Psyllid ID: psy3023

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390--
MAMADSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEGGRPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD
ccccccccccEEEcEEEEEcccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccHHHHHHHHHccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccEEcccccccEEEEccccccccccccccHHHHHccccccccccccccccccccccccccEEEcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccc
cccccccccccEEEEEEEEEccHHHHHHccEEEEEEcccccccccccccccccccccccEcccccccccccccccccccccHHHHcccEEHHHHHHHHHHHHHHHHHHcccEEcccccHHHHHHHHHHcccHHHHHHHHHHHHccccccccccccccccccccccccHHcccccccccccccccEEEcccEEEEEEEccccccccccccccHHHHHHcccccHHHHcccccccccccEEEEEEEcccccccccEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccccccccHHHccccccHHHHHHHHccccccEEccccccEEEcEEEEEEccccccccccccccHHHHHHcccccEccccccc
mamadskaplrcvkkvqfgilspdeirrmsvteggikfpetmeggrpklgglmdprqgvidrssrcqtcagnmtecpghfghidlakpvfhvgfVTKTIKILRCVCFycskllvspshpkvrDVVLKTKGQSRRRQAFIYDLckgkniceggdemdinkdgaedpnslqnkkqghggcgryqpnirrsglDLTAEwkhvnedsqekkipltgkgvllnkkqghggcgryqpnirrsglDLTAEwkhvnedsqekkipltgkgvlldDLTHKLADIIKCNNElirnessgaATHVIAENIKMLQFHVATltdndmpglpramqksgkpLKAIKARLKGkegrirgnlmgkrvdfsartvitpdpnlridqvgvprsiaqnmtfpeivtpfnmd
mamadskaplrcvkkvqfgilspdeirrmsvteggikfpetmeggrpklggLMDPRQGVIDRSSRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSkllvspshpkvrdvvlktkgqsrrrqafiydlckgknicEGGDEMDINKDGAEDPNslqnkkqghggcgryqPNIRRSGLDLTAEWKHVnedsqekkipltgkgvllnkkqghggcgryqpnIRRSGLDLTAEWKHVnedsqekkipltgkgvLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLpramqksgkplkAIKArlkgkegrirgnlmgkrvdfsartvitpdpnlridqvgvprsiaqnmtfpeivtpfnmd
MAMADSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEGGRPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD
**********RCVKKVQFGILSPD*I*************************************SRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICE****************************************DLTAEW**************TGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKHV*******KIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLT**********************************NLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEI*******
*****SKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEGGRPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICE*********************KQGHGGCGRYQPNIRRSGLDLTAEW*************LTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNED******************THKLADIIKCNNELIRNES*GAATHVIAENIKMLQFHVATLTDNDM***************AIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNM*
********PLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEGGRPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPN***********CGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD
**MADSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEGGRPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNIC************************GHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD
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MAMADSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEGGRPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD
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 ?
Query392 2.2.26 [Sep-21-2011]
P04052 1887 DNA-directed RNA polymera yes N/A 0.982 0.204 0.724 1e-165
P08775 1970 DNA-directed RNA polymera no N/A 0.971 0.193 0.673 1e-154
P24928 1970 DNA-directed RNA polymera yes N/A 0.971 0.193 0.673 1e-154
P35074 1853 DNA-directed RNA polymera N/A N/A 0.966 0.204 0.583 1e-129
P16356 1856 DNA-directed RNA polymera yes N/A 0.969 0.204 0.582 1e-128
P35084 1727 DNA-directed RNA polymera yes N/A 0.971 0.220 0.535 1e-108
P36594 1752 DNA-directed RNA polymera yes N/A 0.946 0.211 0.482 2e-99
A5DCV3 1579 DNA-directed RNA polymera N/A N/A 0.951 0.236 0.486 2e-95
P04050 1733 DNA-directed RNA polymera yes N/A 0.946 0.214 0.489 5e-95
Q75A34 1745 DNA-directed RNA polymera yes N/A 0.941 0.211 0.477 9e-93
>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 =  582 bits (1500), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 284/392 (72%), Positives = 327/392 (83%), Gaps = 7/392 (1%)

Query: 4   ADSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEGGRPKLGGLMDPRQGVIDRS 63
            DSKAPLR VK+VQFGILSPDEIRRMSVTEGG++F ETMEGGRPKLGGLMDPRQGVIDR+
Sbjct: 5   TDSKAPLRQVKRVQFGILSPDEIRRMSVTEGGVQFAETMEGGRPKLGGLMDPRQGVIDRT 64

Query: 64  SRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRD 123
           SRCQTCAGNMTECPGHFGHIDLAKPVFH+GF+TKTIKILRCVCFYCSK+LVSP +PK+++
Sbjct: 65  SRCQTCAGNMTECPGHFGHIDLAKPVFHIGFITKTIKILRCVCFYCSKMLVSPHNPKIKE 124

Query: 124 VVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAE-DPNSLQNKKQGHGGCGRYQ 182
           +V+K++GQ R+R A++YDLCKGK ICEGG++MD+ K+  + DP    NKK GHGGCG YQ
Sbjct: 125 IVMKSRGQPRKRLAYVYDLCKGKTICEGGEDMDLTKENQQPDP----NKKPGHGGCGHYQ 180

Query: 183 PNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVL-LNKKQGHGGCGRYQPNIRRSGLD-L 240
           P+IRR+GLDLTAEWKH NEDSQEKKI ++ + V  + K      C     + + +  D +
Sbjct: 181 PSIRRTGLDLTAEWKHQNEDSQEKKIVVSAERVWEILKHITDEECFILGMDPKYARPDWM 240

Query: 241 TAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIK 300
                 V   +    + + G     DDLTHKL+DIIK NNEL +NE+SGAA HVI ENIK
Sbjct: 241 IVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIK 300

Query: 301 MLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVIT 360
           MLQFHVATL DNDMPG+PRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVIT
Sbjct: 301 MLQFHVATLVDNDMPGMPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVIT 360

Query: 361 PDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
           PDPNLRIDQVGVPRSIAQN+TFPE+VTPFN+D
Sbjct: 361 PDPNLRIDQVGVPRSIAQNLTFPELVTPFNID 392
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|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|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|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|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|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|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|P04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPO21 PE=1 SV=2 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

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 ?
Query392
324120560 1803 RNA polymerase II largest subunit [Crypt 0.994 0.216 0.782 1e-178
324120558 1687 RNA polymerase II largest subunit [Gynai 0.974 0.226 0.757 1e-177
324120564 1793 RNA polymerase II largest subunit [Bemis 1.0 0.218 0.774 1e-176
324120548 1862 RNA polymerase II largest subunit [Zorot 0.992 0.208 0.765 1e-176
324120538 1640 RNA polymerase II largest subunit [Eucon 0.997 0.238 0.767 1e-174
324120534 1907 RNA polymerase II largest subunit [Karoo 0.997 0.205 0.764 1e-174
324120532 1904 RNA polymerase II largest subunit [Gallo 0.994 0.204 0.762 1e-174
324120566 1862 RNA polymerase II largest subunit [Urole 0.994 0.209 0.769 1e-173
193700005 1862 PREDICTED: DNA-directed RNA polymerase I 0.994 0.209 0.769 1e-173
322801476 1905 hypothetical protein SINV_09846 [Solenop 0.992 0.204 0.756 1e-173
>gi|324120560|dbj|BAJ78671.1| RNA polymerase II largest subunit [Cryptotympana facialis] Back     alignment and taxonomy information
 Score =  629 bits (1623), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 309/395 (78%), Positives = 336/395 (85%), Gaps = 5/395 (1%)

Query: 1   MAMADSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEGGRPKLGGLMDPRQGVI 60
           MAM+DSKAPLR VK+VQFGILSPDEIRRMSVTEGGI+FPETMEGGRPKLGGLMDPRQGVI
Sbjct: 1   MAMSDSKAPLRSVKRVQFGILSPDEIRRMSVTEGGIRFPETMEGGRPKLGGLMDPRQGVI 60

Query: 61  DRSSRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPK 120
           DR SRCQTCAGNM+ECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPK
Sbjct: 61  DRHSRCQTCAGNMSECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPK 120

Query: 121 VRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGR 180
           ++++V+KTKGQ R+R  F+YDLCKGKNICEGGDEMD+NK+  EDPN+ Q +KQGHGGCGR
Sbjct: 121 IKEIVMKTKGQPRKRLTFVYDLCKGKNICEGGDEMDLNKENIEDPNNPQ-RKQGHGGCGR 179

Query: 181 YQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVL-LNKKQGHGGCGRY--QPNIRRSG 237
           YQPN+RR+GLD+TAEWKH NEDSQEKKI L+ + V  + K      C      P   R  
Sbjct: 180 YQPNLRRTGLDVTAEWKHANEDSQEKKIALSAERVWEIFKHITDEECFILGMDPKFARPD 239

Query: 238 LDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAE 297
             +      V        + + G     DDLTHKL+DIIKCNNELIRNE SGAATHVIAE
Sbjct: 240 W-MIVTVLPVPPLPVRPAVVMYGSARNQDDLTHKLSDIIKCNNELIRNEQSGAATHVIAE 298

Query: 298 NIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSART 357
           NIKMLQFHVATL DNDMPGLPRAMQKSGKPLKA+KARLKGKEGRIRGNLMGKRVDFSART
Sbjct: 299 NIKMLQFHVATLVDNDMPGLPRAMQKSGKPLKALKARLKGKEGRIRGNLMGKRVDFSART 358

Query: 358 VITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
           VITPDPNL IDQVGVPRSIAQNMTFPEIVTPFN+D
Sbjct: 359 VITPDPNLGIDQVGVPRSIAQNMTFPEIVTPFNID 393

Source: Cryptotympana facialis

Species: Cryptotympana facialis

Genus: Cryptotympana

Family: Cicadidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|324120558|dbj|BAJ78670.1| RNA polymerase II largest subunit [Gynaikothrips ficorum] Back     alignment and taxonomy information
>gi|324120564|dbj|BAJ78673.1| RNA polymerase II largest subunit [Bemisia tabaci] Back     alignment and taxonomy information
>gi|324120548|dbj|BAJ78665.1| RNA polymerase II largest subunit [Zorotypus sp. 154-1] Back     alignment and taxonomy information
>gi|324120538|dbj|BAJ78660.1| RNA polymerase II largest subunit [Euconocephalus varius] Back     alignment and taxonomy information
>gi|324120534|dbj|BAJ78658.1| RNA polymerase II largest subunit [Karoophasma biedouwense] Back     alignment and taxonomy information
>gi|324120532|dbj|BAJ78657.1| RNA polymerase II largest subunit [Galloisiana yuasai] Back     alignment and taxonomy information
>gi|324120566|dbj|BAJ78674.1| RNA polymerase II largest subunit [Uroleucon nigrotuberculatum] 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|322801476|gb|EFZ22137.1| hypothetical protein SINV_09846 [Solenopsis invicta] 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 ?
Query392
FB|FBgn0003277 1887 RpII215 "RNA polymerase II 215 0.528 0.109 0.773 8.8e-151
ZFIN|ZDB-GENE-041008-78 1965 polr2a "polymerase (RNA) II (D 0.984 0.196 0.685 4.5e-144
UNIPROTKB|J9NW09 1789 POLR2A "DNA-directed RNA polym 0.984 0.215 0.676 1.1e-142
UNIPROTKB|Q6NX41 566 POLR2A "DNA-directed RNA polym 0.984 0.681 0.676 1.1e-142
UNIPROTKB|I3LJR4 1010 POLR2A "DNA-directed RNA polym 0.984 0.382 0.676 1.1e-142
UNIPROTKB|F1PGS0 1969 POLR2A "DNA-directed RNA polym 0.984 0.196 0.676 2.6e-142
UNIPROTKB|G3MZY8 1970 POLR2A "DNA-directed RNA polym 0.984 0.195 0.676 2.6e-142
UNIPROTKB|P24928 1970 POLR2A "DNA-directed RNA polym 0.984 0.195 0.676 2.6e-142
MGI|MGI:98086 1970 Polr2a "polymerase (RNA) II (D 0.984 0.195 0.676 2.6e-142
RGD|1587326 1970 Polr2a "polymerase (RNA) II (D 0.984 0.195 0.676 2.6e-142
FB|FBgn0003277 RpII215 "RNA polymerase II 215kD subunit" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 917 (327.9 bits), Expect = 8.8e-151, Sum P(2) = 8.8e-151
 Identities = 164/212 (77%), Positives = 192/212 (90%)

Query:     5 DSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEGGRPKLGGLMDPRQGVIDRSS 64
             DSKAPLR VK+VQFGILSPDEIRRMSVTEGG++F ETMEGGRPKLGGLMDPRQGVIDR+S
Sbjct:     6 DSKAPLRQVKRVQFGILSPDEIRRMSVTEGGVQFAETMEGGRPKLGGLMDPRQGVIDRTS 65

Query:    65 RCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDV 124
             RCQTCAGNMTECPGHFGHIDLAKPVFH+GF+TKTIKILRCVCFYCSK+LVSP +PK++++
Sbjct:    66 RCQTCAGNMTECPGHFGHIDLAKPVFHIGFITKTIKILRCVCFYCSKMLVSPHNPKIKEI 125

Query:   125 VLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAE-DPNSLQNKKQGHGGCGRYQP 183
             V+K++GQ R+R A++YDLCKGK ICEGG++MD+ K+  + DPN    KK GHGGCG YQP
Sbjct:   126 VMKSRGQPRKRLAYVYDLCKGKTICEGGEDMDLTKENQQPDPN----KKPGHGGCGHYQP 181

Query:   184 NIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGV 215
             +IRR+GLDLTAEWKH NEDSQEKKI ++ + V
Sbjct:   182 SIRRTGLDLTAEWKHQNEDSQEKKIVVSAERV 213
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
ZFIN|ZDB-GENE-041008-78 polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Danio rerio (taxid:7955)] 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|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|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

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) ?
P16356RPB1_CAEEL2, ., 7, ., 7, ., 60.58290.96930.2047yesN/A
P04052RPB1_DROME2, ., 7, ., 7, ., 60.72440.98210.2040yesN/A
P35084RPB1_DICDI2, ., 7, ., 7, ., 60.53580.97190.2206yesN/A
P24928RPB1_HUMAN2, ., 7, ., 7, ., 4, 80.67330.97190.1934yesN/A

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.7LOW CONFIDENCE prediction!
4th Layer2.7.7.60.737

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 ?
Query392
pfam04997330 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, do 1e-103
smart00663 295 smart00663, RPOLA_N, RNA polymerase I subunit A N- 3e-66
PRK08566 882 PRK08566, PRK08566, DNA-directed RNA polymerase su 3e-57
TIGR02390 867 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer 2e-53
COG0086 808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 7e-44
PRK14977 1321 PRK14977, PRK14977, bifunctional DNA-directed RNA 2e-40
PRK08566 882 PRK08566, PRK08566, DNA-directed RNA polymerase su 1e-38
COG0086 808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 6e-36
TIGR02390 867 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer 3e-34
PRK14977 1321 PRK14977, PRK14977, bifunctional DNA-directed RNA 1e-26
pfam00623 165 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, do 4e-22
PRK14906 1460 PRK14906, PRK14906, DNA-directed RNA polymerase su 5e-19
CHL00018 663 CHL00018, rpoC1, RNA polymerase beta' subunit 2e-18
TIGR02386 1140 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, 6e-18
PRK00566 1156 PRK00566, PRK00566, DNA-directed RNA polymerase su 7e-17
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 6e-16
TIGR02387 619 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase 4e-15
PRK02625 627 PRK02625, rpoC1, DNA-directed RNA polymerase subun 6e-15
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 9e-14
>gnl|CDD|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1 Back     alignment and domain information 
 Score =  306 bits (787), Expect = e-103
 Identities = 141/359 (39%), Positives = 188/359 (52%), Gaps = 51/359 (14%)

Query: 10  LRCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPRQGVIDRSSRCQ 67
           L+ +K++QFGI SP+EIR+ SV E  +  PET      +P+ GGL+D R G I + S C+
Sbjct: 1   LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNYGSLKPEPGGLLDERMGTIKKKSICE 58

Query: 68  TCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLK 127
           TC   +TECPGHFGHI+LAKPVFH+GF  K + ILRCVC  CS LL++ S       V+ 
Sbjct: 59  TCGVEVTECPGHFGHIELAKPVFHIGFFKKILSILRCVCKLCSSLLLNESVKYFFLKVVI 118

Query: 128 TKG--QSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQPNI 185
                 S++R   I +LCK K+IC    E +                    GCG+YQP I
Sbjct: 119 DPKGKNSKKRLKKINNLCKKKSICSKCGEDNGGLK-------------AFEGCGKYQPKI 165

Query: 186 RRSG-LDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEW 244
            + G   + A  K++  +  ++K+       +L   +           I +   D     
Sbjct: 166 SKDGAEAIKALLKNIEIEELKEKLRKLNPEKVLQIFK----------KISKE--DEEILG 213

Query: 245 KHVNEDSQEKK-----------------IPLTGKGVLLDDLTHKLADIIKCNNELIRNES 287
              N      +                 + L G     DDLTHKL DIIK NN L +   
Sbjct: 214 --FNPSGNRPEWMILTVLPVPPPCIRPSVQLDGGRFAEDDLTHKLRDIIKRNNRLKKMLE 271

Query: 288 SGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNL 346
            GA +H+I E  ++LQ HVATL DND+PG P A+QKSG+PLK+I  RLKGKEGR RGNL
Sbjct: 272 EGAPSHIIREEKRLLQEHVATLFDNDIPGQPPALQKSGRPLKSISQRLKGKEGRFRGNL 330

RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand. Length = 330
>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|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|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated 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|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|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2 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|214336 CHL00018, rpoC1, RNA polymerase beta' subunit 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|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit 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|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit Back     alignment and domain information
>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma; 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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 392
KOG0260|consensus 1605 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
PRK08566 882 DNA-directed RNA polymerase subunit A'; Validated 100.0
KOG0261|consensus 1386 100.0
KOG0262|consensus 1640 100.0
COG0086 808 RpoC DNA-directed RNA polymerase, beta' subunit/16 100.0
PF04997337 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; Int 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
PRK02625 627 rpoC1 DNA-directed RNA polymerase subunit gamma; P 100.0
TIGR02387 619 rpoC1_cyan DNA-directed RNA polymerase, gamma subu 100.0
PRK14906 1460 DNA-directed RNA polymerase subunit beta'/alpha do 100.0
CHL00018 663 rpoC1 RNA polymerase beta' subunit 100.0
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 100.0
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 100.0
smart00663 295 RPOLA_N RNA polymerase I subunit A N-terminus. 100.0
>KOG0260|consensus Back     alignment and domain information 
Probab=100.00  E-value=3.4e-93  Score=732.49  Aligned_cols=364  Identities=63%  Similarity=1.009  Sum_probs=341.8

Q ss_pred             CCCCCccccceEEEecCCHHHHHHhhhcccceeCcccccCCccccCCCCCCCCCCCCCCCccccccCCCCCCCCcceEee
Q psy3023           5 DSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEGGRPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGHFGHID   84 (392)
Q Consensus         5 ~~~~~~~~i~~i~F~~~s~eeI~~~Sv~~~~i~~~~~~~~~~p~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhI~   84 (392)
                      .+++|-++|++|+||++|++|||+|||.+  |..|++++.|.|..|||.|||||+.|+...|.|||.++.+||||||||+
T Consensus         7 ~~~~pl~~v~~vqFgi~spdeir~mSV~~--i~~~e~~e~~~pk~ggl~D~RlG~idr~~~CqTC~g~~~~CpGHFGhie   84 (1605)
T KOG0260|consen    7 FSQAPLRTVKSVQFGILSPDEIRRMSVAE--IEFPETMEGGRPKLGGLMDPRLGTIDRDSLCQTCGGNMFECPGHFGHIE   84 (1605)
T ss_pred             cccCcceeeeEEEeeccChhhhhcceeEE--eecccccccCCCCcCCccccccCCCCccchhhhhccccccCCcccceee
Confidence            46899999999999999999999999999  9999999999999999999999999999999999999999999999999


Q ss_pred             cCcchhhhhcHHHHHHHHHHhhhcccccccCCCchHHHHHHHhhhcchHHHHHHHHHHhhccccCCCCCCCCcCCCCCCC
Q psy3023          85 LAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAED  164 (392)
Q Consensus        85 L~~PV~hp~f~~~~~~iL~~iC~~C~~l~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~c~~~~~~~~~~~~~~~  164 (392)
                      ||.|||||+|++++.+||+|+|++|+++++++..+..++.++.... .++++..++.+|+.+..|+...+.+.       
T Consensus        85 LAkPvfH~gFl~kv~kiL~cVC~~C~ki~~~~~~~~~~~~~~~~~~-~k~rl~~v~~vck~k~~ce~g~~~e~-------  156 (1605)
T KOG0260|consen   85 LAKPVFHPGFLKKVKKILRCVCFYCSKILKDKFNPKEDQILRKRYC-SKGRLLMVLDVCKGKVVCEGGIDVES-------  156 (1605)
T ss_pred             eccccccHHHHHHHHHHHHHhhhcchheeecccCcchhhhhhhhcC-CcchHHHHHHhhccceeeeccccccc-------
Confidence            9999999999999999999999999999999988877777775544 77899999999999999976433221       


Q ss_pred             ccccccCCCCCCCCCCCCCccccccceeeeEeeccccccccccccCChHHHHHhhcC-CCCCccc--ccccccccCCCCC
Q psy3023         165 PNSLQNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQ-GHGGCGR--YQPNIRRSGLDLT  241 (392)
Q Consensus       165 ~~~~~~~~~~~~~C~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~p~~v~~i~k~-~~~d~~l--l~p~~~~~~l~~~  241 (392)
                              ..+.+|+..+|.|++.+.+++++|+..+++.++.+..+++++|.++|++ +++|+..  +++.|++      
T Consensus       157 --------~g~sgcg~kqP~i~r~gl~l~a~~k~~~e~~~e~k~~ls~e~V~~i~k~Isded~~~lg~~~~~ar------  222 (1605)
T KOG0260|consen  157 --------DGRSGCGLKQPSIRRLGLDLWAFWKQGDEDSQESKRKLSAERVLEIFKRISDEDIDQLGFKPKIAR------  222 (1605)
T ss_pred             --------cccccccccCCceeccCchhhhhhhccCccCCcccccCcHHHHHHHHHhhchhhhhhhcCCCCcCC------
Confidence                    1467999999999999999999999978888888999999999999999 9999887  8899999      


Q ss_pred             CcccccccccC-----CceeeecCCcccchhhHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHhhhccCCCCC
Q psy3023         242 AEWKHVNEDSQ-----EKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPG  316 (392)
Q Consensus       242 p~~~il~~l~V-----RP~~~~~~~~~~eddlT~~l~~II~~n~~L~~~~~~g~~~~~~~~~~~~LQ~~v~~~~d~~~~~  316 (392)
                      |+||||++|||     ||+++++|..+.+||+|++|.+||+.|..|++.+++|++++++.+...+||.+|++|+||+.+|
T Consensus       223 pewmIlTvLPVPP~~vrP~iv~~~s~rg~DdlthkLadIiK~n~~l~r~e~~ga~~H~i~e~~~LlqfhVat~~Dn~~pg  302 (1605)
T KOG0260|consen  223 PEWMILTVLPVPPPAVRPEIVMQGSARGEDDLTHKLADIIKKNIGLKRNEENGAPAHIIEEYEQLLQFHVATYVDNDIPG  302 (1605)
T ss_pred             CceeEEEEecCCCCcccceeeecccccCcchhHHHHHHHHHHHHHHhhhhhcCCchhhHHHHHhHhhhhhhheecccccC
Confidence            99999999965     8888888888899999999999999999999999999999999999999999999999999999


Q ss_pred             CccccccCCCchhhHhhhhcccccccccccCCccccCccceeecCCCCCccccccchHHhHhhcccCccccCCCCC
Q psy3023         317 LPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD  392 (392)
Q Consensus       317 ~~~~~~~~~~~~~gi~q~L~~K~G~fR~nlmGKRVnfsaRSVIsPDP~l~ideiGvP~~~A~~LT~Pe~Vt~~Ni~  392 (392)
                      .|++.+++++|+++|++||+|||||+|+|||||||||||||||||||||++||||||..||++|||||.||+||++
T Consensus       303 qp~a~qksGrplkSi~arlKgkegriRgnLmGKRvDFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~Nid  378 (1605)
T KOG0260|consen  303 QPQADQKSGRPLKSISARLKGKEGRIRGNLMGKRVDFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNID  378 (1605)
T ss_pred             CcccccccCCcccchhhhhccccchhhhcccccccCcceeeeecCCCCcchhcccCcHHHHhhccCcceeccccHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999985

>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
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated Back     alignment and domain information
>KOG0261|consensus Back     alignment and domain information
>KOG0262|consensus Back     alignment and domain information
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA 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
>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
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional Back     alignment and domain information
>CHL00018 rpoC1 RNA polymerase beta' subunit Back     alignment and domain information
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus 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 ?
Query392
3h0g_A 1752 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 1e-100
1i3q_A 1733 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 4e-96
4a3c_A 1732 Rna Polymerase Ii Initial Transcribing Complex With 4e-96
3j0k_A 1455 Orientation Of Rna Polymerase Ii Within The Human V 4e-96
2waq_A 880 The Complete Structure Of The Archaeal 13-Subunit D 5e-63
2pmz_A 880 Archaeal Rna Polymerase From Sulfolobus Solfataricu 2e-62
3qqc_A436 Crystal Structure Of Archaeal Spt45 BOUND TO THE RN 7e-46
3iyd_D 1413 Three-Dimensional Em Structure Of An Intact Activat 9e-19
3lu0_D 1407 Molecular Model Of Escherichia Coli Core Rna Polyme 9e-19
4gzy_D 1534 Crystal Structures Of Bacterial Rna Polymerase Paus 6e-16
1iw7_D 1524 Crystal Structure Of The Rna Polymerase Holoenzyme 6e-16
1l9u_D 1524 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 2e-15
2gho_D 1233 Recombinant Thermus Aquaticus Rna Polymerase For St 1e-14
1hqm_D 1265 Crystal Structure Of Thermus Aquaticus Core Rna Pol 1e-14
1i6v_D 1264 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 1e-14
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 Back     alignment and structure 
Iteration: 1

 Score =  362 bits (930), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 192/398 (48%), Positives = 256/398 (64%), Gaps = 27/398 (6%)
Query: 6   SKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPRQGVIDRS 63
           S  PLR V++VQFGILSP+EIR MSV +  I+FPETM+  G RP++GGL+DPR G IDR 
Sbjct: 9   SSVPLRRVEEVQFGILSPEEIRSMSVAK--IEFPETMDESGQRPRVGGLLDPRLGTIDRQ 66
Query: 64  SRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRD 123
            +CQTC   M +CPGHFGHI+LAKPVFH+GF++K  KIL CVC+ C KL +  S+PK  D
Sbjct: 67  FKCQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFND 126
Query: 124 VVLKTKGQSRRRQAFIYDLCKGKNICE-----GGDEMDINKDGAEDPNSLQNKKQGHGGC 178
              +     + R   ++++CK K +C+     G D  D++   A           GHGGC
Sbjct: 127 T--QRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDNFDLSNPSA---------NMGHGGC 175
Query: 179 GRYQPNIRRSGLDLTAEWKHVNEDSQ--EKKI--PLTGKGVLLN-KKQGHGGCGRYQPNI 233
           G  QP IR+ GL L   WK   ++S   EK++  PL    +  +   +     G  +   
Sbjct: 176 GAAQPTIRKDGLRLWGSWKRGKDESDLPEKRLLSPLEVHTIFTHISSEDLAHLGLNEQYA 235
Query: 234 RRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATH 293
           R   + +T              +  T +G   DDLTHKL+DIIK N  + R E  GA  H
Sbjct: 236 RPDWMIITVLPVPPPSVRPSISVDGTSRGE--DDLTHKLSDIIKANANVRRCEQEGAPAH 293
Query: 294 VIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDF 353
           +++E  ++LQFHVAT  DN++ G P+A+QKSG+PLK+I+ARLKGKEGR+RGNLMGKRVDF
Sbjct: 294 IVSEYEQLLQFHVATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDF 353
Query: 354 SARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNM 391
           SARTVIT DPNL +D++GVPRSIA+ +T+PE VTP+N+
Sbjct: 354 SARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNI 391
>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|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|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|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP CLAMP DOMAIN Length = 436 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|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 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|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 ?
Query392
3qqc_A436 DNA-directed RNA polymerase subunit B, DNA-direct 1e-154
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 1e-139
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 1e-133
4ayb_A 880 DNA-directed RNA polymerase; transferase, multi-su 1e-119
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 6e-20
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 2e-19
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 5e-19
>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} Length = 436 Back     alignment and structure
 Score =  441 bits (1137), Expect = e-154
 Identities = 118/403 (29%), Positives = 167/403 (41%), Gaps = 59/403 (14%)

Query: 5   DSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEG-GRPKLGGLMDPRQGVIDRS 63
           +     + +  ++FGILSP EIR+MS  E  +  P+T +  G P  GG+MD R GVID  
Sbjct: 61  NLSEGGKVIGSIEFGILSPQEIRKMSAVE--VTVPDTYDDDGYPIEGGVMDKRMGVIDPG 118

Query: 64  SRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPS-HPKVR 122
            RC+TC G   ECPGHFGHI+LA+PV HVGF     +IL   C  C ++ ++     +  
Sbjct: 119 LRCETCGGRAGECPGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYM 178

Query: 123 DVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQ 182
             +   + +       I      K                        ++     CG  Q
Sbjct: 179 KKIELARNRRSEFNE-IIKEIHKKA----------------------KERMVCPHCGAPQ 215

Query: 183 PNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTA 242
             I+     +  E +  +E   E +  L    V    +            I    L L  
Sbjct: 216 YPIKFEKPTIYWEIRK-DEQGNEYRHRLMPTEVRDWLE-----------KIPDKDLPLLG 263

Query: 243 --------EWK-----HVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSG 289
                   EW       V   +    I L       DDLTHKL DII+ NN L +N  +G
Sbjct: 264 LDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDDLTHKLVDIIRINNRLKQNIEAG 323

Query: 290 AATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGK 349
           A   +I +   +LQ+HV T  +N+ PG+P A  KSG+PLK +  RLKGKEGR RGNL G 
Sbjct: 324 APQLIIEDLWDLLQYHVTTYINNEAPGVPPAKHKSGRPLKTLAQRLKGKEGRFRGNLSGG 383

Query: 350 RVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
               +    +               ++       E     N++
Sbjct: 384 AGSGAGSGSVLARAAF-------EITVQHLFEAAEKGEVDNLN 419
>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
>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
>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
>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
>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
>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 ?
Query392
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
3qqc_A436 DNA-directed RNA polymerase subunit B, DNA-direct 100.0
4ayb_A 880 DNA-directed RNA polymerase; transferase, multi-su 100.0
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 100.0
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 100.0
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 100.0
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
Probab=100.00  E-value=3.1e-94  Score=804.32  Aligned_cols=376  Identities=50%  Similarity=0.863  Sum_probs=330.0

Q ss_pred             CCCCCCCccccceEEEecCCHHHHHHhhhcccceeCcccccC--CccccCCCCCCCCCCCCCCCccccccCCCCCCCCcc
Q psy3023           3 MADSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEG--GRPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGHF   80 (392)
Q Consensus         3 ~~~~~~~~~~i~~i~F~~~s~eeI~~~Sv~~~~i~~~~~~~~--~~p~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGHf   80 (392)
                      ..+|.+|.++|++|+||++|+|||+++||++  |+++.+||.  ++|+.|||||||||+.++...|+|||++..+|||||
T Consensus         6 ~~~s~~~~~~i~~i~Fg~~S~eeI~~~Sv~~--I~~~~~~d~~~~~P~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGHF   83 (1752)
T 3h0g_A            6 FSPSSVPLRRVEEVQFGILSPEEIRSMSVAK--IEFPETMDESGQRPRVGGLLDPRLGTIDRQFKCQTCGETMADCPGHF   83 (1752)
T ss_dssp             SCCCSSCCCCCCCBEECCCCHHHHHHHCCCC--CCCTTCTTCSSSSSCCSSSSSSSCCCSSSSCCCTTSCCSSSSCCCCC
T ss_pred             CCCCcCcceeeeeEEEecCCHHHHHHhCeeE--EecccccccccCCCCCCCCcCccccCCCCCCCCCCCCCCCCcCCCcc
Confidence            4689999999999999999999999999999  999999985  599999999999999999999999999999999999


Q ss_pred             eEeecCcchhhhhcHHHHHHHHHHhhhcccccccCCCchHHHHHHHhhhcchHHHHHHHHHHhhccccCCCCCCCCcCCC
Q psy3023          81 GHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKD  160 (392)
Q Consensus        81 GhI~L~~PV~hp~f~~~~~~iL~~iC~~C~~l~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~c~~~~~~~~~~~  160 (392)
                      |||||++|||||+||+.|++||+|+|++|++|++++.++++...++.  ...++|+++++++|+++..|+.+...+.+..
T Consensus        84 GHIELa~PVfHpgF~~~I~kILr~vC~~C~klll~~~~~~f~~~lrl--rd~k~r~~~V~~~ck~k~~Ce~~~~~~~~~~  161 (1752)
T 3h0g_A           84 GHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFNDTQRY--RDPKNRLNAVWNVCKTKMVCDTGLSAGSDNF  161 (1752)
T ss_dssp             EECCCCSCBCCHHHHHHHHHHSSSSCTTTCCCSCCSCSHHHHHHHHS--SCTTTTHHHHHHHHHHCCCCCSSTTCCSSCC
T ss_pred             eeeecccceEeehhhHHHHHHHHHHHHHhcccccccccHHHHHHHHc--cCHHHHHHHHHHHhccccccCCCCcccccch
Confidence            99999999999999999999999999999999999887766554432  2345678999999998889976432221000


Q ss_pred             CCCCccccccCCCCCCCCCCCCCccccccceeeeEeeccccccc-cccccCChHHHHHhhcC-CCCCccc--cccccccc
Q psy3023         161 GAEDPNSLQNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQ-EKKIPLTGKGVLLNKKQ-GHGGCGR--YQPNIRRS  236 (392)
Q Consensus       161 ~~~~~~~~~~~~~~~~~C~~~~~~i~~~~~~~~~~~~~~~~~~~-~~~~~l~p~~v~~i~k~-~~~d~~l--l~p~~~~~  236 (392)
                          .......++.|++|++.+|.||+.+++++.+|+...++.. +.+..|+|++|+++|++ |++|+++  +++.+.+ 
T Consensus       162 ----~~~~~~~~~~~~gCG~~qP~IRKeglkl~~~~k~~k~~~~~~~k~~LtP~eVl~ifk~IsdeD~~lLGl~~~~~r-  236 (1752)
T 3h0g_A          162 ----DLSNPSANMGHGGCGAAQPTIRKDGLRLWGSWKRGKDESDLPEKRLLSPLEVHTIFTHISSEDLAHLGLNEQYAR-  236 (1752)
T ss_dssp             ----CSSCCCCCCSSCSSCCCCCCCEEETTEEECCBCCSSSSCBCSSCCCCCHHHHHHHHHHSCHHHHHHSSCCSSSCC-
T ss_pred             ----hcccccccccCCCcCCcCCcEEeeccEEEEEEcccccccccccceecCHHHHHHHHHhcCHHHHHHhCCCccCCC-
Confidence                0000113457999999999999999988888875332211 24568999999999999 9999998  6677777 


Q ss_pred             CCCCCCccccccccc-----CCceeeecCCcccchhhHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHhhhcc
Q psy3023         237 GLDLTAEWKHVNEDS-----QEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTD  311 (392)
Q Consensus       237 ~l~~~p~~~il~~l~-----VRP~~~~~~~~~~eddlT~~l~~II~~n~~L~~~~~~g~~~~~~~~~~~~LQ~~v~~~~d  311 (392)
                           |+||||++||     |||++.++|+...|||||++|++||+.|+.|++....|++..++.+.|++||.+|++|+|
T Consensus       237 -----PewmiL~vLPVpPp~vRPsv~ldg~~~~edDLt~~l~~II~~N~~Lk~~~~~gap~~~~~~~~~~LQ~~v~~~~d  311 (1752)
T 3h0g_A          237 -----PDWMIITVLPVPPPSVRPSISVDGTSRGEDDLTHKLSDIIKANANVRRCEQEGAPAHIVSEYEQLLQFHVATYMD  311 (1752)
T ss_dssp             -----GGGSSBSSCEECCGGGSCCCCCSSSCCCCCTTTTHHHHHHHHHHHHHGGGGCCSSSTTHHHHHHHHHHHHHHTTC
T ss_pred             -----hhheEeeccccCCCCccCceEcCCCccCCChHHHHHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHhhc
Confidence                 9999999995     488888888778899999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCccccccCCCchhhHhhhhcccccccccccCCccccCccceeecCCCCCccccccchHHhHhhcccCccccCCCC
Q psy3023         312 NDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNM  391 (392)
Q Consensus       312 ~~~~~~~~~~~~~~~~~~gi~q~L~~K~G~fR~nlmGKRVnfsaRSVIsPDP~l~ideiGvP~~~A~~LT~Pe~Vt~~Ni  391 (392)
                      |+.+|.+.+.+++++|++||+|||+||+||||+|||||||||||||||||||||++||||||..||++|||||+||+||+
T Consensus       312 n~~~~~~~~~~~~~rp~k~~~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~evGvP~~~A~~Lt~Pe~vt~~ni  391 (1752)
T 3h0g_A          312 NEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNI  391 (1752)
T ss_dssp             TTCSSCCCCCSSSSCCCCCHHHHHTCSSSSSTTTTSSCCCSSEEEEEEEEETTSCTTBCBCCHHHHTSCCCCCBCCTTTH
T ss_pred             CCCCCCccccccCCCCCcchHhhhhcccccccccccccccCCccceeecCCCCcccceeeChHHHHHhcCCCccccHHHH
Confidence            99998876666678999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q psy3023         392 D  392 (392)
Q Consensus       392 ~  392 (392)
                      +
T Consensus       392 ~  392 (1752)
T 3h0g_A          392 Y  392 (1752)
T ss_dssp             H
T ss_pred             H
Confidence            3
>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
>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
>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
>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
>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
>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

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 392
d1twfa_ 1449 e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c 1e-105
d1smyd_ 1504 e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t 3e-48
d1smyd_ 1504 e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t 0.001
>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 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]

 Score =  337 bits (865), Expect = e-105
 Identities = 187/409 (45%), Positives = 240/409 (58%), Gaps = 51/409 (12%)

Query: 6   SKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPRQGVIDRS 63
           S APLR VK+VQFG+ SP+E+R +SV +  I+FPETM+    R K+GGL DPR G IDR+
Sbjct: 6   SSAPLRTVKEVQFGLFSPEEVRAISVAK--IRFPETMDETQTRAKIGGLNDPRLGSIDRN 63

Query: 64  SRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRD 123
            +CQTC   M ECPGHFGHIDLAKPVFHVGF+ K  K+  CVC +C KLL+   +  +R 
Sbjct: 64  LKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQ 123

Query: 124 VVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQP 183
            +      S++R A I+ LCK K +CE   ++    D          +    GGCG  QP
Sbjct: 124 ALAIKD--SKKRFAAIWTLCKTKMVCE--TDVPSEDDP--------TQLVSRGGCGNTQP 171

Query: 184 NIRRSGLDLTAEWKH---VNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDL 240
            IR+ GL L   WK      +  + +   L+ + +L               NI +     
Sbjct: 172 TIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEIL---------------NIFKHISVK 216

Query: 241 TAEWKHVNEDSQEKK-----------------IPLTGKGVLLDDLTHKLADIIKCNNELI 283
                  NE     +                 I         DDLT KLADI+K N  L 
Sbjct: 217 DFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLE 276

Query: 284 RNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIR 343
             E +GA  H I E   +LQFHVAT  DND+ G P+A+QKSG+P+K+I+ARLKGKEGRIR
Sbjct: 277 TLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIR 336

Query: 344 GNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
           GNLMGKRVDFSARTVI+ DPNL +DQVGVP+SIA+ +T+PE+VTP+N+D
Sbjct: 337 GNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNID 385
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query392
d1twfa_ 1449 RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1smyd_ 1504 RNA-polymerase beta-prime {Thermus thermophilus [T 100.0
d1jmab246 Cellular receptor HveA {Human (Homo sapiens) [TaxI 88.49
>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=3.5e-83  Score=720.82  Aligned_cols=371  Identities=50%  Similarity=0.847  Sum_probs=317.4

Q ss_pred             CCCCCCCCccccceEEEecCCHHHHHHhhhcccceeCcccccC--CccccCCCCCCCCCCCCCCCccccccCCCCCCCCc
Q psy3023           2 AMADSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEG--GRPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGH   79 (392)
Q Consensus         2 ~~~~~~~~~~~i~~i~F~~~s~eeI~~~Sv~~~~i~~~~~~~~--~~p~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGH   79 (392)
                      +-++|.+|.++|++|+|++||+|||++||++|  |++|.+|+.  ++|..|||||||||+++++..|.|||++..+||||
T Consensus         2 ~~~~~~~p~~~i~~i~f~~~s~eeIr~~S~~e--i~~~~~~~~~~~~p~~~Gl~d~rlG~~~~~~~C~tC~~~~~~CpGH   79 (1449)
T d1twfa_           2 GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAK--IRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGH   79 (1449)
T ss_dssp             CCSCCCSCBCCCCEEECCBCCHHHHHHTCCCC--CCCSCCSCTTSCCSCCSSSSCSSSCCCTTCCCSSSCCCCTTSCCCC
T ss_pred             CCCCCcCccceeceEEEEecCHHHHHHhcceE--EcCCCcccCCCCCCCCCCCcchhhCCCCCcCCCCCCCCCCcCCCCC
Confidence            67899999999999999999999999999988  999999974  67999999999999999999999999999999999


Q ss_pred             ceEeecCcchhhhhcHHHHHHHHHHhhhcccccccCCCchHHHHHHHhhhcchHHHHHHHHHHhhccccCCCCCCCCcCC
Q psy3023          80 FGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINK  159 (392)
Q Consensus        80 fGhI~L~~PV~hp~f~~~~~~iL~~iC~~C~~l~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~c~~~~~~~~~~  159 (392)
                      ||||||+.||||||||+.++++|+++|++|++++++.....+...+.  ......+...+.+.++....|.......   
T Consensus        80 fGhIeL~~PV~h~~f~~~~~~~L~~~C~~C~~l~l~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  154 (1449)
T d1twfa_          80 FGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALA--IKDSKKRFAAIWTLCKTKMVCETDVPSE---  154 (1449)
T ss_dssp             CCCEEEEEEEECGGGHHHHHHHHHHBCTTTCCBSCCTTSHHHHHHHT--CCSHHHHHHHHHHHHTTCCBCCSEECCS---
T ss_pred             CEeeEecccchhHHHHHHHHHHHHHhhhccCCEeecccHHHHHHHHh--hcchhhhhHHHHHHhhhheeccccccch---
Confidence            99999999999999999999999999999999999987655544443  1233455667778888776764311100   


Q ss_pred             CCCCCccccccCCCCCCCCCCCCCccccccceeeeEeeccccc---cccccccCChHHHHHhhcC-CCCCccc--ccccc
Q psy3023         160 DGAEDPNSLQNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNED---SQEKKIPLTGKGVLLNKKQ-GHGGCGR--YQPNI  233 (392)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~C~~~~~~i~~~~~~~~~~~~~~~~~---~~~~~~~l~p~~v~~i~k~-~~~d~~l--l~p~~  233 (392)
                         ..    ......|.+|+..++.+++....+..+|+.....   .+.....++|++++++|++ +++++.+  +++..
T Consensus       155 ---~~----~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~~i~~~~~~~l~~~~~~  227 (1449)
T d1twfa_         155 ---DD----PTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVF  227 (1449)
T ss_dssp             ---SC----TTSCEECCSCCCBCCCCEECSSCEEEEECSSSSCTTSCSCEEEEECHHHHHHHHTTSCHHHHHHTTCBTTT
T ss_pred             ---hh----hhhhhhcCCCCcCChhhhhhhHHHHHHHHHhhhcccccchhheeCCHHHHHHHHHhCCHhHHHHhCCCcCC
Confidence               00    0133467899999999988877777776543221   1222347899999999999 9888766  55666


Q ss_pred             cccCCCCCCcccccccccC-----CceeeecCCcccchhhHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHhh
Q psy3023         234 RRSGLDLTAEWKHVNEDSQ-----EKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVAT  308 (392)
Q Consensus       234 ~~~~l~~~p~~~il~~l~V-----RP~~~~~~~~~~eddlT~~l~~II~~n~~L~~~~~~g~~~~~~~~~~~~LQ~~v~~  308 (392)
                      .+      |+||||++|||     ||++..+|+...+||||.+|++||+.|++|++....+++...+.+.|..||.+|+.
T Consensus       228 ~~------p~~~~l~~lpV~P~~~RP~~~~~~~~~~~~dlt~~~~~Ii~~n~~l~~~~~~~~~~~~~~~~~~~LQ~~v~~  301 (1449)
T d1twfa_         228 SR------PEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVAT  301 (1449)
T ss_dssp             BC------GGGGEEEEECCCCTTTSCCCCCSSSCCCCCHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHH
T ss_pred             CC------hHHEEeeeeecCCCCcCCceEeCCCcccCChHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHH
Confidence            67      99999999976     77777777667899999999999999999999999999999999999999999999


Q ss_pred             hccCCCCCCccccccCCCchhhHhhhhcccccccccccCCccccCccceeecCCCCCccccccchHHhHhhcccCccccC
Q psy3023         309 LTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTP  388 (392)
Q Consensus       309 ~~d~~~~~~~~~~~~~~~~~~gi~q~L~~K~G~fR~nlmGKRVnfsaRSVIsPDP~l~ideiGvP~~~A~~LT~Pe~Vt~  388 (392)
                      |+||+.++.+.++.++++|++||+|+|+||+||||+|||||||||||||||||||+|++||||||..||++|||||+||+
T Consensus       302 ~~dn~~~~~~~~~~~~~~~~k~i~~~L~gK~GrfR~nl~GKRVd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~  381 (1449)
T d1twfa_         302 YMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTP  381 (1449)
T ss_dssp             HHCCCSSCCCCCSSCTTCCCCCSTTSCTTTTTTSSGGGTTCSCCSEEEEEEEECTTSCTTEEEEEHHHHTTCEEEEECCT
T ss_pred             hccccccCCchhccccCCCccchhhHhccchhhhhhhccccccccccceeeccCCccceeecccHHHHHhhCCCCeeecH
Confidence            99999988776666667899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy3023         389 FNMD  392 (392)
Q Consensus       389 ~Ni~  392 (392)
                      ||++
T Consensus       382 ~n~~  385 (1449)
T d1twfa_         382 YNID  385 (1449)
T ss_dssp             TTHH
T ss_pred             HHHH
Confidence            9963
>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1jmab2 g.24.1.1 (B:60-105) Cellular receptor HveA {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure