Psyllid ID: psy16768

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----
METNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTARSVTPACEPNSHHDVKKIEFKKQNKILPLVLQNSLTGSSYPANHPDFIGK
cccccEEEEEEEcccHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHcHHcccccccccHHHHHHHHHHHHccccccEEEEcccccccccHHHHHHHHHHHHHHcHHHHHHHHHHccccccccccccEEEccccccccccccccc
ccccccEEEEEccccHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEcHHHHHHHHHHHcccHHHcccccccccHHHHHHHHHHHHHHHHHHcccccHccccccccccccccEEEEEEEEcccccccccccccc
metngkhllktdgiNVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSwmldevksttarsvtpacepnshhdvkkiefkkqnkilplvlqnsltgssypanhpdfigk
metngkhllktdgiNVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTarsvtpacepnshhdvkkiefkkqNKILPLVlqnsltgssypanhpdfigk
METNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTARSVTPACEPNSHHDVKKIEFKKQNKILPLVLQNSLTGSSYPANHPDFIGK
*******LLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVK*********************IEFKKQNKILPLVLQ******************
***NGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMV********VKSTTARSVTPACEPNSHHDVKKIEFKKQNKILPLVLQNSLTGSSYPANHPDF***
METNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTARSVTPACEPNSHHDVKKIEFKKQNKILPLVLQNSLTGSSYPANHPDFIGK
***NGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTARSVTPACEPNSHHDVKKIEFKKQNKILPLVLQNSLTGSSYPANHPDF***
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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METNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTARSVTPACEPNSHHDVKKIEFKKQNKILPLVLQNSLTGSSYPANHPDFIGK
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 ?
Query154 2.2.26 [Sep-21-2011]
P918751642 DNA-directed RNA polymera yes N/A 0.480 0.045 0.675 2e-23
O351341717 DNA-directed RNA polymera yes N/A 0.474 0.042 0.671 2e-22
O956021720 DNA-directed RNA polymera yes N/A 0.474 0.042 0.657 8e-22
O548891716 DNA-directed RNA polymera yes N/A 0.474 0.042 0.657 9e-22
P153981689 DNA-directed RNA polymera yes N/A 0.454 0.041 0.514 1e-15
Q86H361615 DNA-directed RNA polymera yes N/A 0.467 0.044 0.430 1e-13
P109641664 DNA-directed RNA polymera yes N/A 0.506 0.046 0.410 4e-12
Q976A6392 DNA-directed RNA polymera yes N/A 0.636 0.25 0.366 2e-11
C3N7Q1392 DNA-directed RNA polymera yes N/A 0.636 0.25 0.336 6e-10
C3NFS2392 DNA-directed RNA polymera yes N/A 0.636 0.25 0.336 6e-10
>sp|P91875|RPA1_DROME DNA-directed RNA polymerase I subunit RPA1 OS=Drosophila melanogaster GN=RpI1 PE=1 SV=2 Back     alignment and function desciption
 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 50/74 (67%), Positives = 61/74 (82%)

Query: 7    HLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIE 66
             LLKTDGIN+  + Q+  +LDLN+LY NDIH +A TYGIEAA++VI++EV NVF VYGI 
Sbjct: 1498 QLLKTDGINIGEMFQHNKILDLNRLYSNDIHAIARTYGIEAASQVIVKEVSNVFKVYGIT 1557

Query: 67   VDPRHLSLVADYMT 80
            VD RHLSL+ADYMT
Sbjct: 1558 VDRRHLSLIADYMT 1571
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol I. A bridging helix emanates from RPA1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol I 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.
Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6
>sp|O35134|RPA1_MOUSE DNA-directed RNA polymerase I subunit RPA1 OS=Mus musculus GN=Polr1a PE=1 SV=2 Back     alignment and function description
>sp|O95602|RPA1_HUMAN DNA-directed RNA polymerase I subunit RPA1 OS=Homo sapiens GN=POLR1A PE=1 SV=2 Back     alignment and function description
>sp|O54889|RPA1_RAT DNA-directed RNA polymerase I subunit RPA1 OS=Rattus norvegicus GN=Polr1a PE=1 SV=1 Back     alignment and function description
>sp|P15398|RPA1_SCHPO DNA-directed RNA polymerase I subunit rpa1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpa1 PE=1 SV=2 Back     alignment and function description
>sp|Q86H36|RPA1_DICDI DNA-directed RNA polymerase I subunit rpa1 OS=Dictyostelium discoideum GN=polr1a PE=3 SV=1 Back     alignment and function description
>sp|P10964|RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPA190 PE=1 SV=2 Back     alignment and function description
>sp|Q976A6|RPOA2_SULTO DNA-directed RNA polymerase subunit A'' OS=Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) GN=rpoA2 PE=3 SV=2 Back     alignment and function description
>sp|C3N7Q1|RPOA2_SULIY DNA-directed RNA polymerase subunit A'' OS=Sulfolobus islandicus (strain Y.G.57.14 / Yellowstone #1) GN=rpoA2 PE=3 SV=1 Back     alignment and function description
>sp|C3NFS2|RPOA2_SULIN DNA-directed RNA polymerase subunit A'' OS=Sulfolobus islandicus (strain Y.N.15.51 / Yellowstone #2) GN=rpoA2 PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query154
357624352 369 putative DNA-directed RNA polymerase I l 0.480 0.200 0.729 3e-25
312372078 1721 hypothetical protein AND_20631 [Anophele 0.5 0.044 0.636 4e-23
194757042 1643 GF13529 [Drosophila ananassae] gi|190622 0.5 0.046 0.675 8e-23
449273568 910 DNA-directed RNA polymerase I subunit RP 0.538 0.091 0.613 2e-22
195381961 1648 GJ20610 [Drosophila virilis] gi|19414449 0.487 0.045 0.68 3e-22
195583416 1642 GD25674 [Drosophila simulans] gi|1941935 0.506 0.047 0.653 3e-22
195334386 1585 GM20204 [Drosophila sechellia] gi|194125 0.506 0.049 0.653 3e-22
195486012 1642 GE12306 [Drosophila yakuba] gi|194177429 0.506 0.047 0.653 4e-22
195431457 1649 GK15841 [Drosophila willistoni] gi|19415 0.487 0.045 0.68 4e-22
170067707 1692 DNA-directed RNA polymerase I largest su 0.467 0.042 0.680 5e-22
>gi|357624352|gb|EHJ75158.1| putative DNA-directed RNA polymerase I largest subunit [Danaus plexippus] Back     alignment and taxonomy information
 Score =  119 bits (299), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 54/74 (72%), Positives = 67/74 (90%)

Query: 9   LKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVD 68
           LKT+GIN+  +S+Y HLLDLNKLY NDIH +A+TYGIEAAN+VII+E++NVF VYGI VD
Sbjct: 224 LKTEGINIVQMSKYSHLLDLNKLYTNDIHAIANTYGIEAANKVIIKEIQNVFNVYGITVD 283

Query: 69  PRHLSLVADYMTHS 82
           PRHL+LVADYMT++
Sbjct: 284 PRHLTLVADYMTYN 297

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|312372078|gb|EFR20121.1| hypothetical protein AND_20631 [Anopheles darlingi] Back     alignment and taxonomy information
>gi|194757042|ref|XP_001960774.1| GF13529 [Drosophila ananassae] gi|190622072|gb|EDV37596.1| GF13529 [Drosophila ananassae] Back     alignment and taxonomy information
>gi|449273568|gb|EMC83052.1| DNA-directed RNA polymerase I subunit RPA1, partial [Columba livia] Back     alignment and taxonomy information
>gi|195381961|ref|XP_002049701.1| GJ20610 [Drosophila virilis] gi|194144498|gb|EDW60894.1| GJ20610 [Drosophila virilis] Back     alignment and taxonomy information
>gi|195583416|ref|XP_002081518.1| GD25674 [Drosophila simulans] gi|194193527|gb|EDX07103.1| GD25674 [Drosophila simulans] Back     alignment and taxonomy information
>gi|195334386|ref|XP_002033864.1| GM20204 [Drosophila sechellia] gi|194125834|gb|EDW47877.1| GM20204 [Drosophila sechellia] Back     alignment and taxonomy information
>gi|195486012|ref|XP_002091328.1| GE12306 [Drosophila yakuba] gi|194177429|gb|EDW91040.1| GE12306 [Drosophila yakuba] Back     alignment and taxonomy information
>gi|195431457|ref|XP_002063757.1| GK15841 [Drosophila willistoni] gi|194159842|gb|EDW74743.1| GK15841 [Drosophila willistoni] Back     alignment and taxonomy information
>gi|170067707|ref|XP_001868588.1| DNA-directed RNA polymerase I largest subunit [Culex quinquefasciatus] gi|167863791|gb|EDS27174.1| DNA-directed RNA polymerase I largest subunit [Culex quinquefasciatus] 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 ?
Query154
FB|FBgn00199381642 RpI1 "RNA polymerase I subunit 0.474 0.044 0.684 4.9e-21
UNIPROTKB|E1C4T2745 POLR1A "Uncharacterized protei 0.467 0.096 0.666 1.8e-20
UNIPROTKB|E1BIX21717 POLR1A "DNA-directed RNA polym 0.493 0.044 0.688 2.3e-20
UNIPROTKB|F1NJE0917 POLR1A "DNA-directed RNA polym 0.467 0.078 0.666 2.5e-20
ZFIN|ZDB-GENE-030131-52861710 polr1a "polymerase (RNA) I pol 0.467 0.042 0.666 2.9e-20
UNIPROTKB|J9P5G41717 POLR1A "DNA-directed RNA polym 0.493 0.044 0.675 3.7e-20
MGI|MGI:10963971717 Polr1a "polymerase (RNA) I pol 0.493 0.044 0.675 3.7e-20
UNIPROTKB|E2R0G41746 POLR1A "DNA-directed RNA polym 0.493 0.043 0.675 3.8e-20
UNIPROTKB|F1SVC31723 POLR1A "DNA-directed RNA polym 0.493 0.044 0.675 4.7e-20
UNIPROTKB|B9ZVN91659 POLR1A "DNA-directed RNA polym 0.493 0.045 0.662 1.2e-19
FB|FBgn0019938 RpI1 "RNA polymerase I subunit" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 262 (97.3 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 50/73 (68%), Positives = 61/73 (83%)

Query:     8 LLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEV 67
             LLKTDGIN+  + Q+  +LDLN+LY NDIH +A TYGIEAA++VI++EV NVF VYGI V
Sbjct:  1499 LLKTDGINIGEMFQHNKILDLNRLYSNDIHAIARTYGIEAASQVIVKEVSNVFKVYGITV 1558

Query:    68 DPRHLSLVADYMT 80
             D RHLSL+ADYMT
Sbjct:  1559 DRRHLSLIADYMT 1571
GO:0006360 "transcription from RNA polymerase I promoter" evidence=ISS;NAS
GO:0005736 "DNA-directed RNA polymerase I complex" evidence=ISS
GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;NAS
GO:0005634 "nucleus" evidence=NAS
GO:0008270 "zinc ion binding" evidence=IEA
GO:0003677 "DNA binding" evidence=IEA
UNIPROTKB|E1C4T2 POLR1A "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|E1BIX2 POLR1A "DNA-directed RNA polymerase" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F1NJE0 POLR1A "DNA-directed RNA polymerase" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-5286 polr1a "polymerase (RNA) I polypeptide A" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|J9P5G4 POLR1A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:1096397 Polr1a "polymerase (RNA) I polypeptide A" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|E2R0G4 POLR1A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|F1SVC3 POLR1A "DNA-directed RNA polymerase" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|B9ZVN9 POLR1A "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)] 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) ?
O54889RPA1_RAT2, ., 7, ., 7, ., 60.65750.47400.0425yesN/A
O95602RPA1_HUMAN2, ., 7, ., 7, ., 60.65750.47400.0424yesN/A
P91875RPA1_DROME2, ., 7, ., 7, ., 60.67560.48050.0450yesN/A
P15398RPA1_SCHPO2, ., 7, ., 7, ., 60.51420.45450.0414yesN/A
O35134RPA1_MOUSE2, ., 7, ., 7, ., 60.67120.47400.0425yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

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 ?
Query154
cd02735309 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of 2e-36
pfam04998447 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do 3e-21
PRK04309383 PRK04309, PRK04309, DNA-directed RNA polymerase su 5e-14
cd06528363 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Pol 6e-14
cd02736300 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) o 8e-14
cd00630158 cd00630, RNAP_largest_subunit_C, Largest subunit o 1e-12
cd02584410 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of 1e-12
TIGR02389367 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymer 2e-12
PRK14897509 PRK14897, PRK14897, unknown domain/DNA-directed RN 1e-10
PRK14898858 PRK14898, PRK14898, DNA-directed RNA polymerase su 4e-10
PRK149771321 PRK14977, PRK14977, bifunctional DNA-directed RNA 1e-08
cd02737381 cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) 4e-06
COG0086808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 3e-04
>gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain Back     alignment and domain information 
 Score =  126 bits (320), Expect = 2e-36
 Identities = 44/81 (54%), Positives = 61/81 (75%)

Query: 2   ETNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFA 61
               K+L+ T+G+N+  + ++  +LD+N++Y NDIH M +TYGIEAA R I++E+ NVF 
Sbjct: 164 GGKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFK 223

Query: 62  VYGIEVDPRHLSLVADYMTHS 82
           VYGI VDPRHLSL+ADYMT  
Sbjct: 224 VYGIAVDPRHLSLIADYMTFE 244

RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. Length = 309
>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5 Back     alignment and domain information
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A''; Validated Back     alignment and domain information
>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP) Back     alignment and domain information
>gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain Back     alignment and domain information
>gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase (RNAP), C-terminal domain Back     alignment and domain information
>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain Back     alignment and domain information
>gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A'' Back     alignment and domain information
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional Back     alignment and domain information
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; Provisional 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|132724 cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain 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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 154
TIGR02389367 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit 100.0
cd02584410 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryoti 100.0
cd02736300 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryot 100.0
cd02735309 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic 100.0
cd06528363 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (R 100.0
PRK04309383 DNA-directed RNA polymerase subunit A''; Validated 100.0
PRK14897509 unknown domain/DNA-directed RNA polymerase subunit 100.0
cd02737381 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher 100.0
PRK14898858 DNA-directed RNA polymerase subunit A''; Provision 100.0
KOG0262|consensus1640 100.0
PRK149771321 bifunctional DNA-directed RNA polymerase A'/A'' su 99.98
KOG0261|consensus1386 99.95
cd00630158 RNAP_largest_subunit_C Largest subunit of RNA poly 99.95
KOG0260|consensus 1605 99.92
PF04998277 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; Int 99.88
cd02655204 RNAP_beta'_C Largest subunit (beta') of Bacterial 99.88
PRK005661156 DNA-directed RNA polymerase subunit beta'; Provisi 99.69
TIGR023861140 rpoC_TIGR DNA-directed RNA polymerase, beta' subun 99.68
PRK148442836 bifunctional DNA-directed RNA polymerase subunit b 99.62
PRK14906 1460 DNA-directed RNA polymerase subunit beta'/alpha do 99.55
PRK025971331 rpoC2 DNA-directed RNA polymerase subunit beta'; P 99.54
TIGR023881227 rpoC2_cyan DNA-directed RNA polymerase, beta'' sub 99.52
CHL001171364 rpoC2 RNA polymerase beta'' subunit; Reviewed 99.51
PRK096032890 bifunctional DNA-directed RNA polymerase subunit b 99.44
COG0086808 RpoC DNA-directed RNA polymerase, beta' subunit/16 98.38
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A'' Back     alignment and domain information 
Probab=100.00  E-value=5.4e-38  Score=274.56  Aligned_cols=117  Identities=28%  Similarity=0.353  Sum_probs=111.6

Q ss_pred             CCCeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh
Q psy16768          3 TNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS   82 (154)
Q Consensus         3 ~~~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~   82 (154)
                      ++++|+|+|+|+||+++|.++ +||++|++||||++|+++|||||||++|++|+++||+.||++||+|||+||||+||++
T Consensus       221 ~~~~~~l~teG~nl~~v~~~~-~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~  299 (367)
T TIGR02389       221 EGDEYVIYTEGSNLKEVLKLE-GVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWD  299 (367)
T ss_pred             CCCeEEEEEeccCHHHHHcCC-CCccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhcCC
Confidence            467899999999999999995 9999999999999999999999999999999999999999999999999999999999


Q ss_pred             c----cchhhhcccc----------------------ccccccCCcccceeec---CCCCCchhhhh
Q psy16768         83 E----FDLIIMVSKS----------------------WMLDEVKSTTARSVTP---ACEPNSHHDVK  120 (154)
Q Consensus        83 G----~~R~Gm~~~~----------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~  120 (154)
                      |    +||+|++++.                      |+.|+|+|||+||++|   |+|||+|+++.
T Consensus       300 G~~~~i~R~Gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~  366 (367)
T TIGR02389       300 GEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLVM  366 (367)
T ss_pred             ceEEeccccccccCCCCHHHhcChHhHHHHHHHHhhcCCCCcCCChHHHhhcCCCcCCcCCeEEEee
Confidence            9    9999997532                      9999999999999999   99999999875

This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain Back     alignment and domain information
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain Back     alignment and domain information
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain Back     alignment and domain information
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP) Back     alignment and domain information
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated Back     alignment and domain information
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional Back     alignment and domain information
>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain Back     alignment and domain information
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional Back     alignment and domain information
>KOG0262|consensus Back     alignment and domain information
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional Back     alignment and domain information
>KOG0261|consensus Back     alignment and domain information
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain Back     alignment and domain information
>KOG0260|consensus Back     alignment and domain information
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain 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
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional Back     alignment and domain information
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional Back     alignment and domain information
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit Back     alignment and domain information
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed Back     alignment and domain information
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query154
2y0s_C395 Crystal Structure Of Sulfolobus Shibatae Rna Polyme 6e-11
2waq_C395 The Complete Structure Of The Archaeal 13-Subunit D 6e-11
3hkz_C395 The X-Ray Crystal Structure Of Rna Polymerase From 1e-10
2pmz_C392 Archaeal Rna Polymerase From Sulfolobus Solfataricu 1e-10
1i3q_A 1733 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 2e-05
4a3c_A 1732 Rna Polymerase Ii Initial Transcribing Complex With 2e-05
3j0k_A1455 Orientation Of Rna Polymerase Ii Within The Human V 2e-05
3h0g_A 1752 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 2e-05
>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In P21 Space Group Length = 395 Back     alignment and structure 
Iteration: 1

 Score = 63.2 bits (152), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 60/101 (59%), Gaps = 3/101 (2%)
Query: 6   KHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGI 65
           ++++ TDG N++ +   + + D+ K+  N+I  +   +GIEAA  +IIRE+  V A  G+
Sbjct: 248 EYIILTDGSNLSGVLSVKGV-DIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGL 306
Query: 66  EVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTARS 106
           +VD RH+ LVAD MT +   ++  + +  +  E  S  AR+
Sbjct: 307 DVDMRHILLVADVMTRT--GVVRQIGRHGVTGEKNSVLARA 345
>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 395 Back     alignment and structure
>pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea Length = 395 Back     alignment and structure
>pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 392 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|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|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 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 ?
Query154
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 4e-26
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 4e-25
4ayb_C395 DNA-directed RNA polymerase; transferase, multi-su 8e-20
>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
 Score =  102 bits (254), Expect = 4e-26
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 2    ETNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFA 61
            E   + +L+TDGIN+        + D  + Y N    +    GIEA    +++E++NV  
Sbjct: 1305 ERADEWVLETDGINLTEAMTVEGV-DATRTYSNSFVEILQILGIEATRSALLKELRNVIE 1363

Query: 62   VYGIEVDPRHLSLVADYMTHS 82
              G  V+ RHL+L+ D MT  
Sbjct: 1364 FDGSYVNYRHLALLCDVMTSR 1384
>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_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C Length = 395 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query154
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
4ayb_C395 DNA-directed RNA polymerase; transferase, multi-su 100.0
2a6h_D1524 DNA-directed RNA polymerase beta' chain; RNA polym 99.79
1hqm_D1265 DNA-directed RNA polymerase; transferase, transcri 99.74
3lu0_D1407 DNA-directed RNA polymerase subunit beta'; E. coli 99.69
>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=5.6e-36  Score=297.14  Aligned_cols=121  Identities=22%  Similarity=0.272  Sum_probs=116.7

Q ss_pred             CeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc-
Q psy16768          5 GKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE-   83 (154)
Q Consensus         5 ~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G-   83 (154)
                      ++|+|+|||+||+++|.+ ++||++||+||||+||+++|||||||++|++||+.||+.||++||+|||+||||+||++| 
T Consensus      1308 ~~~~l~teG~nL~~v~~~-~gVD~~rt~sNdI~ei~~vlGIEAAR~~Ii~Ei~~v~~~~G~~Vd~RHl~LlaD~MT~~G~ 1386 (1752)
T 3h0g_A         1308 DEWVLETDGINLTEAMTV-EGVDATRTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGH 1386 (1752)
T ss_dssp             EEEEEECCSCCCSTTTSS-SSCCTTTCCCSCHHHHHHHSCHHHHHHHHHHHHHTTSCSSSCCCCHHHHHHHHHHHTSSSS
T ss_pred             ceEEEEecccCHHHHhCc-CCCccccCeeCCHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccCCe
Confidence            489999999999999999 699999999999999999999999999999999999999999999999999999999999 


Q ss_pred             ---cchhhhcccc----------------------ccccccCCcccceeec---CCCCCchhhhhhhhhhc
Q psy16768         84 ---FDLIIMVSKS----------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKKIEFKK  126 (154)
Q Consensus        84 ---~~R~Gm~~~~----------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~~~~~~  126 (154)
                         ||||||++..                      |+.|+|+|||||||+|   ++|||+|+++.+.+.++
T Consensus      1387 ~~~itR~Gi~~~~~s~l~~aSFE~T~~~L~~Aa~~g~~D~l~gvse~Ii~G~~~~~GTG~fdll~~~~~l~ 1457 (1752)
T 3h0g_A         1387 LMAITRHGINRAETGALMRCSFEETVEILMDAAASGEKDDCKGISENIMLGQLAPMGTGAFDIYLDQDMLM 1457 (1752)
T ss_dssp             CCCCCTTSCSCCCSHHHHHHHHSCCTHHHHHHGGGTCCBCCCCSTTGGGTCSCCCSBTTSCEECCCHHHHH
T ss_pred             EEeechhhhccCCCCHHHHhhHHHHHHHHHHHHHhcCcccccChhHHhhcCCCcCCccceEEEEeCHHHhc
Confidence               9999998642                      9999999999999999   99999999999998877
>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
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C 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
>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

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 154
d1twfa_1449 e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c 1e-23
d1smyd_1504 e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t 0.002
>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 = 93.8 bits (232), Expect = 1e-23
 Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 1/79 (1%)

Query: 4    NGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVY 63
              + +L+TDG+N++ +     + D  ++Y N    +    GIEA    + +EV NV A  
Sbjct: 1300 EPEWVLETDGVNLSEVMTVPGI-DPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASD 1358

Query: 64   GIEVDPRHLSLVADYMTHS 82
            G  V+ RH++L+ D MT  
Sbjct: 1359 GSYVNYRHMALLVDVMTTQ 1377
>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 ?
Query154
d1twfa_1449 RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1smyd_1504 RNA-polymerase beta-prime {Thermus thermophilus [T 99.44
>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=3.4e-34  Score=277.67  Aligned_cols=119  Identities=24%  Similarity=0.314  Sum_probs=113.5

Q ss_pred             CCeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc
Q psy16768          4 NGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE   83 (154)
Q Consensus         4 ~~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G   83 (154)
                      +++|+|+|+|+||.++|.+ +.||+++++||||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|
T Consensus      1300 ~~~~vl~teG~nl~~~l~~-~~iD~~~~~sNdI~dil~~lGIEAar~~ii~EI~~V~~~~Gi~Id~rHi~LIad~MT~~G 1378 (1449)
T d1twfa_        1300 EPEWVLETDGVNLSEVMTV-PGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQG 1378 (1449)
T ss_dssp             EEEEEEEEESCCHHHHTTS-TTBCTTTCBCSCHHHHHHHHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTTBS
T ss_pred             CCcEEEEcCcCCHHHHhcc-CCcccccCccCcHHHHHHHHhHHHHHHHHHHHHHHHHHhcCcEECHHHHHHHHHHHCcCC
Confidence            4689999999999999999 589999999999999999999999999999999999999999999999999999999999


Q ss_pred             ----cchhhhcccc----------------------ccccccCCcccceeec---CCCCCchhhhhhhh
Q psy16768         84 ----FDLIIMVSKS----------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKKIE  123 (154)
Q Consensus        84 ----~~R~Gm~~~~----------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~~~  123 (154)
                          +||+||++++                      |+.|+|+|||||||+|   |+|||+|+++.|.+
T Consensus      1379 ~~~~i~R~gi~~~~~S~l~~aSFEeT~~vL~~AAi~g~~D~L~G~senIi~G~~ip~GTG~fdll~d~~ 1447 (1449)
T d1twfa_        1379 GLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEE 1447 (1449)
T ss_dssp             SCCCSSSCSSSCSSCCTTSSCCSSCSHHHHHHHHHHTCEECCCSHHHHHHTTCCCSSGGGSSEEEECSC
T ss_pred             eEeeccHHHhccCCcCHHHHhhchhHHHHHHHHHhcCCcccCCCcHHHeecCCCCCCcccccEEEechh
Confidence                9999996432                      9999999999999999   99999999999876
>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure