Psyllid ID: psy13848

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------41
MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKSRGLIQRLKGKQGRFRGNLSGKRVDFTSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKDPASKGNVKFLRYGNRLKIASELKSAYLVWRVAGSISARGELHPKQKTDKVRSRNGWLSSVLSSSLRFREHETSVIIPPPAIMKPKALWTGKQIFSLILKPNRDCPVNANLKTKGRAYTFKFSIMVKDQFRERNTACKISHVTFCVDSPTEIQQQSGPGNKYSPSYSNRTGTVPSMLI
cHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccEEcccHHHHHHccccccccHHHHHHHHHHHHccccccccccHHHHccccccccccHHHHHHHHcccccccccccHHHHHHHHHHHHccccccccccEEEEcccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccEEEEEEcccccccccccccccccEEEccccHHHHHHHcccccccccccccccccccccccccccHHHHHHHHcccccccccEEEEEEccccccccccccccccccccEEEEcccccEEEEcccHHHHcccccccccccEEEccccccccccc
ccHHHHHHHHHHHHHHHccccccccHHHccccccHHHHHHHccccccEEccccccEEEccEEEEEccccccccccccccHHHHHHccccccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHccccEEEEccccccccEEEEEccccccEEEccEEEEEcccccEcccEcccccccccccccccccccHHHHHHHHHHccccccccHHHHcccccccHHHHHHHHcccHHHHHHHHHHHHHHcHHHHHHHHHHHccccccccccccccEEcccccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccEEEEEEEccccHHHHHcccccccccccccccccccccccc
MIQEDWEWLQLHCALFinsetsgiplnmqpksksrGLIQRLKgkqgrfrgnlsgkrvdftsrtvispdpnlqiyqvgIPEHVAKIltypervhhANKEHLKQLVlngpdkhpglLRAKERLLSEGYSKCEGYIRAMEsgrlqtqpgcsaeETLEAVILKELSVIRDHAGKAClqelhpsngplvmalsgskgsfiNISQMIACVGQqaingkrvpngfdnrslphfdkfskdpaskgnvkflRYGNRLKIASELKSAYLVWRVAGsisargelhpkqktdkvrsrngwlSSVLSSSlrfrehetsviipppaimkpkalwtgKQIFSLilkpnrdcpvnanlktkgrayTFKFSIMVKDQFRerntackishvtfcvdspteiqqqsgpgnkyspsysnrtgtvpsmli
MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKSRGLIQRlkgkqgrfrgnlsgkrvdftsrtvispdpnlqiyqVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHfdkfskdpaskgnvKFLRYGNRLKIASELKSAYLVWRVAGSisargelhpkqktdkvrsrngwlssvlssslrfrehetsviipppaimkpKALWTGKQIFSLILKPNRDCPVNAnlktkgraytfKFSIMVKDQFRERNTACKISHVTFCVDSpteiqqqsgpgnkyspsysnrtgtvpsmli
MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKSRGLIQRLKGKQGRFRGNLSGKRVDFTSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKDPASKGNVKFLRYGNRLKIASELKSAYLVWRVAGSISARGELHPKQKTDKVRSRNGWlssvlssslRFREHETSViipppaimkpkaLWTGKQIFSLILKPNRDCPVNANLKTKGRAYTFKFSIMVKDQFRERNTACKISHVTFCVDSPTEIQQQSGPGNKYSPSYSNRTGTVPSMLI
****DWEWLQLHCALFINSE***********************************RVDFTSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNG*****GLLRAKERLLSEGYSKCEGYIRAME*********CSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGF******************GNVKFLRYGNRLKIASELKSAYLVWRVAGSIS*******************WLSSVLSSSLRFREHETSVIIPPPAIMKPKALWTGKQIFSLILKPNRDCPVNANLKTKGRAYTFKFSIMVKDQFRERNTACKISHVTFCVD*******************************
MIQEDWEWLQLHCALFINS********************RLKGKQGRFRGNLSGKRVDFTSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKDPASKGNVKFLRYGNRLKIASELKSAYLVWRVAGSISARGELHPKQKTDKVRSRNGWLSSVLSSSLRFREHETSVIIPPPAIMKPKALWTGKQIFSLILKPNRDCPVNANLKTKGRAYTFKFSIMVKDQFRERNTACKISHVTFCV***********************TG****MLI
MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKSRGLIQRLKGKQGRFRGNLSGKRVDFTSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKDPASKGNVKFLRYGNRLKIASELKSAYLVWRVAGSISARGEL***********RNGWLSSVLSSSLRFREHETSVIIPPPAIMKPKALWTGKQIFSLILKPNRDCPVNANLKTKGRAYTFKFSIMVKDQFRERNTACKISHVTFCVDSPT****************SNRT********
MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKSRGLIQRLKGKQGRFRGNLSGKRVDFTSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKDPASKGNVKFLRYGNRLKIASELKSAYLVWRVAGSISARGELHPKQKTDKVRSRNGWLSSVLSSSLRFREHETSVIIPPPAIMKPKALWTGKQIFSLILKPNRDCPVNANLKTKGRAYTFKFSIMVKDQFRERNTACKISHVTFCVDSPTEIQQQ***********************
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MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKSRGLIQRLKGKQGRFRGNLSGKRVDFTSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKDPASKGNVKFLRYGNRLKIASELKSAYLVWRVAGSISARGELHPKQKTDKVRSRNGWLSSVLSSSLRFREHETSVIIPPPAIMKPKALWTGKQIFSLILKPNRDCPVNANLKTKGRAYTFKFSIMVKDQFRERNTACKISHVTFCVDSPTEIQQQSGPGNKYSPSYSNRTGTVPSMLI
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 ?
Query409 2.2.26 [Sep-21-2011]
Q5ZL98 1390 DNA-directed RNA polymera yes N/A 0.310 0.091 0.748 1e-50
A4IF62 1390 DNA-directed RNA polymera yes N/A 0.310 0.091 0.748 2e-50
O14802 1390 DNA-directed RNA polymera yes N/A 0.310 0.091 0.748 2e-50
Q86AQ5 1450 DNA-directed RNA polymera yes N/A 0.268 0.075 0.625 3e-38
O94666 1405 DNA-directed RNA polymera yes N/A 0.268 0.078 0.616 2e-35
Q6BI69 1457 DNA-directed RNA polymera yes N/A 0.322 0.090 0.522 3e-32
P04051 1460 DNA-directed RNA polymera yes N/A 0.268 0.075 0.55 1e-31
Q980R2 880 DNA-directed RNA polymera yes N/A 0.312 0.145 0.522 6e-31
P11512 880 DNA-directed RNA polymera yes N/A 0.276 0.128 0.552 3e-30
P31813 905 DNA-directed RNA polymera N/A N/A 0.268 0.121 0.555 8e-29
>sp|Q5ZL98|RPC1_CHICK DNA-directed RNA polymerase III subunit RPC1 OS=Gallus gallus GN=POLR3A PE=2 SV=1 Back     alignment and function desciption
 Score =  201 bits (510), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 95/127 (74%), Positives = 109/127 (85%)

Query: 113 GLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKAC 172
           GLL+AK  LL  GY KC+ YI A+ +G+LQ QPGC+AEETLEA+ILKELSVIRDHAG AC
Sbjct: 708 GLLKAKYELLHAGYKKCDEYIEALNTGKLQQQPGCTAEETLEALILKELSVIRDHAGSAC 767

Query: 173 LQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKD 232
           L+EL  SN PL+MAL GSKGSFINISQMIACVGQQAI+G RVP+GF+NRSLPHF+K SK 
Sbjct: 768 LRELDKSNSPLIMALCGSKGSFINISQMIACVGQQAISGSRVPDGFENRSLPHFEKHSKL 827

Query: 233 PASKGNV 239
           PA+KG V
Sbjct: 828 PAAKGFV 834
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 III which synthesizes small RNAs, such as 5S rRNA and tRNAs. 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 III. A bridging helix emanates from RPC1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol III 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.
Gallus gallus (taxid: 9031)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6
>sp|A4IF62|RPC1_BOVIN DNA-directed RNA polymerase III subunit RPC1 OS=Bos taurus GN=POLR3A PE=2 SV=1 Back     alignment and function description
>sp|O14802|RPC1_HUMAN DNA-directed RNA polymerase III subunit RPC1 OS=Homo sapiens GN=POLR3A PE=1 SV=2 Back     alignment and function description
>sp|Q86AQ5|RPC1_DICDI DNA-directed RNA polymerase III subunit rpc1 OS=Dictyostelium discoideum GN=polr3a PE=3 SV=1 Back     alignment and function description
>sp|O94666|RPC1_SCHPO DNA-directed RNA polymerase III subunit rpc1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc1 PE=2 SV=1 Back     alignment and function description
>sp|Q6BI69|RPC1_DEBHA DNA-directed RNA polymerase III subunit RPC1 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=RPC1 PE=3 SV=2 Back     alignment and function description
>sp|P04051|RPC1_YEAST DNA-directed RNA polymerase III subunit RPC1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPO31 PE=1 SV=1 Back     alignment and function description
>sp|Q980R2|RPOA1_SULSO DNA-directed RNA polymerase subunit A' OS=Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) GN=rpoA1 PE=1 SV=1 Back     alignment and function description
>sp|P11512|RPOA1_SULAC DNA-directed RNA polymerase subunit A' OS=Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) GN=rpoA1 PE=3 SV=2 Back     alignment and function description
>sp|P31813|RPOA1_THECE DNA-directed RNA polymerase subunit A' OS=Thermococcus celer GN=rpoA1 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 ?
Query409
242015075 1364 DNA-directed RNA polymerase III largest 0.784 0.235 0.419 6e-63
345489196 1355 PREDICTED: DNA-directed RNA polymerase I 0.792 0.239 0.402 2e-59
241633681 1394 DNA-directed RNA polymerase II largest s 0.799 0.234 0.401 5e-58
350402598 1385 PREDICTED: DNA-directed RNA polymerase I 0.312 0.092 0.789 3e-53
91092426 1390 PREDICTED: similar to AGAP004703-PA [Tri 0.305 0.089 0.765 4e-52
340711859 1385 PREDICTED: DNA-directed RNA polymerase I 0.312 0.092 0.781 4e-52
328710964 1366 PREDICTED: DNA-directed RNA polymerase I 0.789 0.236 0.372 5e-52
405974578 1368 DNA-directed RNA polymerase III subunit 0.312 0.093 0.742 5e-52
6624245 538 RNA polymerase III largest subunit [Leth 0.298 0.226 0.787 8e-52
380025198 1994 PREDICTED: LOW QUALITY PROTEIN: DNA-dire 0.300 0.061 0.765 1e-51
>gi|242015075|ref|XP_002428200.1| DNA-directed RNA polymerase III largest subunit, putative [Pediculus humanus corporis] gi|212512752|gb|EEB15462.1| DNA-directed RNA polymerase III largest subunit, putative [Pediculus humanus corporis] Back     alignment and taxonomy information
 Score =  248 bits (632), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 156/372 (41%), Positives = 211/372 (56%), Gaps = 51/372 (13%)

Query: 1   MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKSRGLIQRLKGKQGRFRGNLSGKRVDFT 60
           MI EDW++LQLHCAL+INSET+GIPL+MQPK  +RGL+QRLKGKQGRFRGNLSGKRVDF+
Sbjct: 306 MINEDWDFLQLHCALYINSETTGIPLSMQPKKATRGLVQRLKGKQGRFRGNLSGKRVDFS 365

Query: 61  SRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPGLLRAKER 120
           SRTVISPDPNLQI QVG+PEHVAKILT+PE+V+ AN   L++LV NGPD HPG    ++R
Sbjct: 366 SRTVISPDPNLQIDQVGVPEHVAKILTFPEKVNRANIFLLRELVRNGPDTHPGANFVEDR 425

Query: 121 LLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHA--GKACLQELHP 178
               G SK   Y+R     ++ ++             LK   V+  H       L    P
Sbjct: 426 ---NGNSK--RYLRYGNRSKISSE-------------LKFGDVVERHLIDDDIVLFNRQP 467

Query: 179 SNGPL-VMALSGS--KGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKDP-- 233
           S   L +MA      K      ++ +        +G  +     N  LP   +   +   
Sbjct: 468 SLHKLSIMAHRAKVLKHRTFRFNECVCTPYNADFDGDEM-----NLHLPQTLEAKAEALV 522

Query: 234 --ASKGNVKFLRYGNRLKIASE--LKSAYLVWRVAGSISARGELHPKQKTDKVRSRNGWL 289
             ++K N+   R G  L  A++  +  AYL+               ++ T   +++  WL
Sbjct: 523 LMSNKANLATPRNGELLIAATQDFITGAYLL--------------TQKNTFFTQAKANWL 568

Query: 290 SSVLSSSLRFREHETSVIIPPPAIMKPKALWTGKQIFSLILKPNRDCPVNANLKTKGRAY 349
              L+  L  ++    + +PPPAI+KP  LWT KQIFS+ILKPN+ C +  NL+TKG+AY
Sbjct: 569 ---LACILAGKDANLHIDLPPPAIIKPMRLWTAKQIFSVILKPNKKCKIVCNLRTKGKAY 625

Query: 350 TFKFSIMVKDQF 361
           T +  + V D F
Sbjct: 626 TSREEMCVNDSF 637

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|345489196|ref|XP_001602571.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|241633681|ref|XP_002408700.1| DNA-directed RNA polymerase II largest subunit, putative [Ixodes scapularis] gi|215501234|gb|EEC10728.1| DNA-directed RNA polymerase II largest subunit, putative [Ixodes scapularis] Back     alignment and taxonomy information
>gi|350402598|ref|XP_003486538.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|91092426|ref|XP_968165.1| PREDICTED: similar to AGAP004703-PA [Tribolium castaneum] gi|270004743|gb|EFA01191.1| hypothetical protein TcasGA2_TC010518 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|340711859|ref|XP_003394485.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like [Bombus terrestris] Back     alignment and taxonomy information
>gi|328710964|ref|XP_001945328.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|405974578|gb|EKC39212.1| DNA-directed RNA polymerase III subunit RPC1 [Crassostrea gigas] Back     alignment and taxonomy information
>gi|6624245|dbj|BAA88487.1| RNA polymerase III largest subunit [Lethenteron reissneri] Back     alignment and taxonomy information
>gi|380025198|ref|XP_003696364.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase III subunit RPC1-like, partial [Apis florea] 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 ?
Query409
ZFIN|ZDB-GENE-050208-103 1390 polr3a "polymerase (RNA) III ( 0.310 0.091 0.755 1.5e-89
UNIPROTKB|E9PTB6 1342 Polr3a "DNA-directed RNA polym 0.310 0.094 0.748 7.4e-89
UNIPROTKB|F1NIK7 1390 POLR3A "DNA-directed RNA polym 0.310 0.091 0.748 1.4e-88
UNIPROTKB|Q5ZL98 1390 POLR3A "DNA-directed RNA polym 0.310 0.091 0.748 1.4e-88
UNIPROTKB|E2QXD8 1376 POLR3A "DNA-directed RNA polym 0.310 0.092 0.748 2.2e-88
UNIPROTKB|J9P629 1390 POLR3A "DNA-directed RNA polym 0.310 0.091 0.748 2.2e-88
UNIPROTKB|O14802 1390 POLR3A "DNA-directed RNA polym 0.310 0.091 0.748 2.2e-88
UNIPROTKB|A4IF62 1390 POLR3A "DNA-directed RNA polym 0.310 0.091 0.748 2.2e-88
UNIPROTKB|F1S2E6 1390 POLR3A "DNA-directed RNA polym 0.310 0.091 0.748 3.7e-88
FB|FBgn0030687 1383 CG17209 [Drosophila melanogast 0.310 0.091 0.653 2.1e-82
ZFIN|ZDB-GENE-050208-103 polr3a "polymerase (RNA) III (DNA directed) polypeptide A" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
 Score = 497 (180.0 bits), Expect = 1.5e-89, Sum P(2) = 1.5e-89
 Identities = 96/127 (75%), Positives = 110/127 (86%)

Query:   113 GLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKAC 172
             GLL+AK+ LL  GY KC+ YI A+++GRLQ QPGC+AEETLEA+ILKELSVIRDHAG AC
Sbjct:   708 GLLKAKQELLDAGYEKCDEYIDALKTGRLQQQPGCTAEETLEALILKELSVIRDHAGSAC 767

Query:   173 LQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKD 232
             L+EL  SN PL+MAL GSKGSFINISQMIACVGQQAI+G RVP+GF+NRSLPHF K SK 
Sbjct:   768 LRELDKSNSPLIMALCGSKGSFINISQMIACVGQQAISGSRVPDGFENRSLPHFQKHSKL 827

Query:   233 PASKGNV 239
             PA+KG V
Sbjct:   828 PAAKGFV 834
GO:0003677 "DNA binding" evidence=IEA
GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA
GO:0006351 "transcription, DNA-dependent" evidence=IEA
GO:0008270 "zinc ion binding" evidence=IEA
GO:0005634 "nucleus" evidence=IEA
GO:0032549 "ribonucleoside binding" evidence=IEA
GO:0016779 "nucleotidyltransferase activity" evidence=IEA
GO:0016740 "transferase activity" evidence=IEA
UNIPROTKB|E9PTB6 Polr3a "DNA-directed RNA polymerase" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1NIK7 POLR3A "DNA-directed RNA polymerase" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q5ZL98 POLR3A "DNA-directed RNA polymerase III subunit RPC1" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|E2QXD8 POLR3A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|J9P629 POLR3A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|O14802 POLR3A "DNA-directed RNA polymerase III subunit RPC1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|A4IF62 POLR3A "DNA-directed RNA polymerase III subunit RPC1" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F1S2E6 POLR3A "DNA-directed RNA polymerase" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
FB|FBgn0030687 CG17209 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.70.691
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 ?
Query409
PRK08566 882 PRK08566, PRK08566, DNA-directed RNA polymerase su 9e-48
smart00663295 smart00663, RPOLA_N, RNA polymerase I subunit A N- 1e-44
TIGR02390 867 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer 1e-41
pfam05000108 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, do 1e-39
PRK14977 1321 PRK14977, PRK14977, bifunctional DNA-directed RNA 4e-38
COG0086 808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 1e-31
PRK08566882 PRK08566, PRK08566, DNA-directed RNA polymerase su 3e-31
TIGR02390867 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer 7e-30
pfam00623165 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, do 4e-27
COG0086808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 2e-17
pfam04997330 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, do 6e-16
TIGR02386 1140 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, 6e-14
PRK00566 1156 PRK00566, PRK00566, DNA-directed RNA polymerase su 6e-13
PRK14906 1460 PRK14906, PRK14906, DNA-directed RNA polymerase su 3e-12
PRK14977 1321 PRK14977, PRK14977, bifunctional DNA-directed RNA 1e-11
PRK02625627 PRK02625, rpoC1, DNA-directed RNA polymerase subun 2e-11
TIGR02387619 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase 8e-11
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 2e-10
CHL00018663 CHL00018, rpoC1, RNA polymerase beta' subunit 2e-10
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 2e-09
pfam04983158 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, do 3e-06
PRK08566 882 PRK08566, PRK08566, DNA-directed RNA polymerase su 6e-05
TIGR02390 867 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer 0.002
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated Back     alignment and domain information 
 Score =  174 bits (443), Expect = 9e-48
 Identities = 66/117 (56%), Positives = 85/117 (72%), Gaps = 7/117 (5%)

Query: 1   MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS----RGLIQRLKGKQGRFRGNLSGKR 56
           +I++ WE LQ H   + ++E  GIP     + +S    + L QRLKGK+GRFRGNLSGKR
Sbjct: 263 IIEDLWELLQYHVTTYFDNEIPGIP---PARHRSGRPLKTLAQRLKGKEGRFRGNLSGKR 319

Query: 57  VDFTSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG 113
           V+F++RTVISPDPNL I +VG+PE +AK LT PERV   N E L++ VLNGP+KHPG
Sbjct: 320 VNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPG 376

Length = 882
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus 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|218372 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, domain 4 Back     alignment and domain information
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional Back     alignment and domain information
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>gnl|CDD|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|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2 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|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1 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|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; 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|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma; Provisional Back     alignment and domain information
>gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit Back     alignment and domain information
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit Back     alignment and domain information
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3 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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 409
KOG0261|consensus 1386 100.0
TIGR02390868 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit 100.0
PRK14977 1321 bifunctional DNA-directed RNA polymerase A'/A'' su 100.0
PRK08566882 DNA-directed RNA polymerase subunit A'; Validated 100.0
KOG0260|consensus 1605 100.0
KOG0262|consensus 1640 100.0
TIGR02386 1140 rpoC_TIGR DNA-directed RNA polymerase, beta' subun 100.0
PRK14906 1460 DNA-directed RNA polymerase subunit beta'/alpha do 100.0
PRK00566 1156 DNA-directed RNA polymerase subunit beta'; Provisi 100.0
COG0086808 RpoC DNA-directed RNA polymerase, beta' subunit/16 100.0
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 100.0
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 100.0
smart00663295 RPOLA_N RNA polymerase I subunit A N-terminus. 100.0
CHL00018663 rpoC1 RNA polymerase beta' subunit 99.97
PRK02625627 rpoC1 DNA-directed RNA polymerase subunit gamma; P 99.97
TIGR02387619 rpoC1_cyan DNA-directed RNA polymerase, gamma subu 99.97
PF05000108 RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; Int 99.94
TIGR02388 1227 rpoC2_cyan DNA-directed RNA polymerase, beta'' sub 99.91
PRK02597 1331 rpoC2 DNA-directed RNA polymerase subunit beta'; P 99.9
CHL00117 1364 rpoC2 RNA polymerase beta'' subunit; Reviewed 99.88
PF00623166 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; Int 99.88
KOG0262|consensus 1640 99.8
KOG0261|consensus 1386 99.78
TIGR02390 868 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit 99.52
PRK14977 1321 bifunctional DNA-directed RNA polymerase A'/A'' su 99.51
PRK08566 882 DNA-directed RNA polymerase subunit A'; Validated 99.47
PF04998 277 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; Int 99.12
KOG0260|consensus 1605 99.1
PF04983158 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; Int 98.53
COG0086 808 RpoC DNA-directed RNA polymerase, beta' subunit/16 97.02
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 96.75
PRK00566 1156 DNA-directed RNA polymerase subunit beta'; Provisi 95.75
TIGR02386 1140 rpoC_TIGR DNA-directed RNA polymerase, beta' subun 90.66
PRK14906 1460 DNA-directed RNA polymerase subunit beta'/alpha do 88.32
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 87.59
>KOG0261|consensus Back     alignment and domain information 
Probab=100.00  E-value=1.8e-89  Score=727.36  Aligned_cols=286  Identities=58%  Similarity=0.974  Sum_probs=282.2

Q ss_pred             ChhHhHHHHHHHHHHHHcCCCCCCCCCCCCCCCchhhHHHhhcCcceeeecccCCccCCCCCeeecCCCCCCcccccchH
Q psy13848          1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKSRGLIQRLKGKQGRFRGNLSGKRVDFTSRTVISPDPNLQIYQVGIPE   80 (409)
Q Consensus         1 ~i~~~~~~LQ~~v~~~~~~~~~~~~~~~~~~~~~k~~~~~l~gK~G~~R~nl~GKRvdfs~RsVI~pdP~L~~~evgiP~   80 (409)
                      .|+|+||.||.+||.|+||+++|.|..+.+++|.+|++||||||+||||+||+||||||||||||||||||.|||||||.
T Consensus       303 ~imE~Wd~lQl~~AlyINSEl~g~~~~~~p~kp~RGf~QRLKGKqGRFRgNLSGKRVDFSGRTVISPDPNL~IdeVgVP~  382 (1386)
T KOG0261|consen  303 LIMEDWDFLQLQVALYINSELPGIPINMAPKKPTRGFVQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDEVGVPI  382 (1386)
T ss_pred             hhhhhhHHHHHHHHHhhcccCCCCCCCCCCCCchHHHHHHhcccCCceeccccCceeeccCceeeCCCCCcceeeccchH
Confidence            47899999999999999999999999989999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHcCCCceeccccHHHHHHHHHcCCCCCCCc----------------------------------------------
Q psy13848         81 HVAKILTYPERVHHANKEHLKQLVLNGPDKHPGL----------------------------------------------  114 (409)
Q Consensus        81 ~~a~~lt~pe~v~~~N~~~l~~lv~ng~~~~pGa----------------------------------------------  114 (409)
                      .+|+.|||||+||.+|+++||+||.|||++||||                                              
T Consensus       383 rvAkiLTfpE~Vt~~Ni~klr~lV~NGP~vhPGANyv~~r~~~~kr~L~yg~R~kiA~eLk~GdvVERHL~DgDvVLFNR  462 (1386)
T KOG0261|consen  383 RVAKILTFPERVTRANIRKLRQLVRNGPNVHPGANYVVQRGEGFKRFLKYGNRDKIADELKIGDVVERHLMDGDVVLFNR  462 (1386)
T ss_pred             HHHHHhcchhhccHHHHHHHHHHHhcCCCCCCCcchhhhcccchhhHhhcCcHHHHHHhhccchHHHhhcccCCEEEEcC
Confidence            9999999999999999999999999999999999                                              


Q ss_pred             --------------------------------------------------------------------------------
Q psy13848        115 --------------------------------------------------------------------------------  114 (409)
Q Consensus       115 --------------------------------------------------------------------------------  114 (409)
                                                                                                      
T Consensus       463 QPSLHkmSIM~H~akV~p~RTfRFNEcvCtPYNADFDGDEMNlHvPQTEEAraEA~~LMgvknNlvTPr~GEpiiAAtQD  542 (1386)
T KOG0261|consen  463 QPSLHKMSIMSHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIAATQD  542 (1386)
T ss_pred             CchHHHHHHHHHHhhcccCceeeccccccCCcCCCCCcccccccCCchHHHHHHHHHHhccccccccCCCCCceeehhhh
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q psy13848        115 --------------------------------------------------------------------------------  114 (409)
Q Consensus       115 --------------------------------------------------------------------------------  114 (409)
                                                                                                      
T Consensus       543 FiTg~YLlt~KDtF~dRa~~~ql~s~~~d~~~~i~lppPaI~KP~~LwTGKQ~fsvlirpn~~s~v~~Nl~~k~k~~~~~  622 (1386)
T KOG0261|consen  543 FITGGYLLTHKDTFLDRAEFSQLCSYMSDAMTHIDLPPPAILKPVELWTGKQLFSVLIRPNDDSPVRVNLDAKNKNFSLV  622 (1386)
T ss_pred             hhhcceeeecccccccHHHHHHHHHHHhccccccCCCChhhcCceeeeccCEEEEEEeccCCCCceEEeeccccceeecc
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q psy13848        115 --------------------------------------------------------------------------------  114 (409)
Q Consensus       115 --------------------------------------------------------------------------------  114 (409)
                                                                                                      
T Consensus       623 ~~k~~~mc~nDg~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lgnrGFSIGi~DVq  702 (1386)
T KOG0261|consen  623 KGKSFEMCPNDGYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGIDDVQ  702 (1386)
T ss_pred             cCCCcccCCCCCeEEEecchhhhcccccccccCCCccceEeeehhhcchHHHHHHHHHHHHhhhhhccccccccccCCCC
Confidence                                                                                            


Q ss_pred             -----hhhHHHHHHhhhhhHHHHHHHhhcCCCcCCCCCChhhHHHHHHHHHHHHHHHHHHhhhhhcCCCCCcchhhhhcC
Q psy13848        115 -----LRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSG  189 (409)
Q Consensus       115 -----~~~K~~iI~eg~~kc~~~iadf~~GqLe~qpG~t~~EtLE~~v~~~ln~~~~~~g~~~~~~l~p~N~~~~M~~sG  189 (409)
                           .++|+.+++.||.+|+++|.+|..|+|+.||||+.+++||+.+.++|+.+|+++|++|+..|.++|++++|+.||
T Consensus       703 Pg~~L~~~k~~lv~~gY~kc~~~I~e~~kG~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~eL~~~NsPliMa~CG  782 (1386)
T KOG0261|consen  703 PGEILSQEKEELVNRGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSELSTIREEAGKICIRELHPRNSPLIMALCG  782 (1386)
T ss_pred             ccHHHHHHHHHHHHhHHHHHHHHHHHHhccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccChHHHHHhc
Confidence                 568899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcchhhHHHHHHHhcCcccCCcccCCCCCCCCCCCCCCCCCCCCCCCeeecCCcCCcccchhhhhhhhhheeeeccccc
Q psy13848        190 SKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKDPASKGNVKFLRYGNRLKIASELKSAYLVWRVAGSISA  269 (409)
Q Consensus       190 sKGS~~Ni~Qi~~~vGQQ~l~G~Rip~g~~gRtLPhF~~~d~~~~a~GfI~nsf~~GL~p~~~~lk~e~~~h~~~gr~~~  269 (409)
                      ||||.+|++||+||||||.+.|+|+|.||.+|+||||++.+..|+|+|||.|||++||+|      .|||||+|+||   
T Consensus       783 SKGS~INiSQMvACVGQQ~ISG~RvPdGf~dRsLPHF~r~Sk~P~aKGFV~NSFySGLTp------tEFfFHtm~GR---  853 (1386)
T KOG0261|consen  783 SKGSKINISQMVACVGQQIISGHRVPDGFEDRSLPHFERHSKTPAAKGFVANSFYSGLTP------TEFFFHTMSGR---  853 (1386)
T ss_pred             CCCCcccHHHHHHHhhhhhhcCCcCCCccccccCccccccCCCccccchhhhhcccCCCc------hhhheeecccc---
Confidence            999999999999999999999999999999999999999999999999999999999999      99999999999   


Q ss_pred             cccccccccccccccCcchHHHHHHhhhcc
Q psy13848        270 RGELHPKQKTDKVRSRNGWLSSVLSSSLRF  299 (409)
Q Consensus       270 ~gl~~ta~kt~~~tsrsGyl~r~L~~~l~F  299 (409)
                      |||+|||+||    +.+||+||+|+|+||-
T Consensus       854 EGLVDTAVKT----AETGYMqRRLmK~LED  879 (1386)
T KOG0261|consen  854 EGLVDTAVKT----AETGYMQRRLMKSLED  879 (1386)
T ss_pred             cchhhhhhhh----hhhhhHHHHHHHHHHH
Confidence            9999999999    9999999999999987

>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A' Back     alignment and domain information
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional Back     alignment and domain information
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated Back     alignment and domain information
>KOG0260|consensus Back     alignment and domain information
>KOG0262|consensus Back     alignment and domain information
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form Back     alignment and domain information
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional Back     alignment and domain information
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional Back     alignment and domain information
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus Back     alignment and domain information
>CHL00018 rpoC1 RNA polymerase beta' subunit Back     alignment and domain information
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional Back     alignment and domain information
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit Back     alignment and domain information
>PF05000 RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; InterPro: IPR007083 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit Back     alignment and domain information
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional Back     alignment and domain information
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed Back     alignment and domain information
>PF00623 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; InterPro: IPR000722 RNA polymerases catalyse the DNA dependent polymerisation of RNA from DNA, using the four ribonucleoside triphosphates as substrates Back     alignment and domain information
>KOG0262|consensus Back     alignment and domain information
>KOG0261|consensus Back     alignment and domain information
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A' Back     alignment and domain information
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional Back     alignment and domain information
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated 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
>KOG0260|consensus Back     alignment and domain information
>PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional Back     alignment and domain information
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form Back     alignment and domain information
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional Back     alignment and domain information
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional 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 ?
Query409
2pmz_A 880 Archaeal Rna Polymerase From Sulfolobus Solfataricu 4e-32
2pmz_A880 Archaeal Rna Polymerase From Sulfolobus Solfataricu 6e-18
2waq_A 880 The Complete Structure Of The Archaeal 13-Subunit D 7e-32
2waq_A880 The Complete Structure Of The Archaeal 13-Subunit D 5e-18
4a3c_A 1732 Rna Polymerase Ii Initial Transcribing Complex With 1e-27
4a3c_A 1732 Rna Polymerase Ii Initial Transcribing Complex With 7e-19
1i3q_A 1733 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 1e-27
1i3q_A 1733 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 7e-19
3j0k_A 1455 Orientation Of Rna Polymerase Ii Within The Human V 1e-27
3j0k_A 1455 Orientation Of Rna Polymerase Ii Within The Human V 7e-19
3h0g_A 1752 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 3e-26
3h0g_A 1752 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 7e-22
1i6v_D 1264 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 6e-09
1hqm_D 1265 Crystal Structure Of Thermus Aquaticus Core Rna Pol 6e-09
2gho_D 1233 Recombinant Thermus Aquaticus Rna Polymerase For St 6e-09
1l9u_D 1524 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 6e-09
3iyd_D 1413 Three-Dimensional Em Structure Of An Intact Activat 7e-09
3lu0_D 1407 Molecular Model Of Escherichia Coli Core Rna Polyme 7e-09
4gzy_D 1534 Crystal Structures Of Bacterial Rna Polymerase Paus 9e-09
1iw7_D 1524 Crystal Structure Of The Rna Polymerase Holoenzyme 9e-09
3qqc_A436 Crystal Structure Of Archaeal Spt45 BOUND TO THE RN 9e-07
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 880 Back     alignment and structure 
Iteration: 1

 Score =  135 bits (340), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 69/132 (52%), Positives = 91/132 (68%), Gaps = 4/132 (3%)
Query: 1   MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS-RGLIQRLKGKQGRFRGNLSGKRVDF 59
           +I++ W+ LQ H A + ++E  G+P +     +  R L QRLKGK+GRFRGNLSGKRVDF
Sbjct: 261 IIEDLWDLLQYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDF 320
Query: 60  TSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG---LLR 116
           +SRTVISPDPN+ I +VG+PE +AK LT PER+   N E L+Q V+NGPDK PG   ++R
Sbjct: 321 SSRTVISPDPNISIDEVGVPEIIAKTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIR 380
Query: 117 AKERLLSEGYSK 128
              R +   Y K
Sbjct: 381 PDGRRIDLRYVK 392
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 880 Back     alignment and structure
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 880 Back     alignment and structure
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 880 Back     alignment and structure
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt Dna-Rna Hybrid Length = 1732 Back     alignment and structure
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt Dna-Rna Hybrid Length = 1732 Back     alignment and structure
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1733 Back     alignment and structure
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1733 Back     alignment and structure
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455 Back     alignment and structure
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455 Back     alignment and structure
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 Back     alignment and structure
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 Back     alignment and structure
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1264 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|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For Structural Studies Length = 1233 Back     alignment and structure
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1524 Back     alignment and structure
>pdb|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|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP CLAMP DOMAIN Length = 436 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 ?
Query409
3qqc_A436 DNA-directed RNA polymerase subunit B, DNA-direct 1e-53
4ayb_A880 DNA-directed RNA polymerase; transferase, multi-su 1e-51
4ayb_A 880 DNA-directed RNA polymerase; transferase, multi-su 7e-47
4ayb_A 880 DNA-directed RNA polymerase; transferase, multi-su 7e-12
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 3e-47
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 1e-46
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 6e-05
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 1e-46
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 3e-46
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 5e-05
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 2e-13
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 2e-13
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 5e-12
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 7e-07
>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 =  183 bits (466), Expect = 1e-53
 Identities = 33/114 (28%), Positives = 48/114 (42%), Gaps = 8/114 (7%)

Query: 1   MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS-RGLIQRLKGKQGRFRGNLSGKRVDF 59
           +I++ W+ LQ H   +IN+E  G+P       +  + L QRLKGK+GRFRGNLSG     
Sbjct: 328 IIEDLWDLLQYHVTTYINNEAPGVPPAKHKSGRPLKTLAQRLKGKEGRFRGNLSGGAGSG 387

Query: 60  TSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG 113
                +                V  +    E+    N   + + VL G   H  
Sbjct: 388 AGSGSVLARAAF-------EITVQHLFEAAEKGEVDNLNGVIENVLIGQKHHHH 434
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880 Back     alignment and structure
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880 Back     alignment and structure
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880 Back     alignment and structure
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 Back     alignment and structure
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 Back     alignment and structure
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 Back     alignment and structure
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 Back     alignment and structure
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 Back     alignment and structure
>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
>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
>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
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query409
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 100.0
4ayb_A880 DNA-directed RNA polymerase; transferase, multi-su 100.0
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 100.0
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 100.0
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 100.0
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 100.0
3qqc_A436 DNA-directed RNA polymerase subunit B, DNA-direct 99.77
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 99.32
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 99.3
4ayb_A 880 DNA-directed RNA polymerase; transferase, multi-su 99.25
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 95.34
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 93.29
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 90.2
>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=1.7e-77  Score=691.05  Aligned_cols=292  Identities=39%  Similarity=0.642  Sum_probs=279.2

Q ss_pred             hhHhHHHHHHHHHHHHcCCCCCCCCCCCC-CCCchhhHHHhhcCcceeeecccCCccCCCCCeeecCCCCCCcccccchH
Q psy13848          2 IQEDWEWLQLHCALFINSETSGIPLNMQP-KSKSRGLIQRLKGKQGRFRGNLSGKRVDFTSRTVISPDPNLQIYQVGIPE   80 (409)
Q Consensus         2 i~~~~~~LQ~~v~~~~~~~~~~~~~~~~~-~~~~k~~~~~l~gK~G~~R~nl~GKRvdfs~RsVI~pdP~L~~~evgiP~   80 (409)
                      +.+.|++||.||++||||+.+|.|.+.++ ++|+|+|+||||||+||||+|||||||||||||||+|||||++||||||.
T Consensus       295 ~~~~~~~LQ~~v~~~~dn~~~~~~~~~~~~~rp~k~~~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~evGvP~  374 (1752)
T 3h0g_A          295 VSEYEQLLQFHVATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGVPR  374 (1752)
T ss_dssp             HHHHHHHHHHHHHHTTCTTCSSCCCCCSSSSCCCCCHHHHHTCSSSSSTTTTSSCCCSSEEEEEEEEETTSCTTBCBCCH
T ss_pred             HHHHHHHHHHHHHHhhcCCCCCCccccccCCCCCcchHhhhhcccccccccccccccCCccceeecCCCCcccceeeChH
Confidence            56889999999999999999999876544 58999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHcCCCceeccccHHHHHHHHHcCCCCCCCc----------------------------------------------
Q psy13848         81 HVAKILTYPERVHHANKEHLKQLVLNGPDKHPGL----------------------------------------------  114 (409)
Q Consensus        81 ~~a~~lt~pe~v~~~N~~~l~~lv~ng~~~~pGa----------------------------------------------  114 (409)
                      .||++|||||+|++||+++|++||.||++.||||                                              
T Consensus       375 ~~A~~Lt~Pe~vt~~ni~~l~~lv~nG~~~~pga~~v~~~~~~~~~l~~~~~~~~~~l~~g~~v~r~l~~gd~Vl~NRqP  454 (1752)
T 3h0g_A          375 SIAKTLTYPETVTPYNIYQLQELVRNGPDEHPGAKYIIRDTGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQP  454 (1752)
T ss_dssp             HHHTSCCCCCBCCTTTHHHHHHHHHHCTTSSSCEEEEECTTCCBCCTTTTCSCCCCCCCSSCEEEECCCSCCEEEEECSS
T ss_pred             HHHHhcCCCccccHHHHHHHHHHHHcCCccccCceeeecCCCcEeechhhchhhhhhcCcCcEEEeeeccCCeEEEecCc
Confidence            9999999999999999999999999999999998                                              


Q ss_pred             --------------------------------------------------------------------------------
Q psy13848        115 --------------------------------------------------------------------------------  114 (409)
Q Consensus       115 --------------------------------------------------------------------------------  114 (409)
                                                                                                      
T Consensus       455 tLHr~sima~~~~v~~gktirlh~~vC~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~v  534 (1752)
T 3h0g_A          455 SLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTL  534 (1752)
T ss_dssp             CCSGGGEEEEECCCCSSSSEEEEGGGSGGGTCCSSSCEEEEECCCSTTHHHHHHHTCCTTTTSEETTTTEESCCCCTHHH
T ss_pred             ccchhhcccccceeecCceeeechhhCCCccCccccceeeeeccCCHHHHHHHHHHhcCccceecCCCCCceeeecchhh
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q psy13848        115 --------------------------------------------------------------------------------  114 (409)
Q Consensus       115 --------------------------------------------------------------------------------  114 (409)
                                                                                                      
T Consensus       535 lg~y~lT~~~~f~~~~e~~~l~~~~~~~~~~~~~pai~kp~~~wtGkqifs~ilp~~~~~~~~~~~~~~~~~~d~~v~i~  614 (1752)
T 3h0g_A          535 AGVRKFSLRDNFLTRNAVMNIMLWVPDWDGILPPPVILKPKVLWTGKQILSLIIPKGINLIRDDDKQSLSNPTDSGMLIE  614 (1752)
T ss_dssp             HHHHHHHSTTCEEETHHHHGGGGCSSSCCSSCCCCSBCSSSCEEETTHHHHTTSCSSBCEECCCSSCCSSCTTTCSEEEC
T ss_pred             hheeeeccccccCCHHHHHHHHHhhcccCCccCccceecCcCCCchhhHHhhhCcCCCCceeccccccCcCCCcCeEEEE
Confidence                                                                                            


Q ss_pred             -------------------------------------------------------------------hhhHHHHHHhhhh
Q psy13848        115 -------------------------------------------------------------------LRAKERLLSEGYS  127 (409)
Q Consensus       115 -------------------------------------------------------------------~~~K~~iI~eg~~  127 (409)
                                                                                         .+++.++|+++++
T Consensus       615 ~gell~g~l~K~~lg~~~~~li~~i~~~~G~~~~~~~ld~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~a~~  694 (1752)
T 3h0g_A          615 NGEIIYGVVDKKTVGASQGGLVHTIWKEKGPEICKGFFNGIQRVVNYWLLHNGFSIGIGDTIADADTMKEVTRTVKEARR  694 (1752)
T ss_dssp             BSCEEEECCSHHHHSSCTTCHHHHSSSSSCTTTHHHHHHHHHHHHHHHHHHHCCCCCGGGGSCCSHHHHHHHHHHHTTTH
T ss_pred             cCeEEecccchHHhccCcccHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhcCceechhhcccCHHHHHHHHHHHHHHHH
Confidence                                                                               2346789999999


Q ss_pred             hHHHHHHHhhcCCCcCCCCCChhhHHHHHHHHHHHHHHHHHHhhhhhcCCCCCcchhhhhcCCCcchhhHHHHHHHhcCc
Q psy13848        128 KCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQ  207 (409)
Q Consensus       128 kc~~~iadf~~GqLe~qpG~t~~EtLE~~v~~~ln~~~~~~g~~~~~~l~p~N~~~~M~~sGsKGS~~Ni~Qi~~~vGQQ  207 (409)
                      +|.+++++|+.|.|+..||++.+|++|++++++|+++++++++.|++.+++.|++++|+.||||||++|++||+||||||
T Consensus       695 ~v~~~~~~~~~g~l~~~~g~~~~e~~e~~v~~~l~~~~~~~~~~~~~~l~~~N~~~~M~~SGakGs~~ni~Q~~~~~Gqq  774 (1752)
T 3h0g_A          695 QVAECIQDAQHNRLKPEPGMTLRESFEAKVSRILNQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQ  774 (1752)
T ss_dssp             HHHHHHTTTTTTCCCCCSSCCTTHHHHHHHHHHHHHHHHHHHHHHHTTSCSSCTTTHHHHHCSSCCHHHHHHHHTCCCCC
T ss_pred             HHHHHHHHHHcCCCccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHhhhccccCHHHHHHHHhccCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCcccCCCCCCCCCCCCCCCCCCCCCCCeeecCCcCCcccchhhhhhhhhheeeeccccccccccccccccccccCcc
Q psy13848        208 AINGKRVPNGFDNRSLPHFDKFSKDPASKGNVKFLRYGNRLKIASELKSAYLVWRVAGSISARGELHPKQKTDKVRSRNG  287 (409)
Q Consensus       208 ~l~G~Rip~g~~gRtLPhF~~~d~~~~a~GfI~nsf~~GL~p~~~~lk~e~~~h~~~gr~~~~gl~~ta~kt~~~tsrsG  287 (409)
                      .++|+|||+||.+|+||||.++|.+|+++|||.|||++||+|      .|||||||+||   |||+|||+||    +++|
T Consensus       775 ~~~GkrIp~g~~~rtLP~f~k~d~~~~a~GfV~~sF~~GL~p------~EfFfhtmggR---eGLiDTAvKT----A~SG  841 (1752)
T 3h0g_A          775 IVEGKRIPFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTP------QEFFFHAMAGR---EGLIDTAVKT----AETG  841 (1752)
T ss_dssp             CSTTSSSCCCSTTSSSTTSCSSCCSTTTSSCCSSCTTTCCCH------HHHHHHHHHHT---TTTTHHHHTT----THHH
T ss_pred             ccCCccCCCCCCCccCCCCCCCCCCcccCcchhhcccCCCCH------HHHHHHhhhhh---hhhhHhhhhc----CcCc
Confidence            999999999999999999999999999999999999999999      99999999999   9999999999    9999


Q ss_pred             hHHHHHHhhhcc----ccccCCC
Q psy13848        288 WLSSVLSSSLRF----REHETSV  306 (409)
Q Consensus       288 yl~r~L~~~l~F----~~~~~~~  306 (409)
                      ||||||++.|+.    +|++.|.
T Consensus       842 YLqRRLVk~leDv~V~YDgTVRn  864 (1752)
T 3h0g_A          842 YIQRRLVKAMEDVMVRYDGTVRN  864 (1752)
T ss_dssp             HHHHHHHHHHTTCEEETTTEEEC
T ss_pred             hhHHHHHHHHhheEEeeCCeeEc
Confidence            999999999987    4554443
>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
>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
>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
>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
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Back     alignment and structure
>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 409
d1twfa_ 1449 e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c 5e-29
d1twfa_ 1449 e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c 1e-19
d1smyd_ 1504 e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t 5e-29
d1smyd_ 1504 e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t 5e-05
>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 =  117 bits (294), Expect = 5e-29
 Identities = 58/113 (51%), Positives = 79/113 (69%), Gaps = 1/113 (0%)

Query: 2   IQEDWEWLQLHCALFINSETSGIPLNMQP-KSKSRGLIQRLKGKQGRFRGNLSGKRVDFT 60
           I+E    LQ H A +++++ +G P  +Q      + +  RLKGK+GR RGNL GKRVDF+
Sbjct: 288 IEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFS 347

Query: 61  SRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG 113
           +RTVIS DPNL++ QVG+P+ +AK LTYPE V   N + L QLV NGP++HPG
Sbjct: 348 ARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPG 400
>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 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
>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 ?
Query409
d1twfa_ 1449 RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1smyd_ 1504 RNA-polymerase beta-prime {Thermus thermophilus [T 100.0
d1twfa_ 1449 RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta 98.99
d1smyd_ 1504 RNA-polymerase beta-prime {Thermus thermophilus [T 95.74
>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=3e-69  Score=619.11  Aligned_cols=285  Identities=40%  Similarity=0.631  Sum_probs=273.7

Q ss_pred             hhHhHHHHHHHHHHHHcCCCCCCCCCCCC-CCCchhhHHHhhcCcceeeecccCCccCCCCCeeecCCCCCCcccccchH
Q psy13848          2 IQEDWEWLQLHCALFINSETSGIPLNMQP-KSKSRGLIQRLKGKQGRFRGNLSGKRVDFTSRTVISPDPNLQIYQVGIPE   80 (409)
Q Consensus         2 i~~~~~~LQ~~v~~~~~~~~~~~~~~~~~-~~~~k~~~~~l~gK~G~~R~nl~GKRvdfs~RsVI~pdP~L~~~evgiP~   80 (409)
                      +.+.|..||.+|+.|+||+.++.+..... ++++|||+|||+||+||||+|||||||||||||||+|||+|.++|||||.
T Consensus       288 ~~~~~~~LQ~~v~~~~dn~~~~~~~~~~~~~~~~k~i~~~L~gK~GrfR~nl~GKRVd~s~RsVI~pdp~l~~~evGvP~  367 (1449)
T d1twfa_         288 IEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPK  367 (1449)
T ss_dssp             HHHHHHHHHHHHHHHHCCCSSCCCCCSSCTTCCCCCSTTSCTTTTTTSSGGGTTCSCCSEEEEEEEECTTSCTTEEEEEH
T ss_pred             HHHHHHHHHHHHHHhccccccCCchhccccCCCccchhhHhccchhhhhhhccccccccccceeeccCCccceeecccHH
Confidence            46789999999999999999988865544 58999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHcCCCceeccccHHHHHHHHHcCCCCCCCc----------------------------------------------
Q psy13848         81 HVAKILTYPERVHHANKEHLKQLVLNGPDKHPGL----------------------------------------------  114 (409)
Q Consensus        81 ~~a~~lt~pe~v~~~N~~~l~~lv~ng~~~~pGa----------------------------------------------  114 (409)
                      .||.+||+||.||+||+++|+++|.|||+.||||                                              
T Consensus       368 ~~A~~Lt~pe~v~~~n~~~l~~~v~ng~~~~pga~~~~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~Vl~NRqP  447 (1449)
T d1twfa_         368 SIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQP  447 (1449)
T ss_dssp             HHHTTCEEEEECCTTTHHHHHHHHHHTTTSSSCEEEEECTTCCEEETTSCTTTTCCCCCTTCEEEEECCTTCEEEEECSS
T ss_pred             HHHhhCCCCeeecHHHHHHHHHHHHcCCccCCcccceecccCceEEEecchhhhhhhcccccEEEEEEecCeeEEecCcc
Confidence            9999999999999999999999999999999999                                              


Q ss_pred             --------------------------------------------------------------------------------
Q psy13848        115 --------------------------------------------------------------------------------  114 (409)
Q Consensus       115 --------------------------------------------------------------------------------  114 (409)
                                                                                                      
T Consensus       448 tLHr~si~a~~~~v~~~ktirl~~~vc~~yNADFDGDeMnvhvPqs~~A~aEa~~Lm~~~~nilsp~~G~pi~~~~QD~~  527 (1449)
T d1twfa_         448 SLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTL  527 (1449)
T ss_dssp             CCSGGGEEEEEEEEESSSSEEECGGGHHHHTCCSSSCEEEEECCCSHHHHHHHHHHTBGGGGSEETTTTEESCCCCHHHH
T ss_pred             chhhhccccceeEeecCceEEeccccccccccccccceEEEEccCCHHHHHHHHHHhhhhcccccccCCceeeeeccchh
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q psy13848        115 --------------------------------------------------------------------------------  114 (409)
Q Consensus       115 --------------------------------------------------------------------------------  114 (409)
                                                                                                      
T Consensus       528 lg~y~LT~~~~f~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~tgkqi~s~~l~~~~~~~~~~~~~~~~~~~~~~~~i~  607 (1449)
T d1twfa_         528 CGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLII  607 (1449)
T ss_dssp             HHHHHHHSTTCEEEHHHHHHHHHHSTTCCSCCCCCSBCSSSCEEEHHHHHHHHSCTTCCEEECCTTCCTTCTTCCSEEEE
T ss_pred             hhhhhhhcccccCCHHHHHHHHHhcccccccccCCeEEeeeeccccceEEEEEccCCceeeeccCCccccccCCceEEEE
Confidence                                                                                            


Q ss_pred             -------------------------------------------------------------------hhhHHHHHHhhhh
Q psy13848        115 -------------------------------------------------------------------LRAKERLLSEGYS  127 (409)
Q Consensus       115 -------------------------------------------------------------------~~~K~~iI~eg~~  127 (409)
                                                                                         .+++.+++.++++
T Consensus       608 ~g~l~~g~l~k~~~g~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~Gfs~gi~D~~~~~~~~~~~~~~~~~~~~  687 (1449)
T d1twfa_         608 DGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKK  687 (1449)
T ss_dssp             TTEEEESCCCHHHHSSCTTSHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHTTCBCCCGGGGCCCHHHHHHHHHHHHHHHH
T ss_pred             CCeeeeccchhhhcccccccccccccccccHHHHHHHHHHHHHHHHHHHHhcchheeeccccccchhhHHHHHHHHHHhh
Confidence                                                                               2345667788888


Q ss_pred             hHHHHHHHhhcCCCcCCCCCChhhHHHHHHHHHHHHHHHHHHhhhhhcCCCCCcchhhhhcCCCcchhhHHHHHHHhcCc
Q psy13848        128 KCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQ  207 (409)
Q Consensus       128 kc~~~iadf~~GqLe~qpG~t~~EtLE~~v~~~ln~~~~~~g~~~~~~l~p~N~~~~M~~sGsKGS~~Ni~Qi~~~vGQQ  207 (409)
                      ++.++..+|+.|.++..++.+..+.+|..+++.|+++++++++.+...++++|++++|+.||||||.+|+.||++|+|||
T Consensus       688 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~v~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGakGs~~n~~Qi~g~~Gqq  767 (1449)
T d1twfa_         688 KVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQ  767 (1449)
T ss_dssp             HHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHTSSCCHHHHHHHHSCCEEC
T ss_pred             hHHHHHHHHHHhhhccccCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccchHhheeccccCCccchHHHHhhhhhh
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCcccCCCCCCCCCCCCCCCCCCCCCCCeeecCCcCCcccchhhhhhhhhheeeeccccccccccccccccccccCcc
Q psy13848        208 AINGKRVPNGFDNRSLPHFDKFSKDPASKGNVKFLRYGNRLKIASELKSAYLVWRVAGSISARGELHPKQKTDKVRSRNG  287 (409)
Q Consensus       208 ~l~G~Rip~g~~gRtLPhF~~~d~~~~a~GfI~nsf~~GL~p~~~~lk~e~~~h~~~gr~~~~gl~~ta~kt~~~tsrsG  287 (409)
                      .++|+|||.++.||+||||.++|.+|+++|||.+||++||+|      .|||||||+||   +||+|||+||    |++|
T Consensus       768 ~~~g~ri~~~~~~r~lp~f~~~~~~~~~~GfI~~sf~~GL~p------~Eyf~h~~~gR---eGLiDTAvkT----a~sG  834 (1449)
T d1twfa_         768 SVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTP------QEFFFHAMGGR---EGLIDTAVKT----AETG  834 (1449)
T ss_dssp             CBTTBSCCCCBTTBSSTTSCTTCCSTTTTTEECSCTTTCCCH------HHHHHHHHHHH---HHHHHHHHHH----HHHH
T ss_pred             cccCccccccccccccccCCCCCCCccccCcccchhhhhhcc------hheeeeeccch---hhhhhhcccc----cccH
Confidence            999999999999999999999999999999999999999999      99999999999   9999999999    9999


Q ss_pred             hHHHHHHhhhcc
Q psy13848        288 WLSSVLSSSLRF  299 (409)
Q Consensus       288 yl~r~L~~~l~F  299 (409)
                      ||||||+++|+.
T Consensus       835 Yl~RrLvk~led  846 (1449)
T d1twfa_         835 YIQRRLVKALED  846 (1449)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHhcC
Confidence            999999999987
>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure