999988888999999999    999999999999999999999999 


Q ss_pred             -------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHHHHHHh-hccccCccccCCC
Q 019610          122 -------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVSQLLNCIGARN  174 (338)
Q Consensus       122 -------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~~~l~~-~~~~~g~~~~~~~  174 (338)
                                               ||||||+|+++||+ ++.|.+.|+|||...+.+++.+.|.+ ||+++|+      
T Consensus       380 ~eDMPft~~G~~PDiIiNPhg~PSRMTiGql~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~------  453 (605)
T PRK07225        380 QEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGK------  453 (605)
T ss_pred             cccCCcCCCCCcccEEECcccccccCcHHHHHHHHHHHHHHhcCceEeecCCCCchHHHHHHHHHHhCcCCCCe------
Confidence                                     99999999999999 88999999999999999999999999 9999998      


Q ss_pred             CCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCccccccCCceeeee
Q 019610          175 SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGE  254 (338)
Q Consensus       175 ~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfGE  254 (338)
                         |.||||              +||++|+++||+|++|||||+|||+||+|+|++||++.|||||++||+|+|||||||
T Consensus       454 ---e~my~G--------------~TG~~~~~~if~G~~yYqrL~HmV~DK~haR~~Gp~~~lTrQP~~GR~r~GG~RfGE  516 (605)
T PRK07225        454 ---EVMYDG--------------ITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGE  516 (605)
T ss_pred             ---EEEEcC--------------CCCCEecccEEEeehheeechhhhcchhhhccCCCCcccccCCccccccCCCeeeee
Confidence               999999              999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccchhhhhhchHHhhhhhh----------ccccccccccc--ccCCeeecccCCCCccccccChHhHHHHHHHHhhhcCC
Q 019610          255 MKCDCLIAHGASGNLHERL----------KCKNVANVIQR--VVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI  322 (338)
Q Consensus       255 ME~daLiahGAs~~L~ErL----------~c~~~~~~~~~--~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i  322 (338)
                      ||||||+|||||++|+|||          .|..|+.+...  .....+|+.|.++..+.++.+|||||||+||| +||||
T Consensus       517 MErd~lia~Gas~~L~Erl~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPya~kll~~EL-~sm~i  595 (605)
T PRK07225        517 MERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDEL-KSLGI  595 (605)
T ss_pred             eehhhhhhhhhHHHHHHHHhccCcceeEEeecCcCcceehhcccCceeecccCCCCceeeccCChhHHHHHHHH-HHCCc
Confidence            9999999999999999999          77788766532  22357799999988999999999999999999 99999


Q ss_pred             eEEEEeee
Q 019610          323 TLKFDTQL  330 (338)
Q Consensus       323 ~~~~~~~~  330 (338)
                      +++|.++.
T Consensus       596 ~~~l~~~~  603 (605)
T PRK07225        596 APRLELED  603 (605)
T ss_pred             eeEEEecc
Confidence            99999873

>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B Back     alignment and domain information
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] 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
>CHL00207 rpoB RNA polymerase beta subunit; Provisional 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
>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
>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
>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 ?
Query338
1i3q_B1224 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 5e-31
3h0g_B1210 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 2e-30
2waq_B1131 The Complete Structure Of The Archaeal 13-Subunit D 2e-22
2pmz_B1124 Archaeal Rna Polymerase From Sulfolobus Solfataricu 7e-21
1i6v_C1118 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 2e-08
1hqm_C1119 Crystal Structure Of Thermus Aquaticus Core Rna Pol 2e-08
1ynj_C1119 Taq Rna Polymerase-Sorangicin Complex Length = 1119 2e-08
1l9u_C1118 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 2e-08
1iw7_C1119 Crystal Structure Of The Rna Polymerase Holoenzyme 4e-08
3lu0_C1342 Molecular Model Of Escherichia Coli Core Rna Polyme 1e-06
3iyd_C1342 Three-Dimensional Em Structure Of An Intact Activat 1e-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 =  131 bits (330), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 119/408 (29%), Positives = 176/408 (43%), Gaps = 104/408 (25%)
Query: 1    MNQASLECGVFRSESYKAEVDNKD------IQVKSRP----------------SDDMLNF 38
            MNQ+S++ G+FRS  +++ +D +        +   +P                 DD L  
Sbjct: 841  MNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIA 900
Query: 39   GKIQSKSGDIVIGKYAEIGADH---------------SIKLKHTERGLVLKVLLSSNDDG 83
              ++    D++IGK   I  D                S  L+ TE G+V +VL+++N DG
Sbjct: 901  PGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG 960
Query: 84   KNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFL---EQTP---------------- 124
              F  V +R +        +GDKF+S HGQKG +G     E  P                
Sbjct: 961  LKFVKVRVRTT----KIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHA 1016
Query: 125  -------AQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSG 176
                   A L+E  L K  A  G    A+PF   T           +S+LL   G ++ G
Sbjct: 1017 IPSRMTVAHLIECLLSKVAALSGNEGDASPFTDIT--------VEGISKLLREHGYQSRG 1068
Query: 177  ITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPL 236
               ++  +    L               + IF   T+YQ+  HM +DK+  R  G  Q L
Sbjct: 1069 FEVMYNGHTGKKLM--------------AQIFFGPTYYQRLRHMVDDKIHARARGPMQVL 1114
Query: 237  TGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVA------------NVIQR 284
            T +PV  R R GG+ FGEM+ DC+IAHGA+  L ERL   + A             VI +
Sbjct: 1115 TRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAK 1174
Query: 285  VVGGPY-CRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLS 331
            +    + C+ C++  DI + ++PY AKLL QEL  +M IT +  T  S
Sbjct: 1175 LNHNQFECKGCDNKIDIYQIHIPYAAKLLFQEL-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|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|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex 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|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 ?
Query338
1twf_B1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 1e-66
3h0g_B1210 DNA-directed RNA polymerase II subunit RPB2; trans 1e-65
4ayb_B1131 DNA-directed RNA polymerase; transferase, multi-su 3e-65
2a6h_C1119 DNA-directed RNA polymerase beta chain; RNA polyme 5e-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 =  225 bits (576), Expect = 1e-66
 Identities = 115/414 (27%), Positives = 164/414 (39%), Gaps = 120/414 (28%)

Query: 1    MNQASLECGVFRSE---SYKAEVDNKDIQVKSR---PSDDMLNFGKIQS----------- 43
            MNQ+S++ G+FRS    SY  +     + +      P        K  +           
Sbjct: 841  MNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIA 900

Query: 44   -----KSGDIVIGKYAEIGA---------------DHSIKLKHTERGLVLKVLLSSNDDG 83
                    D++IGK   I                 D S  L+ TE G+V +VL+++N DG
Sbjct: 901  PGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG 960

Query: 84   KNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFL----------------------- 120
              F  V +R          +GDKF+S HGQKG +G                         
Sbjct: 961  LKFVKVRVRT----TKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHA 1016

Query: 121  ---EQTPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSG 176
                 T A L+E  L K  A  G    A+PF      +  E     +S+LL   G ++ G
Sbjct: 1017 IPSRMTVAHLIECLLSKVAALSGNEGDASPF----TDITVEG----ISKLLREHGYQSRG 1068

Query: 177  ITFIFKHYFLFCLFEC--------PMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFR 228
                         FE          +          + IF   T+YQ+  HM +DK+  R
Sbjct: 1069 -------------FEVMYNGHTGKKL---------MAQIFFGPTYYQRLRHMVDDKIHAR 1106

Query: 229  NTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KC 275
              G  Q LT +PV  R R GG+ FGEM+ DC+IAHGA+  L ERL              C
Sbjct: 1107 ARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGIC 1166

Query: 276  KNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQ 329
              +  + +       C+ C++  DI + ++PY AKLL QEL  +M IT +  T 
Sbjct: 1167 GLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQEL-MAMNITPRLYTD 1219
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query338
1twf_B1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 100.0
4ayb_B1131 DNA-directed RNA polymerase; transferase, multi-su 100.0
3h0g_B1210 DNA-directed RNA polymerase II subunit RPB2; trans 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 98.62
3tbi_B228 DNA-directed RNA polymerase subunit beta; transcri 98.47
>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=7.6e-91  Score=764.34  Aligned_cols=301  Identities=36%  Similarity=0.522  Sum_probs=258.5

Q ss_pred             CcccccccccceeeeEEEEEeec--------cccccC---------------CCCCCcccccccccCCCCeEEEEeccCC
Q 019610            1 MNQASLECGVFRSESYKAEVDNK--------DIQVKS---------------RPSDDMLNFGKIQSKSGDIVIGKYAEIG   57 (338)
Q Consensus         1 iNKsSidRG~f~s~~Ykte~~~~--------~~~~~~---------------~~~~~~~~~g~~~v~~gDvligk~~~~~   57 (338)
                      |||+|||||||||+.|+++..+.        +.+++|               +|+||++.+|. .|++|||||||++|++
T Consensus       841 in~~sv~rg~~~s~~~~~y~~~~~~~~~~~~e~~~~P~~~~~~~~~~~~~~~LD~dGiv~~G~-~V~~gDilvgK~~p~~  919 (1224)
T 1twf_B          841 MNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGV-RVSGEDVIIGKTTPIS  919 (1224)
T ss_dssp             EEHHHHHTTTTCEEEEEEEEECCCCSCTTCCCEESCCCCSSSCBCCSSCGGGCCTTSBCCTTC-EECTTCEEECEECCCC
T ss_pred             hhhhHHhcCCeeEEEEEEEEEEeeeCCCCceeEecCCChhhccCccHHHHhhcccCCccCCcc-EecCCCEEEEEecCCC
Confidence            69999999999999998876431        223322               56789999998 8999999999999843


Q ss_pred             ---------------ceeEEEecCCCceeEEEEEEEeCCCCCeeEEEEEeeccccccccccccccccccCCcceeeeec-
Q 019610           58 ---------------ADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE-  121 (338)
Q Consensus        58 ---------------~d~s~~~~~~e~g~Vd~V~~~~~~~g~~~v~v~ir~~~~~~R~~~iGDKfssRHGqKGvvs~i~-  121 (338)
                                     +|+|++++++|.|+||+|.++++++|.+.|+|++|+    +|.|++|||||||||||||||+|+ 
T Consensus       920 ~~~~~~~~~~~~~~~rd~s~~~~~~e~g~Vd~V~~~~~~~g~~~vkV~ir~----~R~p~iGDKfasRHGqKGvis~i~p  995 (1224)
T 1twf_B          920 PDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRT----TKIPQIGDKFASRHGQKGTIGITYR  995 (1224)
T ss_dssp             -------------CCBBCCEECCTTCCEEEEEEEEEECSSSCEEEEEEEEE----EECCCTTCEEECTTSCEEEEEEEEC
T ss_pred             ccccccccccccCccceeEEEeeCCCCeEEEEEEEEecCCCCEEEEEEEEe----cCCCCchhhhhhhccCcceeeeecc
Confidence                           689999999999999999999999999999999999    999999999999999999999999 


Q ss_pred             -------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHHHHHHh-hccccCccccCCC
Q 019610          122 -------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVSQLLNCIGARN  174 (338)
Q Consensus       122 -------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~~~l~~-~~~~~g~~~~~~~  174 (338)
                                               ||||||+|+++||+ ++.|...|+|||++.+++++++.|++ ||+++|+      
T Consensus       996 ~eDMPf~~dG~~pDiIiNPhg~PSRMtiGqllE~~lgka~~~~G~~~datpF~~~~~~~i~~~L~~~g~~~~G~------ 1069 (1224)
T 1twf_B          996 REDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGF------ 1069 (1224)
T ss_dssp             TTTSCEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSSSCCHHHHHHHHHTTTSCTTSE------
T ss_pred             cccCCcCCCCCCccEEeCCCcCccccccchhHHHHhhHHHHhcCceeecCCCCCccHHHHHHHHHHcCCCCCCC------
Confidence                                     99999999999999 88999999999999999999999999 9998888      


Q ss_pred             CCeEEEeeCCcccccccCCCcccccceeeeeeEEEeeeeeeccccccCccceeeeecCCcccccCCccccccCCceeeee
Q 019610          175 SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGE  254 (338)
Q Consensus       175 ~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfGE  254 (338)
                         |.||||              +||++|+++||+|++|||||+|||+||+||||+|||+.|||||++||+|+|||||||
T Consensus      1070 ---e~ly~G--------------~TG~~~~~~i~vG~~YyqkL~HmV~DKihaRs~GP~~~lT~QP~~Gr~r~GG~RfGE 1132 (1224)
T 1twf_B         1070 ---EVMYNG--------------HTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGE 1132 (1224)
T ss_dssp             ---ECEECT--------------TTCCBCSSCEEEEEEEEEEBSSCGGGTCEEECCCC----------------CCCCCH
T ss_pred             ---EEeecC--------------CCCCCccceEEEehhHhhcchhhcccCceEEeeCCCcccccCCCcccccCCceecch
Confidence               999999              999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccchhhhhhchHHhhhhhh----------cccccccccc---cccCCeeecccCCCCccccccChHhHHHHHHHHhhhcC
Q 019610          255 MKCDCLIAHGASGNLHERL----------KCKNVANVIQ---RVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMG  321 (338)
Q Consensus       255 ME~daLiahGAs~~L~ErL----------~c~~~~~~~~---~~~~~~~c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~  321 (338)
                      ||||||+|||||++|+|||          .|..||.+.+   .....++|+.|.++.++.++.+|||||||+||| +|||
T Consensus      1133 MErd~L~a~Gaa~~L~ErL~~~SD~~~~~vC~~cG~~~~~~~~~~~~~~c~~c~~~~~i~~~~iPysfklL~~EL-~sm~ 1211 (1224)
T 1twf_B         1133 MERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQEL-MAMN 1211 (1224)
T ss_dssp             HHHHHHHHHTCHHHHHHHHCCSSCCCEEEEESSSCSSCCEEETTTTEEEBTTTTBSSSEEEEECCHHHHHHHHHH-HHTT
T ss_pred             hhhhhHHhccHHHHHHHHHhcCCccceeEeeccCCCeeeecccccCceECCcCCCCCccccccCCHhHHHHHHHH-HHCC
Confidence            9999999999999999999          3444454421   122346799998888999999999999999999 9999


Q ss_pred             CeEEEEeee
Q 019610          322 ITLKFDTQL  330 (338)
Q Consensus       322 i~~~~~~~~  330 (338)
                      |++++.++.
T Consensus      1212 i~~~l~~~~ 1220 (1224)
T 1twf_B         1212 ITPRLYTDR 1220 (1224)
T ss_dssp             BCCEEESCS
T ss_pred             CeeEEEecc
Confidence            999999874
>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
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} 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 338
d1twfb_1207 e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces c 3e-50
d1smyc_1119 e.29.1.1 (C:) RNA-polymerase beta {Thermus thermop 2e-38
>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 =  177 bits (450), Expect = 3e-50
 Identities = 115/406 (28%), Positives = 167/406 (41%), Gaps = 104/406 (25%)

Query: 1    MNQASLECGVFRS---ESYKAEVDNKDIQVKSRPS-------------------DDMLNF 38
            MNQ+S++ G+FRS    SY  +     + +                        DD L  
Sbjct: 824  MNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIA 883

Query: 39   GKIQSKSGDIVIGKYAEIGADH---------------SIKLKHTERGLVLKVLLSSNDDG 83
              ++    D++IGK   I  D                S  L+ TE G+V +VL+++N DG
Sbjct: 884  PGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG 943

Query: 84   KNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FLEQ------------ 122
              F  V +R          +GDKF+S HGQKG +G         F  +            
Sbjct: 944  LKFVKVRVRT----TKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHA 999

Query: 123  -----TPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSG 176
                 T A L+E  L K  A  G    A+PF      +  E     +S+LL   G ++ G
Sbjct: 1000 IPSRMTVAHLIECLLSKVAALSGNEGDASPF----TDITVEG----ISKLLREHGYQSRG 1051

Query: 177  ITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPL 236
               ++                       + IF   T+YQ+  HM +DK+  R  G  Q L
Sbjct: 1052 FEVMY----------NGHTGKKL----MAQIFFGPTYYQRLRHMVDDKIHARARGPMQVL 1097

Query: 237  TGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KCKNVANVIQ 283
            T +PV  R R GG+ FGEM+ DC+IAHGA+  L ERL              C  +  + +
Sbjct: 1098 TRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAK 1157

Query: 284  RVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQ 329
                   C+ C++  DI + ++PY AKLL QEL  +M IT +  T 
Sbjct: 1158 LNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELM-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 ?
Query338
d1smyc_1119 RNA-polymerase beta {Thermus thermophilus [TaxId: 100.0
d1twfb_1207 RBP2 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} 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: RNA-polymerase beta
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=1.7e-89  Score=746.30  Aligned_cols=307  Identities=23%  Similarity=0.314  Sum_probs=267.7

Q ss_pred             CcccccccccceeeeEEEEEeecc-------ccc-----------cCCCCCCcccccccccCCCCeEEEEeccCC-----
Q 019610            1 MNQASLECGVFRSESYKAEVDNKD-------IQV-----------KSRPSDDMLNFGKIQSKSGDIVIGKYAEIG-----   57 (338)
Q Consensus         1 iNKsSidRG~f~s~~Ykte~~~~~-------~~~-----------~~~~~~~~~~~g~~~v~~gDvligk~~~~~-----   57 (338)
                      |||||+|||||||+.|+++..+..       ...           ..+|+||++.+|+ .|++|||||||++|..     
T Consensus       690 iNkssidRG~~~s~~~k~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~G~-~v~~gdili~k~~~~~~~~~~  768 (1119)
T d1smyc_         690 ISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGA-EVKPGDILVGRTSFKGESEPT  768 (1119)
T ss_dssp             EETHHHHTTCSCEEEEEEEEEEEECCTTCCCBCCSCCTTSCSTTTGGGTTTSBCCTTC-BCCTTCEEECCEECSSSSSCC
T ss_pred             hcchhhhccccceeeeeEEEeeeeeccCCCceecccCcCcChhhHhhccccCCcCCCC-EeCCCCEEEEEeccCCCCCCC
Confidence            699999999999999888754311       000           1257889999998 7899999999988632     


Q ss_pred             -----------------ceeEEEecCCCceeEEEEEEEeCCCC--------CeeEEEEEeeccccccccccccccccccC
Q 019610           58 -----------------ADHSIKLKHTERGLVLKVLLSSNDDG--------KNFAVVSIRQSVNMVHSACLGDKFSSMHG  112 (338)
Q Consensus        58 -----------------~d~s~~~~~~e~g~Vd~V~~~~~~~g--------~~~v~v~ir~~~~~~R~~~iGDKfssRHG  112 (338)
                                       +|+|+++++++.|+|++|.+..++++        ...++|++|+    .|+|+||||||||||
T Consensus       769 ~~~~~~~~~~~~~~~~~k~~s~~~~~~~~g~v~~v~~~~~~~~~~~~~~~~~~~vkv~~r~----~R~p~iGDKfssRHG  844 (1119)
T d1smyc_         769 PEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQ----KRKLQVGDKLANRHG  844 (1119)
T ss_dssp             HHHHHHHHHHHSCSCCCEECCEECCSSCCCEEEEEEEECSSCSSCCCCTTEEEEEEEEEEE----EECCCTTCEEECTTS
T ss_pred             hHHhhhhcccccccceeeeeeeccCCCCCCEEEEEEEEeccccccccCCCcceEEEEEEee----eeeccccchhhhhcc
Confidence                             68999999999999999999876543        2579999999    999999999999999


Q ss_pred             Ccceeeeec--------------------------cChhHHHHHHhhhh-hccCCceeecCCCCCCHHHHHHHHHh-hcc
Q 019610          113 QKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITEQHQS-FVS  164 (338)
Q Consensus       113 qKGvvs~i~--------------------------MtiGql~E~~~gk~-a~~g~~~~~tpF~~~~~~~i~~~l~~-~~~  164 (338)
                      ||||||+||                          ||||||+|+++||+ |+.|.+.|+|||+..+.+++.+.|.+ ++.
T Consensus       845 QKGv~g~i~~~eDMPft~~Gi~PDiIiNPhg~PSRMTiG~liE~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~l~~~~~~  924 (1119)
T d1smyc_         845 NKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEV  924 (1119)
T ss_dssp             CEEEEEEEECTTTSCBCSSSCBCSEEECSTTTTTTTBTHHHHHHHHHHHHHHTTCEEECCSSSSCCHHHHHHHHHHHHHH
T ss_pred             CCccceeeechhhCccccCCcceeEEeccccccccccHHHHHHHHHHHHHhhcCceeeccCCCCCcHHHHHHHHHHHHHh
Confidence            999999999                          99999999999999 88999999999999999999999887 554


Q ss_pred             ccCccc----------------------------------cCCCCCeEEEeeCCcccccccCCCcccccceeeeeeEEEe
Q 019610          165 QLLNCI----------------------------------GARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTW  210 (338)
Q Consensus       165 ~~g~~~----------------------------------~~~~~gke~l~~g~~~~~~~~~p~~~~~tG~~~~~~if~G  210 (338)
                      ++++.+                                  +++.+|+|.||||              +||++|+++||+|
T Consensus       925 ~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~G~e~my~G--------------~TG~~~~~~If~G  990 (1119)
T d1smyc_         925 YFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDG--------------RTGEPIEGPIVVG  990 (1119)
T ss_dssp             HHHHHHHTTCCCBHHHHHHHHHHHTTTSSCTTSCHHHHHHHHHHTTEECCBCT--------------TTSCBCSSCEEEE
T ss_pred             hccccccccccccchhHHHHHHHhhcccCCCCCChHHHHhhccCCCCEEEECC--------------CCCCEeCCeEEEE
Confidence            432221                                  1234688999999              9999999999999


Q ss_pred             eeeeeccccccCccceeeeecCCcccccCCccccccCCceeeeeccchhhhhhchHHhhhhhhcccccccccccccCCee
Q 019610          211 ITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPY  290 (338)
Q Consensus       211 ~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~GR~r~GG~RfGEME~daLiahGAs~~L~ErL~c~~~~~~~~~~~~~~~  290 (338)
                      |+|||||+|||+||+|||++||++.|||||++||+|+|||||||||||||||||||++|+|||..+|| ++..+..   .
T Consensus       991 ~~yYqrL~HmV~DK~haRs~Gp~~~lTrQP~~GRsr~GGlR~GEMErd~LiahGas~~L~erl~~~SD-~~~~~~~---~ 1066 (1119)
T d1smyc_         991 QMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSD-DIEGRNA---A 1066 (1119)
T ss_dssp             EEEEEEBCCCGGGSCEEESSCCBCSSSCCBCCCSSSCCCEEECHHHHHHHHHTTCHHHHHHHHTTTTT-CHHHHHH---H
T ss_pred             echhhccchhhCcCceeeccCCCchhhCCCCCcccCCCCccchhhHhHHHHHHHHHHHHHHHhhcccc-cccceeE---E
Confidence            99999999999999999999999999999999999999999999999999999999999999988888 4555442   3


Q ss_pred             ecccCCCCccccccChHhHHHHHHHHhhhcCCeEEEEeeec
Q 019610          291 CRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLS  331 (338)
Q Consensus       291 c~~c~~~~~i~~~~ipy~~k~L~~EL~~sm~i~~~~~~~~~  331 (338)
                      |..|.++.++.++.+|||||||+||| +||||++++.++..
T Consensus      1067 ~~~~~~~~~i~~v~iPyafKlL~qEL-~sm~i~~~l~~~~~ 1106 (1119)
T d1smyc_        1067 YEAIIKGEDVPEPSVPESFRVLVKEL-QALALDVQTLDEKD 1106 (1119)
T ss_dssp             HHHHHHTCCCCCCCCCHHHHHHHHHH-HHSSCEEEEECSSS
T ss_pred             ECCeECCCCCCCCCCChHHHHHHHHH-HHCCCCeEEEecCC
Confidence            44455667899999999999999999 99999999987765
>d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure