Psyllid ID: psy1131

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---
MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD
cHHHHHccccccccccEEEcccccEEEEcccccccccccccccEEEEEcccccEEEEEccccccccccccccEEEcccccccccHHHHHHHHccccccccccEEEcccccEEEEEccccccccccccccEEEEEcccccEEEEcccccccccccccccEEEccccEEEEccccccccccccccccccccccccHHHHHHHHHHHccccEEEcccccccEEEEEEHHHHHHHHHcccccccccEEHHHHcccEEcccccccccccccccEEEEcccccccccEEccccccccccccccccccccccHHHHHHHHHHHcccccEEEEcccccEEEEEEEEEEEEEEccccccccc
ccHHHccccccccccEEEEEccccEEEEccccccccEEEEccEEEEEEEEccccEEEcccccccHHHHHHHHccccccccccHcHHHHHHHHcccccccccEEEEEccccEEEEEEcccccccEEcccEEEEEEcccccEEEEcccccHHHHHHcccEEEEccccEEEEEEEEccccccccccccccccccccHHHHHHHHHHHcccccccccccccccEEHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHccccccccccEEEEEEcccccccccccccccccccccccHHHHHHHHHHHHcccccEcccccccEEEEEHHHHHHHHHHHHHcHccc
mfelvrrgnsqypgakyivrdngeridlrfhpkpsdlhlqcgykverhirdgdlvifnrqptlhkmsmmghrvrvlpwstfrmNLRMFELVRrgnsqypgakyivrdngeridlrfhpkpsdlhlqcgykverhirdgdlvifnrqptlhkmsmmghrvrvlpwstfrmnlsctspynadfdgdemnlhvpqsmetraevenihvtprqiitpqnnrpvmgIVQDTLTAVRKMTKRDVFLDKVERHirdgdlvifnrqptlhkmsmmghrvrvlpwstfrmnlsctspynadfdgdemnlhvpqsmetraevenihvtprqiitpqnnrpvmgIVQDTLTAVRKMTKRDVFLD
mfelvrrgnsqypgakyivrdNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQptlhkmsmmghRVRVLPWSTFRMNLRMFELvrrgnsqypgaKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQptlhkmsmmGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVtprqiitpqnnrpvmGIVQDTLTAVRkmtkrdvfldkverhirdgdlvifnrqptlhkmsmmGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVtprqiitpqnnrpvmgIVQDTLtavrkmtkrdvfld
MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD
*************GAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDG****************VENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDG******************NIHVTPRQIITPQNNRPVMGIVQDTLTAV***********
MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD
MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD
MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD
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MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD
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 ?
Query353 2.2.26 [Sep-21-2011]
P04052 1887 DNA-directed RNA polymera yes N/A 0.444 0.083 0.929 1e-84
P24928 1970 DNA-directed RNA polymera yes N/A 0.450 0.080 0.823 3e-77
P08775 1970 DNA-directed RNA polymera yes N/A 0.450 0.080 0.823 3e-77
P16356 1856 DNA-directed RNA polymera yes N/A 0.441 0.084 0.762 3e-72
P35074 1853 DNA-directed RNA polymera N/A N/A 0.441 0.084 0.756 5e-72
P35084 1727 DNA-directed RNA polymera yes N/A 0.444 0.090 0.719 2e-65
P36594 1752 DNA-directed RNA polymera yes N/A 0.464 0.093 0.654 2e-63
Q75A34 1745 DNA-directed RNA polymera yes N/A 0.441 0.089 0.660 4e-60
A5DCV3 1579 DNA-directed RNA polymera N/A N/A 0.441 0.098 0.666 2e-59
P18616 1839 DNA-directed RNA polymera yes N/A 0.470 0.090 0.609 2e-59
>sp|P04052|RPB1_DROME DNA-directed RNA polymerase II subunit RPB1 OS=Drosophila melanogaster GN=RpII215 PE=3 SV=4 Back     alignment and function desciption
 Score =  313 bits (803), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 146/157 (92%), Positives = 152/157 (96%)

Query: 86  RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 145
           RM ELVRRGNSQYPGAKYIVRDNGERIDLRFHPK SDLHLQCGYKVERH+RD DLVIFNR
Sbjct: 393 RMQELVRRGNSQYPGAKYIVRDNGERIDLRFHPKSSDLHLQCGYKVERHLRDDDLVIFNR 452

Query: 146 QPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV 205
           QPTLHKMSMMGHRV+VLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIH+
Sbjct: 453 QPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHI 512

Query: 206 TPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDK 242
           TPRQIITPQ N+PVMGIVQDTLTAVRKMTKRDVF+ +
Sbjct: 513 TPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITR 549
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.
Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6
>sp|P24928|RPB1_HUMAN DNA-directed RNA polymerase II subunit RPB1 OS=Homo sapiens GN=POLR2A PE=1 SV=2 Back     alignment and function description
>sp|P08775|RPB1_MOUSE DNA-directed RNA polymerase II subunit RPB1 OS=Mus musculus GN=Polr2a PE=1 SV=3 Back     alignment and function description
>sp|P16356|RPB1_CAEEL DNA-directed RNA polymerase II subunit RPB1 OS=Caenorhabditis elegans GN=ama-1 PE=1 SV=3 Back     alignment and function description
>sp|P35074|RPB1_CAEBR DNA-directed RNA polymerase II subunit RPB1 OS=Caenorhabditis briggsae GN=rpb-1 PE=3 SV=2 Back     alignment and function description
>sp|P35084|RPB1_DICDI DNA-directed RNA polymerase II subunit rpb1 OS=Dictyostelium discoideum GN=polr2a PE=2 SV=2 Back     alignment and function description
>sp|P36594|RPB1_SCHPO DNA-directed RNA polymerase II subunit rpb1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb1 PE=1 SV=1 Back     alignment and function description
>sp|Q75A34|RPB1_ASHGO DNA-directed RNA polymerase II subunit RPB1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=RPB1 PE=3 SV=2 Back     alignment and function description
>sp|A5DCV3|RPB1_PICGU DNA-directed RNA polymerase II subunit RPB1 (Fragments) OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=RPB1 PE=3 SV=2 Back     alignment and function description
>sp|P18616|RPB1_ARATH DNA-directed RNA polymerase II subunit RPB1 OS=Arabidopsis thaliana GN=RPB205 PE=1 SV=3 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 ?
Query353
324120550 1844 RNA polymerase II largest subunit [Tenod 0.444 0.085 0.961 1e-86
324120560 1803 RNA polymerase II largest subunit [Crypt 0.444 0.087 0.955 4e-86
324120558 1687 RNA polymerase II largest subunit [Gynai 0.456 0.095 0.944 8e-86
324120582 1677 RNA polymerase II largest subunit [Erete 0.444 0.093 0.949 8e-86
193700005 1862 PREDICTED: DNA-directed RNA polymerase I 0.441 0.083 0.942 2e-85
324120566 1862 RNA polymerase II largest subunit [Urole 0.441 0.083 0.942 2e-85
340722779 1902 PREDICTED: DNA-directed RNA polymerase I 0.444 0.082 0.949 2e-85
324120552 1598 RNA polymerase II largest subunit [Blatt 0.444 0.098 0.949 2e-85
383857287 1904 PREDICTED: DNA-directed RNA polymerase I 0.444 0.082 0.949 3e-85
328722767 1958 PREDICTED: DNA-directed RNA polymerase I 0.444 0.080 0.929 3e-85
>gi|324120550|dbj|BAJ78666.1| RNA polymerase II largest subunit [Tenodera aridifolia] Back     alignment and taxonomy information
 Score =  326 bits (835), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 151/157 (96%), Positives = 156/157 (99%)

Query: 86  RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 145
           +M+ELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR
Sbjct: 395 KMYELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 454

Query: 146 QPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV 205
           QPTLHKMSMMGHRV+VLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV
Sbjct: 455 QPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV 514

Query: 206 TPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDK 242
           TPRQIITPQ N+PVMGIVQDTLTAVRKMTKRDVFL+K
Sbjct: 515 TPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFLEK 551

Source: Tenodera aridifolia

Species: Tenodera aridifolia

Genus: Tenodera

Family: Mantidae

Order: Mantodea

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|324120560|dbj|BAJ78671.1| RNA polymerase II largest subunit [Cryptotympana facialis] Back     alignment and taxonomy information
>gi|324120558|dbj|BAJ78670.1| RNA polymerase II largest subunit [Gynaikothrips ficorum] Back     alignment and taxonomy information
>gi|324120582|dbj|BAJ78682.1| RNA polymerase II largest subunit [Eretes sticticus] Back     alignment and taxonomy information
>gi|193700005|ref|XP_001943054.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|324120566|dbj|BAJ78674.1| RNA polymerase II largest subunit [Uroleucon nigrotuberculatum] Back     alignment and taxonomy information
>gi|340722779|ref|XP_003399779.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Bombus terrestris] gi|350424170|ref|XP_003493710.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|324120552|dbj|BAJ78667.1| RNA polymerase II largest subunit [Blattella nipponica] Back     alignment and taxonomy information
>gi|383857287|ref|XP_003704136.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|328722767|ref|XP_001943949.2| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Acyrthosiphon pisum] 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 ?
Query353
FB|FBgn0003277 1887 RpII215 "RNA polymerase II 215 0.444 0.083 0.929 1e-77
UNIPROTKB|Q6NX41566 POLR2A "DNA-directed RNA polym 0.447 0.279 0.829 5.3e-72
UNIPROTKB|I3LJR4 1010 POLR2A "DNA-directed RNA polym 0.450 0.157 0.823 8.6e-72
UNIPROTKB|J9NW09 1789 POLR2A "DNA-directed RNA polym 0.450 0.088 0.823 2.1e-70
UNIPROTKB|F1PGS0 1969 POLR2A "DNA-directed RNA polym 0.450 0.080 0.823 2.5e-70
UNIPROTKB|G3MZY8 1970 POLR2A "DNA-directed RNA polym 0.450 0.080 0.823 2.5e-70
UNIPROTKB|P24928 1970 POLR2A "DNA-directed RNA polym 0.450 0.080 0.823 2.5e-70
MGI|MGI:98086 1970 Polr2a "polymerase (RNA) II (D 0.450 0.080 0.823 2.5e-70
RGD|1587326 1970 Polr2a "polymerase (RNA) II (D 0.450 0.080 0.823 2.5e-70
ZFIN|ZDB-GENE-041008-78 1965 polr2a "polymerase (RNA) II (D 0.450 0.080 0.811 4.1e-70
FB|FBgn0003277 RpII215 "RNA polymerase II 215kD subunit" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 786 (281.7 bits), Expect = 1.0e-77, Sum P(2) = 1.0e-77
 Identities = 146/157 (92%), Positives = 152/157 (96%)

Query:    86 RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 145
             RM ELVRRGNSQYPGAKYIVRDNGERIDLRFHPK SDLHLQCGYKVERH+RD DLVIFNR
Sbjct:   393 RMQELVRRGNSQYPGAKYIVRDNGERIDLRFHPKSSDLHLQCGYKVERHLRDDDLVIFNR 452

Query:   146 QPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV 205
             QPTLHKMSMMGHRV+VLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIH+
Sbjct:   453 QPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHI 512

Query:   206 TPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDK 242
             TPRQIITPQ N+PVMGIVQDTLTAVRKMTKRDVF+ +
Sbjct:   513 TPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITR 549
GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISS;NAS;IDA
GO:0005703 "polytene chromosome puff" evidence=IDA
GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS;NAS
GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;NAS
GO:0005634 "nucleus" evidence=IDA
GO:0003677 "DNA binding" evidence=IEA
GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IGI
GO:0005700 "polytene chromosome" evidence=IDA
UNIPROTKB|Q6NX41 POLR2A "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|I3LJR4 POLR2A "DNA-directed RNA polymerase" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|J9NW09 POLR2A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|F1PGS0 POLR2A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|G3MZY8 POLR2A "DNA-directed RNA polymerase" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|P24928 POLR2A "DNA-directed RNA polymerase II subunit RPB1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:98086 Polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1587326 Polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-041008-78 polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q980R2RPOA1_SULSO2, ., 7, ., 7, ., 60.50940.43340.1738yesN/A
P08775RPB1_MOUSE2, ., 7, ., 7, ., 60.82380.45040.0807yesN/A
P35084RPB1_DICDI2, ., 7, ., 7, ., 60.71970.44470.0909yesN/A
P16356RPB1_CAEEL2, ., 7, ., 7, ., 60.76280.44190.0840yesN/A
P04050RPB1_YEAST2, ., 7, ., 7, ., 60.64740.44190.0900yesN/A
P04052RPB1_DROME2, ., 7, ., 7, ., 60.92990.44470.0832yesN/A
P24928RPB1_HUMAN2, ., 7, ., 7, ., 4, 80.82380.45040.0807yesN/A
P36594RPB1_SCHPO2, ., 7, ., 7, ., 60.65470.46450.0936yesN/A
Q8SSC4RPB1_ENCCU2, ., 7, ., 7, ., 60.55740.48440.1069yesN/A
P18616RPB1_ARATH2, ., 7, ., 7, ., 60.60980.47020.0902yesN/A
Q75A34RPB1_ASHGO2, ., 7, ., 7, ., 60.66020.44190.0893yesN/A

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.7LOW CONFIDENCE prediction!
4th Layer2.7.7.6LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query353
smart00663295 smart00663, RPOLA_N, RNA polymerase I subunit A N- 3e-72
smart00663295 smart00663, RPOLA_N, RNA polymerase I subunit A N- 9e-61
PRK08566 882 PRK08566, PRK08566, DNA-directed RNA polymerase su 2e-59
pfam00623165 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, do 5e-59
TIGR02390 867 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer 3e-55
PRK14977 1321 PRK14977, PRK14977, bifunctional DNA-directed RNA 1e-49
PRK08566 882 PRK08566, PRK08566, DNA-directed RNA polymerase su 4e-47
pfam00623165 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, do 7e-46
TIGR02390 867 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer 6e-43
COG0086 808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 6e-43
COG0086 808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 1e-41
PRK14977 1321 PRK14977, PRK14977, bifunctional DNA-directed RNA 2e-39
pfam00623165 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, do 1e-33
smart00663295 smart00663, RPOLA_N, RNA polymerase I subunit A N- 3e-32
PRK08566 882 PRK08566, PRK08566, DNA-directed RNA polymerase su 2e-31
TIGR02390 867 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer 2e-28
PRK14977 1321 PRK14977, PRK14977, bifunctional DNA-directed RNA 7e-24
COG0086 808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 3e-15
TIGR02386 1140 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, 1e-12
TIGR02386 1140 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, 1e-12
pfam04983158 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, do 1e-12
TIGR02387619 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase 2e-12
CHL00018 663 CHL00018, rpoC1, RNA polymerase beta' subunit 5e-12
pfam04983 158 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, do 6e-12
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 9e-12
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 2e-11
PRK14906 1460 PRK14906, PRK14906, DNA-directed RNA polymerase su 4e-11
TIGR02387619 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase 5e-11
PRK14906 1460 PRK14906, PRK14906, DNA-directed RNA polymerase su 6e-11
PRK02625627 PRK02625, rpoC1, DNA-directed RNA polymerase subun 1e-10
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 3e-10
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 3e-10
PRK02625627 PRK02625, rpoC1, DNA-directed RNA polymerase subun 9e-10
CHL00018663 CHL00018, rpoC1, RNA polymerase beta' subunit 3e-09
PRK00566 1156 PRK00566, PRK00566, DNA-directed RNA polymerase su 7e-09
PRK00566 1156 PRK00566, PRK00566, DNA-directed RNA polymerase su 3e-08
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus Back     alignment and domain information 
 Score =  226 bits (578), Expect = 3e-72
 Identities = 75/147 (51%), Positives = 101/147 (68%), Gaps = 6/147 (4%)

Query: 86  RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPK-PSDLHLQCGYKVERHIRDGDLVIFN 144
           ++ +LVR G     GAKYI+R  G++ +L+   K     HL+ G  VERH+ DGD+V+FN
Sbjct: 154 KLRKLVRNGP---NGAKYIIR--GKKTNLKLAKKSKIANHLKIGDIVERHVIDGDVVLFN 208

Query: 145 RQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIH 204
           RQPTLH+MS+  HRVRVL   T R+N    SPYNADFDGDEMNLHVPQS+E RAE   + 
Sbjct: 209 RQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELM 268

Query: 205 VTPRQIITPQNNRPVMGIVQDTLTAVR 231
           + P  I++P+N +P++G +QD L  + 
Sbjct: 269 LVPNNILSPKNGKPIIGPIQDMLLGLY 295

Length = 295
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus Back     alignment and domain information
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated Back     alignment and domain information
>gnl|CDD|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2 Back     alignment and domain information
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A' Back     alignment and domain information
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional Back     alignment and domain information
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated Back     alignment and domain information
>gnl|CDD|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2 Back     alignment and domain information
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A' Back     alignment and domain information
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional Back     alignment and domain information
>gnl|CDD|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2 Back     alignment and domain information
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus Back     alignment and domain information
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated Back     alignment and domain information
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A' Back     alignment and domain information
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional Back     alignment and domain information
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form Back     alignment and domain information
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form Back     alignment and domain information
>gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3 Back     alignment and domain information
>gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit Back     alignment and domain information
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit Back     alignment and domain information
>gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3 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|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional Back     alignment and domain information
>gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit Back     alignment and domain information
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional Back     alignment and domain information
>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma; 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|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma; Provisional Back     alignment and domain information
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit Back     alignment and domain information
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional Back     alignment and domain information
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 353
PRK14977 1321 bifunctional DNA-directed RNA polymerase A'/A'' su 100.0
KOG0262|consensus 1640 100.0
KOG0261|consensus 1386 100.0
TIGR02390 868 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit 100.0
PRK08566 882 DNA-directed RNA polymerase subunit A'; Validated 100.0
KOG0260|consensus 1605 100.0
smart00663295 RPOLA_N RNA polymerase I subunit A N-terminus. 100.0
CHL00018663 rpoC1 RNA polymerase beta' subunit 100.0
PRK02625627 rpoC1 DNA-directed RNA polymerase subunit gamma; P 100.0
TIGR02387619 rpoC1_cyan DNA-directed RNA polymerase, gamma subu 100.0
PRK00566 1156 DNA-directed RNA polymerase subunit beta'; Provisi 100.0
TIGR02386 1140 rpoC_TIGR DNA-directed RNA polymerase, beta' subun 100.0
PRK14906 1460 DNA-directed RNA polymerase subunit beta'/alpha do 100.0
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 100.0
PF00623166 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; Int 100.0
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 100.0
COG0086 808 RpoC DNA-directed RNA polymerase, beta' subunit/16 100.0
PRK14977 1321 bifunctional DNA-directed RNA polymerase A'/A'' su 100.0
TIGR02390 868 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit 100.0
KOG0261|consensus 1386 100.0
CHL00018 663 rpoC1 RNA polymerase beta' subunit 100.0
PRK08566 882 DNA-directed RNA polymerase subunit A'; Validated 100.0
TIGR02387619 rpoC1_cyan DNA-directed RNA polymerase, gamma subu 100.0
PRK02625627 rpoC1 DNA-directed RNA polymerase subunit gamma; P 100.0
smart00663295 RPOLA_N RNA polymerase I subunit A N-terminus. 100.0
TIGR02386 1140 rpoC_TIGR DNA-directed RNA polymerase, beta' subun 100.0
PRK00566 1156 DNA-directed RNA polymerase subunit beta'; Provisi 100.0
KOG0260|consensus 1605 100.0
PRK14906 1460 DNA-directed RNA polymerase subunit beta'/alpha do 100.0
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 100.0
KOG0262|consensus 1640 100.0
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 100.0
COG0086 808 RpoC DNA-directed RNA polymerase, beta' subunit/16 99.94
PF00623166 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; Int 99.93
PF04983158 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; Int 97.75
PF05183579 RdRP: RNA dependent RNA polymerase; InterPro: IPR0 83.54
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional Back     alignment and domain information 
Probab=100.00  E-value=9.1e-62  Score=537.45  Aligned_cols=215  Identities=38%  Similarity=0.612  Sum_probs=191.7

Q ss_pred             cceeEeecCCCccccceeeeeeeeeccccc----------------------------ccch-HHHHHHHhCCCCCCCce
Q psy1131          52 GDLVIFNRQPTLHKMSMMGHRVRVLPWSTF----------------------------RMNL-RMFELVRRGNSQYPGAK  102 (353)
Q Consensus        52 ~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf----------------------------~~N~-~Lr~lV~nGp~~~pGA~  102 (353)
                      |-.|.|++|+|+||+|||||||++++|+|+                            .+|. +||++|.|||+.||||+
T Consensus       309 ~i~qrLkgKeGrfR~nlmGKRVdfSaRtVIspDP~L~i~EVGvP~~iA~~LT~Pe~Vt~~Ni~~l~~lv~nG~~~~pGA~  388 (1321)
T PRK14977        309 SLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGAN  388 (1321)
T ss_pred             HHHHHhccccccccccccccccccccceeEeCCCCcccccccCHHHHHHhCCCCEEEchhhHHHHHHHHHcCCcccCCcc
Confidence            567899999999999999999999888762                            3454 89999999999999999


Q ss_pred             EEEeCCCceEEeecCCCCCc-------cccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeeeecccCC
Q psy1131         103 YIVRDNGERIDLRFHPKPSD-------LHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTS  175 (353)
Q Consensus       103 ~v~~~~g~~~~l~~~~~~~~-------~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~  175 (353)
                      ||++++|.++.+++..+...       ..|++||+|+|||.|||+|||||||||||+|||||+|++++++||||||++|+
T Consensus       389 ~i~~~~g~~~~l~~~~~~~~~~~~~~a~~L~~g~iV~Rhl~dGD~VL~NRQPSLHk~Simah~vkvl~~kT~Rln~~vC~  468 (1321)
T PRK14977        389 AIRKGDGTKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCP  468 (1321)
T ss_pred             eEEcCCCceeeehhhhhccchhHHHHHHhcccCcEEEEEeecCcEEEeccCCccccccceEEEEEEecCceEEecccccC
Confidence            99999999998887654332       46899999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeeccccccc--cCccee
Q psy1131         176 PYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHI--RDGDLV  253 (353)
Q Consensus       176 ~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l--~d~d~v  253 (353)
                      ||||||||||||+|+|||++|||||.+||++++|++||++|+|++|++||+++|+|+||.+|.|+++++++.  ......
T Consensus       469 pyNADFDGDEMNlHvPQS~eArAEa~~Lm~v~~niisP~~G~Pi~gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~~~~~  548 (1321)
T PRK14977        469 PYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGIT  548 (1321)
T ss_pred             cccCCcccceeeeecCCCHHHHHHHHHHHhhhhcEecCCCCCeeEEeehhhhhhhhhhccCcccCCHHHHHHHHHhCCCc
Confidence            999999999999999999999999999999999999999999999999999999999999999999998752  111122


Q ss_pred             eecCCcccc-cccc
Q psy1131         254 IFNRQPTLH-KMSM  266 (353)
Q Consensus       254 I~nrqPtIh-k~s~  266 (353)
                      ...++|+|. +|..
T Consensus       549 ~~lp~PaI~~kp~~  562 (1321)
T PRK14977        549 DPLPEPAIKTKDGP  562 (1321)
T ss_pred             cccCCCceecCCCC
Confidence            234778888 5533

>KOG0262|consensus Back     alignment and domain information
>KOG0261|consensus Back     alignment and domain information
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A' Back     alignment and domain information
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated Back     alignment and domain information
>KOG0260|consensus Back     alignment and domain information
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus Back     alignment and domain information
>CHL00018 rpoC1 RNA polymerase beta' subunit Back     alignment and domain information
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional Back     alignment and domain information
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit Back     alignment and domain information
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional Back     alignment and domain information
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form Back     alignment and domain information
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional Back     alignment and domain information
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>PF00623 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; InterPro: IPR000722 RNA polymerases catalyse the DNA dependent polymerisation of RNA from DNA, using the four ribonucleoside triphosphates as substrates Back     alignment and domain information
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional Back     alignment and domain information
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A' Back     alignment and domain information
>KOG0261|consensus Back     alignment and domain information
>CHL00018 rpoC1 RNA polymerase beta' subunit Back     alignment and domain information
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated Back     alignment and domain information
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit Back     alignment and domain information
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional Back     alignment and domain information
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus Back     alignment and domain information
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form Back     alignment and domain information
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional Back     alignment and domain information
>KOG0260|consensus Back     alignment and domain information
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional Back     alignment and domain information
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>KOG0262|consensus Back     alignment and domain information
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>PF00623 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; InterPro: IPR000722 RNA polymerases catalyse the DNA dependent polymerisation of RNA from DNA, using the four ribonucleoside triphosphates as substrates Back     alignment and domain information
>PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>PF05183 RdRP: RNA dependent RNA polymerase; InterPro: IPR007855 This entry represents various eukaryotic RNA-dependent RNA polymerases (RDRP; 2 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 ?
Query353
3h0g_A 1752 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 1e-64
3h0g_A 1752 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 3e-48
3j0k_A 1455 Orientation Of Rna Polymerase Ii Within The Human V 2e-60
3j0k_A 1455 Orientation Of Rna Polymerase Ii Within The Human V 1e-44
1i3q_A 1733 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 2e-60
1i3q_A 1733 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 1e-44
4a3c_A 1732 Rna Polymerase Ii Initial Transcribing Complex With 2e-60
4a3c_A 1732 Rna Polymerase Ii Initial Transcribing Complex With 1e-44
2waq_A 880 The Complete Structure Of The Archaeal 13-Subunit D 3e-40
2waq_A 880 The Complete Structure Of The Archaeal 13-Subunit D 2e-30
2pmz_A 880 Archaeal Rna Polymerase From Sulfolobus Solfataricu 6e-40
2pmz_A 880 Archaeal Rna Polymerase From Sulfolobus Solfataricu 4e-30
3iyd_D 1413 Three-Dimensional Em Structure Of An Intact Activat 5e-14
3lu0_D 1407 Molecular Model Of Escherichia Coli Core Rna Polyme 5e-14
4gzy_D 1534 Crystal Structures Of Bacterial Rna Polymerase Paus 1e-09
1iw7_D 1524 Crystal Structure Of The Rna Polymerase Holoenzyme 1e-09
2gho_D 1233 Recombinant Thermus Aquaticus Rna Polymerase For St 1e-09
1l9u_D 1524 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 1e-09
1hqm_D 1265 Crystal Structure Of Thermus Aquaticus Core Rna Pol 1e-09
1i6v_D 1264 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 2e-09
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 Back     alignment and structure 
Iteration: 1

 Score =  243 bits (620), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 110/168 (65%), Positives = 141/168 (83%), Gaps = 4/168 (2%)
Query: 75  VLPWSTFRMNLRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERH 134
           V P++ +++     ELVR G  ++PGAKYI+RD GERIDLR+H +  D+ L+ G++VERH
Sbjct: 386 VTPYNIYQLQ----ELVRNGPDEHPGAKYIIRDTGERIDLRYHKRAGDIPLRYGWRVERH 441
Query: 135 IRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSM 194
           IRDGD+VIFNRQP+LHKMSMMGHR+RV+P+STFR+NLS TSPYNADFDGDEMN+HVPQS 
Sbjct: 442 IRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSE 501
Query: 195 ETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDK 242
           ETRAE++ I + P+QI++PQ+N+PVMGIVQDTL  VRK + RD FL +
Sbjct: 502 ETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTR 549
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 Back     alignment and structure
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455 Back     alignment and structure
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455 Back     alignment and structure
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1733 Back     alignment and structure
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1733 Back     alignment and structure
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt Dna-Rna Hybrid Length = 1732 Back     alignment and structure
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt Dna-Rna Hybrid Length = 1732 Back     alignment and structure
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 880 Back     alignment and structure
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 880 Back     alignment and structure
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 880 Back     alignment and structure
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 880 Back     alignment and structure
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1413 Back     alignment and structure
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1407 Back     alignment and structure
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused Elongation Complexes Length = 1534 Back     alignment and structure
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1524 Back     alignment and structure
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For Structural Studies Length = 1233 Back     alignment and structure
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1524 Back     alignment and structure
>pdb|1HQM|D Chain D, 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 = 1265 Back     alignment and structure
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1264 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 ?
Query353
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 1e-76
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 9e-54
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 4e-38
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 1e-75
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 9e-54
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 3e-37
4ayb_A 880 DNA-directed RNA polymerase; transferase, multi-su 2e-66
4ayb_A 880 DNA-directed RNA polymerase; transferase, multi-su 1e-50
4ayb_A 880 DNA-directed RNA polymerase; transferase, multi-su 3e-28
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 4e-11
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 7e-11
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 9e-11
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 2e-08
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 2e-08
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 Back     alignment and structure
 Score =  255 bits (653), Expect = 1e-76
 Identities = 105/174 (60%), Positives = 136/174 (78%), Gaps = 5/174 (2%)

Query: 86  RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 145
           R+ +LVR G +++PGAKY++RD+G+RIDLR+  +  D+ LQ G+KVERHI D D V+FNR
Sbjct: 387 RLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNR 446

Query: 146 QPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV 205
           QP+LHKMSMM HRV+V+P+STFR+NLS TSPYNADFDGDEMNLHVPQS ETRAE+  +  
Sbjct: 447 QPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCA 506

Query: 206 TPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVE-----RHIRDGDLVI 254
            P QI++PQ+N+P MGIVQDTL  +RK+T RD F++  +       + D D VI
Sbjct: 507 VPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVI 560
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 Back     alignment and structure
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 Back     alignment and structure
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 Back     alignment and structure
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 Back     alignment and structure
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 Back     alignment and structure
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880 Back     alignment and structure
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880 Back     alignment and structure
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880 Back     alignment and structure
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Length = 1265 Back     alignment and structure
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524 Back     alignment and structure
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524 Back     alignment and structure
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Length = 1407 Back     alignment and structure
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Length = 1407 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query353
4ayb_A 880 DNA-directed RNA polymerase; transferase, multi-su 100.0
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 100.0
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 100.0
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 100.0
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 100.0
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 100.0
4ayb_A 880 DNA-directed RNA polymerase; transferase, multi-su 100.0
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 100.0
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 100.0
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 100.0
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 100.0
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 100.0
3qqc_A436 DNA-directed RNA polymerase subunit B, DNA-direct 95.13
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Back     alignment and structure
Probab=100.00  E-value=2.8e-60  Score=513.08  Aligned_cols=222  Identities=39%  Similarity=0.631  Sum_probs=197.1

Q ss_pred             CCcEEeeeccccceeEeecCCCccccceeeeeeeeeccccc----------------------------ccch-HHHHHH
Q psy1131          41 CGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF----------------------------RMNL-RMFELV   91 (353)
Q Consensus        41 ~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf----------------------------~~N~-~Lr~lV   91 (353)
                      .+.+..+.|.    |.|++|+|+||+|||||||++++|+|+                            ++|. +|+++|
T Consensus       290 ~~~rp~ksl~----~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~e~GvP~~~A~~Lt~Pe~vt~~N~~~l~~~v  365 (880)
T 4ayb_A          290 RSGRPLRTLA----QRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVGVPEIIARTLTVPERITPWNIEKLRQFV  365 (880)
T ss_dssp             TTSCCCCCHH----HHHHSSSSTHHHHTSSEECSSEEEEEEEECTTSCSSEEEECHHHHTTSEEEEECCTTTHHHHHHHH
T ss_pred             CCCCcccchh----hhhcccchhhhhcccceeecccCceeeeCCCCccccccCCcHHHHHhCCCCeEEcHHHHHHHHHHH
Confidence            3445556664    599999999999999999999988872                            3454 899999


Q ss_pred             HhCCCCCCCceEEEeCCCceEEeecCCCCCc--cccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeee
Q psy1131          92 RRGNSQYPGAKYIVRDNGERIDLRFHPKPSD--LHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRM  169 (353)
Q Consensus        92 ~nGp~~~pGA~~v~~~~g~~~~l~~~~~~~~--~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~  169 (353)
                      .|||+.||||+++++++|.++.+++......  ..|++||+|+||+.|||+|||||||||||+|||||++++++|+||||
T Consensus       366 ~ng~~~~pga~~~i~~~~~~~~l~~~~~~~~~~~~l~~g~~V~rhl~dgd~VLlNRqPTLHr~si~a~~~~l~~gktirl  445 (880)
T 4ayb_A          366 INGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYVVERHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRL  445 (880)
T ss_dssp             HHTTSSSSCEEEEECSSCCEEEGGGCSSCTTHHHHCCTTCEEEEECCTTCEEEEECSSCCSGGGEEEEEEEECSSSSEEE
T ss_pred             HcCCccccchhhhhhccceEEEeecchhhhHHHHhccccceEeeeeecCcEEEecCCCcccccceeeeeeecccCceeee
Confidence            9999999999999999999999987654433  25899999999999999999999999999999999999999999999


Q ss_pred             ecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeeccccccc--
Q psy1131         170 NLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHI--  247 (353)
Q Consensus       170 ~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l--  247 (353)
                      ||+||+||||||||||||+|||||++||+||++||++++|++||++|+|+++++||+++|+|+||.++.|+++++++.  
T Consensus       446 hp~vC~~yNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~vlg~y~lT~~~~~~~~~~~~~~~  525 (880)
T 4ayb_A          446 NLLVCPPYNADFDGDEMNLHVPQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQIL  525 (880)
T ss_dssp             CGGGHHHHTCCSSSCEEEEECCCSHHHHHHHHHHSBSGGGCBCSSSSSBCSCCCSHHHHHHHHHTSSSCEECHHHHHHHH
T ss_pred             ccccccccccCcccceeEEeccCCHHHHHHHHHHHhChhccccCCCCCccccccccHHHHhHHhhcCcccCCHHHHhhhh
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999987652  


Q ss_pred             cCcceeeecCCcccccccc
Q psy1131         248 RDGDLVIFNRQPTLHKMSM  266 (353)
Q Consensus       248 ~d~d~vI~nrqPtIhk~s~  266 (353)
                      ...+..+...+|++.++..
T Consensus       526 ~~~~~~~~~~~p~i~~~~~  544 (880)
T 4ayb_A          526 GVADVKIDLGEPAILAPRE  544 (880)
T ss_dssp             TTSCCCCCCCSCSEESSSE
T ss_pred             cccceecccCccceeccee
Confidence            2334445567788887654
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Back     alignment and structure
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Back     alignment and structure
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Back     alignment and structure
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Back     alignment and structure
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Back     alignment and structure
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Back     alignment and structure
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Back     alignment and structure
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Back     alignment and structure
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* 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

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 353
d1smyd_ 1504 e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t 5e-45
d1smyd_ 1504 e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t 8e-44
d1smyd_ 1504 e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t 1e-16
d1twfa_ 1449 e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c 1e-43
d1twfa_ 1449 e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c 9e-32
d1twfa_ 1449 e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c 2e-19
>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504 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-prime
domain: RNA-polymerase beta-prime
species: Thermus thermophilus [TaxId: 274]

 Score =  163 bits (412), Expect = 5e-45
 Identities = 31/156 (19%), Positives = 68/156 (43%), Gaps = 12/156 (7%)

Query: 86  RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 145
            + ++  +G    P  K   R    + D++             +     +  G +V+ NR
Sbjct: 656 LLKKMEEKGI--APNVKAARRMLERQRDIKDE----------VWDALEEVIHGKVVLLNR 703

Query: 146 QPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV 205
            PTLH++ +   +  ++   + +++      +NADFDGD+M +HVP S   +AE     +
Sbjct: 704 APTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQML 763

Query: 206 TPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 241
           +   +++P +  P+    +D +  +  +T+      
Sbjct: 764 SAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKK 799
>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504 Back     information, alignment and structure
>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504 Back     information, alignment and structure
>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 Back     information, alignment and structure
>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 Back     information, alignment and structure
>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 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 ?
Query353
d1twfa_ 1449 RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1smyd_ 1504 RNA-polymerase beta-prime {Thermus thermophilus [T 100.0
d1smyd_ 1504 RNA-polymerase beta-prime {Thermus thermophilus [T 100.0
d1twfa_ 1449 RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
>d1twfa_ e.29.1.2 (A:) RBP1 {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-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.4e-56  Score=501.30  Aligned_cols=213  Identities=51%  Similarity=0.807  Sum_probs=192.0

Q ss_pred             eeEeecCCCccccceeeeeeeeeccccc----------------------------ccch-HHHHHHHhCCCCCCCceEE
Q psy1131          54 LVIFNRQPTLHKMSMMGHRVRVLPWSTF----------------------------RMNL-RMFELVRRGNSQYPGAKYI  104 (353)
Q Consensus        54 ~~~~~~~~~l~r~~~mGkRv~v~p~~vf----------------------------~~N~-~Lr~lV~nGp~~~pGA~~v  104 (353)
                      .|.|++|+|+||+|||||||+++.|+|+                            .+|. +|+++|.|||+.||||+++
T Consensus       325 ~~~L~gK~GrfR~nl~GKRVd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~~n~~~l~~~v~ng~~~~pga~~~  404 (1449)
T d1twfa_         325 RARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYV  404 (1449)
T ss_dssp             TTSCTTTTTTSSGGGTTCSCCSEEEEEEEECTTSCTTEEEEEHHHHTTCEEEEECCTTTHHHHHHHHHHTTTSSSCEEEE
T ss_pred             hhHhccchhhhhhhccccccccccceeeccCCccceeecccHHHHHhhCCCCeeecHHHHHHHHHHHHcCCccCCcccce
Confidence            4599999999999999999999888872                            3454 8999999999999999999


Q ss_pred             EeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeeeecccCCCCCCCCCCC
Q psy1131         105 VRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGD  184 (353)
Q Consensus       105 ~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~~~NADFDGD  184 (353)
                      ++++|.++.+++........++.||+|+||+.+||+|||||||||||+|||||+|++++++||||||++|+|||||||||
T Consensus       405 ~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~Vl~NRqPtLHr~si~a~~~~v~~~ktirl~~~vc~~yNADFDGD  484 (1449)
T d1twfa_         405 IRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGD  484 (1449)
T ss_dssp             ECTTCCEEETTSCTTTTCCCCCTTCEEEEECCTTCEEEEECSSCCSGGGEEEEEEEEESSSSEEECGGGHHHHTCCSSSC
T ss_pred             ecccCceEEEecchhhhhhhcccccEEEEEEecCeeEEecCccchhhhccccceeEeecCceEEeccccccccccccccc
Confidence            99999999998877766778999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeeccccccc---cCcceeeecCCccc
Q psy1131         185 EMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHI---RDGDLVIFNRQPTL  261 (353)
Q Consensus       185 emnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l---~d~d~vI~nrqPtI  261 (353)
                      |||+|+|||++|++||+.||++.+|+++|++|+|+++++||+++|+|+||.+++|+++++++.   .-.+.....++|++
T Consensus       485 eMnvhvPqs~~A~aEa~~Lm~~~~nilsp~~G~pi~~~~QD~~lg~y~LT~~~~f~~~~~~~~~~~~~~~~~~~~~~p~~  564 (1449)
T d1twfa_         485 EMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAI  564 (1449)
T ss_dssp             EEEEECCCSHHHHHHHHHHTBGGGGSEETTTTEESCCCCHHHHHHHHHHHSTTCEEEHHHHHHHHHHSTTCCSCCCCCSB
T ss_pred             eEEEEccCCHHHHHHHHHHhhhhcccccccCCceeeeeccchhhhhhhhhcccccCCHHHHHHHHHhcccccccccCCeE
Confidence            999999999999999999999999999999999999999999999999999999999887641   11112223467888


Q ss_pred             ccccc
Q psy1131         262 HKMSM  266 (353)
Q Consensus       262 hk~s~  266 (353)
                      .++..
T Consensus       565 ~~~~~  569 (1449)
T d1twfa_         565 IKPKP  569 (1449)
T ss_dssp             CSSSC
T ss_pred             Eeeee
Confidence            77643
>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure