Psyllid ID: psy16766

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-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-
MVYPSVNFNHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITPEDQQHRAIMKEKIITRQEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSNQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITPEGNY
cccccccccccccccccccccccccccccccccHHHHHHHccccccccHHHHHHHHHHHHccccccccccEEEcccccEEEEccccHHHHHHHHHHHcccccccHHHHHHHHHHHcccccccHHHcccccHHHHHHccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHccccccHHHHHHHHHccccHHHHHHcccccccHHHHHHHHHHHcHHHHHHHHHHccccccccccccccEEEEEEcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHccccccccccHHHHHHHHHHHHccccccccccEEEcccccEEEEccccHHHHHHHHHHcccccccc
ccccccccccccccccEEEEccccccccccccccHHHHHHccccccccHHcHHHHHHHHHcccccccccEEEEcccccEEEEEEcccccHHHHHHHHcccccEEEEEcccccEEEcccccEEEEEEEEccHHHHHHccccccccccccccccccccccccccccccccccccEcccccccccccccccccEEcccccccHHHHHHHHHHHHHHHHHcccEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHcccccccccccEEEEccccEEEEEEccccccccccccccccccccccccccccEccHHHHHHHHHHccHHHHHHHHHccccccccHHHccccEEEEEEcccccccccEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHccccccEcccccccEEEcEEEEEEccccccccccccccHHHHHHccccccccHHcHHHHHHHHHcccccccccEEEEcccccEEEEEEccccccccEEHEEccccccc
mvypsvnfnhahvfphrsvitpdpylnidsigvplefaktltypvpvtpwnVTLLRKMVingpnvypganmiqnedgsvvrisSSQAVQRESLAKRLITPEDQQHRAIMKEKIITRQEVVPEILKLKYYTDQEVKQLSVVKVfspitfnslghtipgglydlamgpisergdpcttcgnnytkckghighielpvpvintLFFRDVQLLLKLSCFlchkinipatsQLLFINQIKLLDAGYVTQAKDLEETLfneenlrlhpAQLVQLVDSHVQSILAHGtkicdindykggeELRSAFVAQVLSRHVKrkcifcatpinaiSYQQRKIIKSFKIDKDNLDQSLDKSLNKSSNQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSlvvppnnlrplsmeqmppvehsrNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGirgdtlnnkLQNSWHELQYNVDLLMDAKLNinkttgahqiDGLKQMLDGKTGMIRQNMmgkrvnfagrsvitpdpylnidsigvplefaktltypvpvtpwnVTLLRKMVingpnvypganmiqnedgsvvrisSSQAVQRESLAKRlitpegny
MVYPSVNFNHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLakrlitpedqqhraimkekiitrqevVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCatpinaisyqQRKIIKSFKIDKDNLDQSldkslnkssnqiirKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTtgahqidglKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISssqavqreslakrlitpegny
MVYPSVNFNHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITPEDQQHRAIMKEKIITRQEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSNQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITPEGNY
*****VNFNHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQ*********************************AIMKEKIITRQEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSFKID************************QGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPP*******************KLYQSILYSCGSLKSVIMAM********LSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMI********************************
*VYPSVNFNHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITPEDQQHRAIMKEKIITRQEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFN*****LHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVK***************QQRKIIKSF*****************************YVMASEVEADFKKLWTNEHLFLKCLIPVLDT*KELIATDIMFIRSLVVPPNNL***************NKLYQSILYSCGSLKSVIMA*******************DTLNNKLQNSWHELQYNVDLLMD******************QMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESL****I******
MVYPSVNFNHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITPEDQQHRAIMKEKIITRQEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSNQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITPEGNY
*VYPSVNFNHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITPEDQQHRAIMKEKIITRQEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSFKID************************QGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITP****
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MVYPSVNFNHAHVFPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITPEDQQHRAIMKEKIITRQEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSNQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITPEGNY
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 ?
Query621 2.2.26 [Sep-21-2011]
P91875 1642 DNA-directed RNA polymera yes N/A 0.774 0.292 0.362 3e-85
O35134 1717 DNA-directed RNA polymera yes N/A 0.772 0.279 0.329 2e-71
O95602 1720 DNA-directed RNA polymera yes N/A 0.758 0.273 0.332 8e-68
O54889 1716 DNA-directed RNA polymera yes N/A 0.756 0.273 0.323 4e-67
P10964 1664 DNA-directed RNA polymera yes N/A 0.764 0.285 0.306 9e-63
P15398 1689 DNA-directed RNA polymera yes N/A 0.787 0.289 0.284 2e-53
Q86H36 1615 DNA-directed RNA polymera yes N/A 0.771 0.296 0.303 3e-52
P31813 905 DNA-directed RNA polymera N/A N/A 0.610 0.418 0.262 5e-35
P25202 1741 DNA-directed RNA polymera N/A N/A 0.698 0.249 0.245 7e-32
P08775 1970 DNA-directed RNA polymera no N/A 0.621 0.195 0.278 7e-29
>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 =  316 bits (810), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 186/513 (36%), Positives = 289/513 (56%), Gaps = 32/513 (6%)

Query: 119 VVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCG 178
           + P  L+   +TDQE+++LSVVKV + ITF++LGH IPGGLYD+ MG      DPC TC 
Sbjct: 11  MFPSDLEFAVFTDQEIRKLSVVKVITGITFDALGHAIPGGLYDIRMGSYGRCMDPCGTC- 69

Query: 179 NNYTKCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLD 238
                C GH+GHIEL  PV N  F + VQ LL + C  C+K+ +      + + Q++L+D
Sbjct: 70  LKLQDCPGHMGHIELGTPVYNPFFIKFVQRLLCIFCLHCYKLQMKDHECEIIMLQLRLID 129

Query: 239 AGYVTQAKDLEETLFNEENLRLHPAQLV-----QLVDSHVQSI--LAHGTKICDINDYKG 291
           AGY+ +A++LE  LF  E +  +   LV      +V  H+ ++  L    +    N  K 
Sbjct: 130 AGYIIEAQELE--LFKSEIVCQNTENLVAIKNGDMVHPHIAAMYKLLEKNEKNSSNSTKT 187

Query: 292 GEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKS 351
              LR+A     L R + +KC  C   +  + Y  R+++  F +   ++ + +       
Sbjct: 188 SCSLRTAITHSALQR-LGKKCRHCNKSMRFVRYMHRRLV--FYVTLADIKERVGTGAETG 244

Query: 352 SNQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLD------TTKELIATDIMFI 405
               +       + A E     ++++ N    LK L+PVL       T  +    D+ F+
Sbjct: 245 GQNKV-------IFADECRRYLRQIYANYPELLKLLVPVLGLSNTDLTQGDRSPVDLFFM 297

Query: 406 RSLVVPPNNLRPLSMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQ--SDLLSEA 463
            +L V P   RPL+M       + +  +Y +I+ +   L  V+  MK  ++  ++    A
Sbjct: 298 DTLPVTPPRARPLNMVGDMLKGNPQTDIYINIIENNHVLNVVLKYMKGGQEKLTEEAKAA 357

Query: 464 LKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGKTGMIRQN 523
            + ++G+T + KL  +W  LQ +VD+L+D  ++    +G    +GLKQ+++ K+G+IR +
Sbjct: 358 YQTLKGETAHEKLYTAWLALQMSVDVLLDVNMSREMKSG----EGLKQIIEKKSGLIRSH 413

Query: 524 MMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVY 583
           MMGKRVN+A R+VITPDP +N+D IG+P  FAK L+YPVPVT WNVT LRKMV+NGP+V+
Sbjct: 414 MMGKRVNYAARTVITPDPNINVDEIGIPDIFAKKLSYPVPVTEWNVTELRKMVMNGPDVH 473

Query: 584 PGANMIQNEDGSVVRISSSQAVQRESLAKRLIT 616
           PGAN IQ+++G    I +  A +RESLAK L++
Sbjct: 474 PGANYIQDKNGFTTYIPADNASKRESLAKLLLS 506
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|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|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|P31813|RPOA1_THECE DNA-directed RNA polymerase subunit A' OS=Thermococcus celer GN=rpoA1 PE=3 SV=1 Back     alignment and function description
>sp|P25202|RPC1_GIAIN DNA-directed RNA polymerase III subunit RPC1 OS=Giardia intestinalis GN=RPOA3 PE=3 SV=1 Back     alignment and function description
>sp|P08775|RPB1_MOUSE DNA-directed RNA polymerase II subunit RPB1 OS=Mus musculus GN=Polr2a PE=1 SV=3 Back     alignment and function description

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 ?
Query621
328784193 1708 PREDICTED: DNA-directed RNA polymerase I 0.792 0.288 0.409 1e-98
380020146 1706 PREDICTED: LOW QUALITY PROTEIN: DNA-dire 0.792 0.288 0.407 2e-98
350414724 1713 PREDICTED: DNA-directed RNA polymerase I 0.797 0.288 0.394 3e-98
340715117 1713 PREDICTED: LOW QUALITY PROTEIN: DNA-dire 0.797 0.288 0.393 4e-98
345483754 1706 PREDICTED: DNA-directed RNA polymerase I 0.790 0.287 0.377 8e-93
383860778 1702 PREDICTED: DNA-directed RNA polymerase I 0.813 0.296 0.375 1e-91
307202220 1687 DNA-directed RNA polymerase I subunit RP 0.772 0.284 0.382 3e-91
157134596 1686 DNA-directed RNA polymerase I largest su 0.772 0.284 0.350 2e-87
91084933 1619 PREDICTED: similar to DNA-directed RNA p 0.763 0.292 0.369 1e-85
195486012 1642 GE12306 [Drosophila yakuba] gi|194177429 0.772 0.292 0.371 1e-84
>gi|328784193|ref|XP_001121092.2| PREDICTED: DNA-directed RNA polymerase I subunit RPA1 [Apis mellifera] Back     alignment and taxonomy information
 Score =  367 bits (941), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 213/520 (40%), Positives = 314/520 (60%), Gaps = 28/520 (5%)

Query: 114 ITRQEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDP 173
           +T + + P+ L    +T  +++ LSV K+ +P++FN LGH + GGLYD A+GP+ E  DP
Sbjct: 11  LTPKHLDPKCLMFSMFTANDIRNLSVAKIRTPLSFNILGHPLKGGLYDPALGPLLESSDP 70

Query: 174 CTTCGNNYTKCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQ 233
           C TCG N  KC GH GHIELP+PVIN LF + + +L+KL+C  C  + IP+  +LL   +
Sbjct: 71  CGTCGCNVFKCPGHFGHIELPMPVINPLFHKGLCMLIKLACLNCFNLQIPSYVKLLLSAK 130

Query: 234 IKLLDAGYVTQAKDLEE----TLFNEENLRLHPAQLVQ-LVDSHVQSILAHGT------- 281
           +KLL  GY++  + LE+     +FN +N      Q VQ ++D++++++L           
Sbjct: 131 LKLLQQGYLSDLESLEQEVMIVVFNSDNPYNVDIQSVQNVIDNYIENLLNKQRFNQSFVQ 190

Query: 282 -KICDINDYKGGEELRSAFVAQVLSRHVKRK-CIFCATPINAISYQQRKIIKSFKIDKDN 339
               DIN      +  +  V  VL ++   K C++C  PI+ I+  + KI+ + KI   N
Sbjct: 191 YDETDINTKNINTQWHTC-VENVLKQYTTPKICVYCEEPISKITTLKNKIMTT-KIS--N 246

Query: 340 LDQSLDKSLNKSSNQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIA 399
           L     +S       +I K +   +M  + +   +KLW NE  FLK +IP          
Sbjct: 247 LSNETIQS-----RGVIHKLDTIMIMPDQSKDYLRKLWQNEKNFLKVIIPCFGMVDIEYP 301

Query: 400 TDIMFIRSLVVPPNNLRPLSMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDL 459
           TDI F   + V P  +RP++      +EH ++++Y+SI+  C  L+++I  +++ +   L
Sbjct: 302 TDIFFFEVIPVLPPIVRPVNFINGQMIEHPQSQVYKSIIQDCLVLRNIIQTIQDGDTEQL 361

Query: 460 LSEA---LKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGK 516
             E       I+G+T   KL N+W  LQ NVD LMD   ++N+TT +    GLKQ+++ K
Sbjct: 362 PEEGKVVYDHIKGNTAIEKLHNAWQNLQVNVDHLMDR--DMNRTTDSANCQGLKQVIEKK 419

Query: 517 TGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMV 576
            G+IR +MMGKRVNFA RSVITPDP LNID IG+P  FA  LTYP PVTPWNV  LR++V
Sbjct: 420 EGIIRMHMMGKRVNFAARSVITPDPNLNIDEIGIPEAFALKLTYPTPVTPWNVVQLRQLV 479

Query: 577 INGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLIT 616
           +NGPN++PGA MI+NEDGS+ RIS S A+QRE++AKRL+T
Sbjct: 480 LNGPNIHPGAVMIENEDGSIQRISISDAIQREAIAKRLLT 519

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|380020146|ref|XP_003693956.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase I subunit RPA1-like [Apis florea] Back     alignment and taxonomy information
>gi|350414724|ref|XP_003490399.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA1-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|340715117|ref|XP_003396066.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase I subunit RPA1-like [Bombus terrestris] Back     alignment and taxonomy information
>gi|345483754|ref|XP_001602617.2| PREDICTED: DNA-directed RNA polymerase I subunit RPA1-like [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|383860778|ref|XP_003705866.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA1-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|307202220|gb|EFN81707.1| DNA-directed RNA polymerase I subunit RPA1 [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|157134596|ref|XP_001663321.1| DNA-directed RNA polymerase I largest subunit [Aedes aegypti] gi|108870419|gb|EAT34644.1| AAEL013134-PA [Aedes aegypti] Back     alignment and taxonomy information
>gi|91084933|ref|XP_970918.1| PREDICTED: similar to DNA-directed RNA polymerase I largest subunit [Tribolium castaneum] gi|270008555|gb|EFA05003.1| hypothetical protein TcasGA2_TC015082 [Tribolium castaneum] 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

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 ?
Query621
FB|FBgn0019938 1642 RpI1 "RNA polymerase I subunit 0.771 0.291 0.365 4.3e-78
ZFIN|ZDB-GENE-030131-5286 1710 polr1a "polymerase (RNA) I pol 0.357 0.129 0.387 9.4e-63
UNIPROTKB|E2R0G4 1746 POLR1A "DNA-directed RNA polym 0.339 0.120 0.387 2.4e-62
UNIPROTKB|F1SVC3 1723 POLR1A "DNA-directed RNA polym 0.339 0.122 0.382 1.2e-61
CGD|CAL0001661 1665 RPA190 [Candida albicans (taxi 0.405 0.151 0.373 3.9e-59
SGD|S000005868 1664 RPA190 "RNA polymerase I large 0.454 0.169 0.358 1.3e-56
POMBASE|SPBC4C3.05c 1689 nuc1 "DNA-directed RNA polymer 0.423 0.155 0.352 1.2e-55
UNIPROTKB|G4NBX7 1719 MGG_01158 "DNA-directed RNA po 0.442 0.159 0.364 5.2e-51
WB|WBGene00012999 1737 rpoa-1 [Caenorhabditis elegans 0.394 0.141 0.334 3.9e-49
TAIR|locus:2076661 1670 NRPA1 "nuclear RNA polymerase 0.239 0.089 0.417 6.6e-49
FB|FBgn0019938 RpI1 "RNA polymerase I subunit" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 797 (285.6 bits), Expect = 4.3e-78, P = 4.3e-78
 Identities = 187/511 (36%), Positives = 290/511 (56%)

Query:   121 PEILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNN 180
             P  L+   +TDQE+++LSVVKV + ITF++LGH IPGGLYD+ MG      DPC TC   
Sbjct:    13 PSDLEFAVFTDQEIRKLSVVKVITGITFDALGHAIPGGLYDIRMGSYGRCMDPCGTC-LK 71

Query:   181 YTKCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAG 240
                C GH+GHIEL  PV N  F + VQ LL + C  C+K+ +      + + Q++L+DAG
Sbjct:    72 LQDCPGHMGHIELGTPVYNPFFIKFVQRLLCIFCLHCYKLQMKDHECEIIMLQLRLIDAG 131

Query:   241 YVTQAKDLEETLFNEENLRLHPAQLV-----QLVDSHVQSI--LAHGTKICDINDYKGGE 293
             Y+ +A++LE  LF  E +  +   LV      +V  H+ ++  L    +    N  K   
Sbjct:   132 YIIEAQELE--LFKSEIVCQNTENLVAIKNGDMVHPHIAAMYKLLEKNEKNSSNSTKTSC 189

Query:   294 ELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSN 353
              LR+A     L R + +KC  C   +  + Y  R+++  F +   ++ + +         
Sbjct:   190 SLRTAITHSALQR-LGKKCRHCNKSMRFVRYMHRRLV--FYVTLADIKERVGTGAETGGQ 246

Query:   354 QIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVL-----DTTK-ELIATDIMFIRS 407
               +       + A E     ++++ N    LK L+PVL     D T+ +    D+ F+ +
Sbjct:   247 NKV-------IFADECRRYLRQIYANYPELLKLLVPVLGLSNTDLTQGDRSPVDLFFMDT 299

Query:   408 LVVPPNNLRPLSMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQ--SDLLSEALK 465
             L V P   RPL+M       + +  +Y +I+ +   L  V+  MK  ++  ++    A +
Sbjct:   300 LPVTPPRARPLNMVGDMLKGNPQTDIYINIIENNHVLNVVLKYMKGGQEKLTEEAKAAYQ 359

Query:   466 GIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGKTGMIRQNMM 525
              ++G+T + KL  +W  LQ +VD+L+D  ++    +G    +GLKQ+++ K+G+IR +MM
Sbjct:   360 TLKGETAHEKLYTAWLALQMSVDVLLDVNMSREMKSG----EGLKQIIEKKSGLIRSHMM 415

Query:   526 GKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPG 585
             GKRVN+A R+VITPDP +N+D IG+P  FAK L+YPVPVT WNVT LRKMV+NGP+V+PG
Sbjct:   416 GKRVNYAARTVITPDPNINVDEIGIPDIFAKKLSYPVPVTEWNVTELRKMVMNGPDVHPG 475

Query:   586 ANMIQNEDGSVVRISSSQAVQRESLAKRLIT 616
             AN IQ+++G    I +  A +RESLAK L++
Sbjct:   476 ANYIQDKNGFTTYIPADNASKRESLAKLLLS 506
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
ZFIN|ZDB-GENE-030131-5286 polr1a "polymerase (RNA) I polypeptide A" [Danio rerio (taxid:7955)] 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
CGD|CAL0001661 RPA190 [Candida albicans (taxid:5476)] Back     alignment and assigned GO terms
SGD|S000005868 RPA190 "RNA polymerase I largest subunit A190" [Saccharomyces cerevisiae (taxid:4932)] Back     alignment and assigned GO terms
POMBASE|SPBC4C3.05c nuc1 "DNA-directed RNA polymerase I complex large subunit Nuc1" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
UNIPROTKB|G4NBX7 MGG_01158 "DNA-directed RNA polymerase" [Magnaporthe oryzae 70-15 (taxid:242507)] Back     alignment and assigned GO terms
WB|WBGene00012999 rpoa-1 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
TAIR|locus:2076661 NRPA1 "nuclear RNA polymerase A1" [Arabidopsis thaliana (taxid:3702)] 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 ?
Query621
smart00663295 smart00663, RPOLA_N, RNA polymerase I subunit A N- 2e-44
PRK08566 882 PRK08566, PRK08566, DNA-directed RNA polymerase su 1e-33
TIGR02390 867 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer 3e-31
pfam00623165 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, do 6e-30
PRK14977 1321 PRK14977, PRK14977, bifunctional DNA-directed RNA 6e-27
COG0086 808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 8e-26
pfam00623165 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, do 1e-23
PRK08566882 PRK08566, PRK08566, DNA-directed RNA polymerase su 2e-22
pfam04997330 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, do 2e-21
TIGR02390867 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer 8e-20
smart00663295 smart00663, RPOLA_N, RNA polymerase I subunit A N- 5e-19
COG0086 808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 1e-18
TIGR02390 867 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer 6e-17
PRK08566 882 PRK08566, PRK08566, DNA-directed RNA polymerase su 2e-16
PRK14977 1321 PRK14977, PRK14977, bifunctional DNA-directed RNA 2e-15
CHL00018 663 CHL00018, rpoC1, RNA polymerase beta' subunit 8e-13
PRK14977 1321 PRK14977, PRK14977, bifunctional DNA-directed RNA 2e-12
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 4e-11
TIGR02387 619 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase 2e-10
PRK02625 627 PRK02625, rpoC1, DNA-directed RNA polymerase subun 3e-10
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 5e-10
PRK14906 1460 PRK14906, PRK14906, DNA-directed RNA polymerase su 1e-09
TIGR02386 1140 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, 4e-09
COG0086808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 2e-07
PRK00566 1156 PRK00566, PRK00566, DNA-directed RNA polymerase su 4e-07
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus Back     alignment and domain information 
 Score =  159 bits (406), Expect = 2e-44
 Identities = 68/193 (35%), Positives = 88/193 (45%), Gaps = 24/193 (12%)

Query: 403 MFIRSLVVPPNNLRPL-SMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLS 461
           M +  L VPP  LRP   ++     E     L + I+             +N     LL 
Sbjct: 3   MILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIK------------RNNRLKRLLE 50

Query: 462 EALKGIRGDTLNNKLQNSWHELQYNVDLLMD-AKLNINKTTGAHQIDGLKQMLDGKTGMI 520
                I        ++N    LQ  VD L+D   L          +  L Q L GK G  
Sbjct: 51  LGAPSII-------IRNEKRLLQEAVDTLIDNEGLPRANQKSGRPLKSLSQRLKGKEGRF 103

Query: 521 RQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGP 580
           RQN++GKRV+F+ RSVITPDP L ++ +GVP E A  LT+P  VTP N+  LRK+V NGP
Sbjct: 104 RQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNGP 163

Query: 581 NVYPGANMIQNED 593
               GA  I    
Sbjct: 164 ---NGAKYIIRGK 173

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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 621
KOG0262|consensus 1640 100.0
PRK08566 882 DNA-directed RNA polymerase subunit A'; Validated 100.0
TIGR02390 868 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit 100.0
PRK14977 1321 bifunctional DNA-directed RNA polymerase A'/A'' su 100.0
KOG0261|consensus 1386 100.0
KOG0260|consensus 1605 100.0
COG0086 808 RpoC DNA-directed RNA polymerase, beta' subunit/16 100.0
PF04997337 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; Int 100.0
TIGR02386 1140 rpoC_TIGR DNA-directed RNA polymerase, beta' subun 100.0
PRK00566 1156 DNA-directed RNA polymerase subunit beta'; Provisi 100.0
smart00663295 RPOLA_N RNA polymerase I subunit A N-terminus. 100.0
PRK02625 627 rpoC1 DNA-directed RNA polymerase subunit gamma; P 100.0
TIGR02387 619 rpoC1_cyan DNA-directed RNA polymerase, gamma subu 100.0
CHL00018 663 rpoC1 RNA polymerase beta' subunit 100.0
PRK14906 1460 DNA-directed RNA polymerase subunit beta'/alpha do 100.0
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 100.0
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 100.0
KOG0261|consensus 1386 100.0
KOG0262|consensus 1640 100.0
PRK14977 1321 bifunctional DNA-directed RNA polymerase A'/A'' su 100.0
TIGR02390868 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit 100.0
PRK08566882 DNA-directed RNA polymerase subunit A'; Validated 100.0
KOG0260|consensus 1605 100.0
smart00663295 RPOLA_N RNA polymerase I subunit A N-terminus. 100.0
PF00623166 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; Int 99.97
PF00623166 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; Int 99.93
CHL00018663 rpoC1 RNA polymerase beta' subunit 99.91
PRK02625627 rpoC1 DNA-directed RNA polymerase subunit gamma; P 99.9
TIGR02387619 rpoC1_cyan DNA-directed RNA polymerase, gamma subu 99.9
TIGR02386 1140 rpoC_TIGR DNA-directed RNA polymerase, beta' subun 99.89
PRK00566 1156 DNA-directed RNA polymerase subunit beta'; Provisi 99.88
PRK14906 1460 DNA-directed RNA polymerase subunit beta'/alpha do 99.87
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 99.85
COG0086808 RpoC DNA-directed RNA polymerase, beta' subunit/16 99.85
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 99.83
>KOG0262|consensus Back     alignment and domain information 
Probab=100.00  E-value=4.6e-114  Score=962.42  Aligned_cols=498  Identities=36%  Similarity=0.609  Sum_probs=420.2

Q ss_pred             ccccCcce-EEEecCChHHHHhhcccccccccccCCCCCccccCccCCCCCccccCCCccCCCCCCccccCCcccccCCC
Q psy16766        116 RQEVVPEI-LKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIELP  194 (621)
Q Consensus       116 ~p~~~~~g-~ef~~~s~eei~~lSv~~I~~~~~~d~~g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfGhI~L~  194 (621)
                      +|+..|-. ++|++|+++||+++||++|++|.+||+.|+|+.|||||++||+ .+..+.|.||++...+||||||||+||
T Consensus         7 ~pv~~~~~~v~Fg~yt~~ei~klSv~kIt~p~~~D~lGhPi~GGLYDl~LGp-~~~~~~C~TC~~~~~~CPGH~GHIeL~   85 (1640)
T KOG0262|consen    7 MPVMSFQPSVSFGSYTDQEIRKLSVKKITNPITFDNLGHPIPGGLYDLALGP-LDNSDVCSTCNQDELNCPGHMGHIELP   85 (1640)
T ss_pred             CcccccccceeeeccCHHHHhhcceeEecCceeecccCCCCCCcccccccCC-ccchhhhhhhcchhhcCCCccCeeeec
Confidence            57766655 9999999999999999999999999999999999999999997 788899999999999999999999999


Q ss_pred             cccccchhhHhHHHHHhhccccccCcccCcchHHHHHHHHhhccccchHHHHhHHHhh--hhccccCcChHHHHHHHHHH
Q psy16766        195 VPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETL--FNEENLRLHPAQLVQLVDSH  272 (621)
Q Consensus       195 ~Pv~hp~f~~~v~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkll~~G~l~~a~~L~~~~--~~~~~~~~~~~~~~~~~~~~  272 (621)
                      .|||||+||+.+|++||+.|++||+|+++..+.+.+.+||++++.|++.+|.+|+.+.  ..+++.+.+..++......+
T Consensus        86 ~pvynPlfF~~ly~lLr~sCl~Chhf~~k~~~v~~~~cqLrll~~G~i~ea~~Le~i~~~~~~d~~d~~~~~~k~~~~~~  165 (1640)
T KOG0262|consen   86 VPVYNPLFFDFLYNLLRGSCLFCHHFRCKNVDVHILFCQLRLLEYGLIEEAEDLESITSETVEDNEDESLNEIKSCRAQY  165 (1640)
T ss_pred             ccccCHHHHHHHHHHHHHHHHhhhhcccCcHHHHHHHHHHHHHHhchHHHHHHHHHhhhhhhccCcchhHHHHHhhhhhh
Confidence            9999999999999999999999999999999999999999999999999999999987  46666654444444444445


Q ss_pred             HHHHHhhccccccCCCCcchHHHHHHHHHHHHhhh-cCCCCCCCCCCCceeecccceEEEEeeccc--------------
Q psy16766        273 VQSILAHGTKICDINDYKGGEELRSAFVAQVLSRH-VKRKCIFCATPINAISYQQRKIIKSFKIDK--------------  337 (621)
Q Consensus       273 ~~~~~~~~~~~~~~~~~k~~~~~r~~i~~~~~~~~-~~kkC~~C~~~~p~irk~~~~~i~~~~~~~--------------  337 (621)
                      +.+.+.+.........+++..+.+++++.+|++.+ ..++|+||+..+|.+||+++.++++.....              
T Consensus       166 v~~~i~~~~~~~~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~~p~~rk~~~~kv~~~~~~~~~~~~~~~~~~i~~  245 (1640)
T KOG0262|consen  166 VTEAISEALLDKSEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHSNPKLRKDGFRKVFIDALSSKVGANVIRGAKIKK  245 (1640)
T ss_pred             ccHHHHHHhhcCCCccchhhHHHHHHHHHHHHHHhhccccCCcccCCCchhhccccceeeeehhcccccccchhheeeeh
Confidence            44444433333333347788999999999999988 889999999999999999999998632210              


Q ss_pred             ccc-chhhhh----hhccc--chh---------hhhhccccccCHHHHHHHHhhcchhhHHHHhhhcccCCC-cccCCCC
Q psy16766        338 DNL-DQSLDK----SLNKS--SNQ---------IIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDT-TKELIAT  400 (621)
Q Consensus       338 ~~~-~~~~d~----~~e~~--~~~---------~~~~~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~-~~~~~~~  400 (621)
                      +.. .+.+|+    +.|..  +.+         +.......||+|.|||+||+.||.+|.++|..||+..+. .+...|.
T Consensus       246 ~~~~~~~~d~~~~G~~E~~~~g~d~~e~~~~~~~~~~t~~~~l~~tevR~~l~~lf~ne~~~l~~lf~l~~~~~~k~~p~  325 (1640)
T KOG0262|consen  246 DVGSKGFEDSGIDGSNEVEEDGKDLFEKSTEPAEFEKTGKKYLLPTEVREHLRDLFKNEGELLSYLFPLWDSGSGKIDPS  325 (1640)
T ss_pred             hcccccccccccCCccccccccccccccccccccccccccccccHHHHHHHHHHHHhhhHHHHHHhhccccccccccCcc
Confidence            000 001111    00100  000         011123469999999999999999999999999993331 1234578


Q ss_pred             ceEEEEeeecCCCCCccccccCCCccccchhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHH
Q psy16766        401 DIMFIRSLVVPPNNLRPLSMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSW  480 (621)
Q Consensus       401 d~ffl~~lpVpP~~~RP~~~~~~~~~ed~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w  480 (621)
                      |+|||+.|||||++|||++++||...||+||..|.+||+.|..|++++..+. +.-....+..++..+|  +.++++++|
T Consensus       326 d~FFld~l~VpPtrfRP~s~~gd~~~en~Qt~~L~kVle~s~~i~~~~~~m~-~kl~~~~k~~l~~~~g--~~~kl~~aw  402 (1640)
T KOG0262|consen  326 DMFFLDNLLVPPTRFRPPSMLGDEVHENPQTLNLNKVLESSVLIRKLLKDMK-GKLDEELKLILERLRG--IFSKLINAW  402 (1640)
T ss_pred             ceeeeeccccCCcccCCchhcchhhhcChHHHHHHHHHHHHHHHHHHHHHhh-hccCHHHHHHHHhhhh--HHHHHHHHH
Confidence            8999999999999999999999999999999999999999999999886655 3222222445566677  678999999


Q ss_pred             HHHHHHHHHhhcccccC-CCCCCCCCccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccchHHHHhhCC
Q psy16766        481 HELQYNVDLLMDAKLNI-NKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLT  559 (621)
Q Consensus       481 ~~LQ~~V~~~~d~~~~~-~~~~~~k~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT  559 (621)
                      .+||.+||.+||++  + ++.+... .+||||+||||||+||+|||||||||||||||||||||++||||||+.||++||
T Consensus       403 ~~LQ~~vn~lfDs~--~~~k~~r~~-~pGikQiLEKKeGLFRkhMMGKRVN~AaRSVIsPDPnI~tnEIGIP~vFA~KLT  479 (1640)
T KOG0262|consen  403 LQLQASVNVLFDSK--MASKWSRDS-PPGIKQILEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEIGIPPVFAKKLT  479 (1640)
T ss_pred             HHHHHHHHHHhccc--cccccccCC-CchHHHHHHHhhhhHHHHhhccccchhhccccCCCCCccccccCCchHHHhhcc
Confidence            99999999999999  6 4444443 489999999999999999999999999999999999999999999999999999


Q ss_pred             cCcccCHHHHHHHHHHHHcCCCCCCcceEEEcCCCcEEEeCCCchHhHHHHHHHhcCCCCC
Q psy16766        560 YPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRLITPEGN  620 (621)
Q Consensus       560 ~PE~VT~~Ni~~Lr~lV~NGp~~~PGA~~i~~~~G~~~~L~~~~~~~R~~~A~~L~~~~~~  620 (621)
                      ||||||+||+++||++|+|||++||||+||+++||+++.|..++.++|+|+|+|||||+.|
T Consensus       480 yPepVt~~NV~elr~aViNGP~~hPGA~~iqd~dg~~t~l~~~~~~qR~alA~qLLtpst~  540 (1640)
T KOG0262|consen  480 YPEPVTPWNVNELRKAVINGPDVHPGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTG  540 (1640)
T ss_pred             CCCcCCcccHHHHHHHHhcCCCCCCCcceeecCCCceeecCCCCHHHHHHHHHHhhccccC
Confidence            9999999999999999999999999999999999999999999999999999999998765

>PRK08566 DNA-directed RNA polymerase subunit A'; Validated 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
>KOG0261|consensus Back     alignment and domain information
>KOG0260|consensus Back     alignment and domain information
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA Back     alignment and domain information
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form Back     alignment and domain information
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional Back     alignment and domain information
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus 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
>CHL00018 rpoC1 RNA polymerase beta' subunit 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
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>KOG0261|consensus 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
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A' Back     alignment and domain information
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated Back     alignment and domain information
>KOG0260|consensus Back     alignment and domain information
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus Back     alignment and domain information
>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
>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
>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
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form Back     alignment and domain information
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional Back     alignment and domain information
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional Back     alignment and domain information
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] 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 ?
Query621
2pmz_A 880 Archaeal Rna Polymerase From Sulfolobus Solfataricu 5e-25
2waq_A 880 The Complete Structure Of The Archaeal 13-Subunit D 1e-24
3j0k_A 1455 Orientation Of Rna Polymerase Ii Within The Human V 4e-21
4a3c_A 1732 Rna Polymerase Ii Initial Transcribing Complex With 5e-21
1i3q_A 1733 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 5e-21
3h0g_A 1752 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 1e-20
3qqc_A436 Crystal Structure Of Archaeal Spt45 BOUND TO THE RN 5e-14
3iyd_D 1413 Three-Dimensional Em Structure Of An Intact Activat 6e-11
3lu0_D 1407 Molecular Model Of Escherichia Coli Core Rna Polyme 6e-11
4gzy_D 1534 Crystal Structures Of Bacterial Rna Polymerase Paus 5e-09
1iw7_D 1524 Crystal Structure Of The Rna Polymerase Holoenzyme 5e-09
1i6v_D 1264 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 4e-08
1l9u_D 1524 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 5e-08
1hqm_D 1265 Crystal Structure Of Thermus Aquaticus Core Rna Pol 5e-08
2gho_D 1233 Recombinant Thermus Aquaticus Rna Polymerase For St 5e-08
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 880 Back     alignment and structure 
Iteration: 1

 Score =  112 bits (281), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 61/142 (42%), Positives = 83/142 (58%), Gaps = 5/142 (3%)
Query: 476 LQNSWHELQYNVDLLMDAK---LNINKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFA 532
           +++ W  LQY+V    D +   L  +K      +  L Q L GK G  R N+ GKRV+F+
Sbjct: 262 IEDLWDLLQYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFS 321
Query: 533 GRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNE 592
            R+VI+PDP ++ID +GVP   AKTLT P  +TPWN+  LR+ VINGP+ +PGAN +   
Sbjct: 322 SRTVISPDPNISIDEVGVPEIIAKTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIRP 381
Query: 593 DGSVVRISSSQAVQRESLAKRL 614
           DG   RI       R+ LA  L
Sbjct: 382 DGR--RIDLRYVKDRKELASTL 401
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 880 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|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|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 Back     alignment and structure
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP CLAMP DOMAIN Length = 436 Back     alignment and structure
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1413 Back     alignment and structure
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1407 Back     alignment and structure
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused Elongation Complexes Length = 1534 Back     alignment and structure
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1524 Back     alignment and structure
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1264 Back     alignment and structure
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1524 Back     alignment and structure
>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase- Includes Complete Structure With Side-Chains (Except For Disordered Regions)-Further Refined From Original Deposition-Contains Additional Sequence Information Length = 1265 Back     alignment and structure
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For Structural Studies Length = 1233 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 ?
Query621
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 5e-90
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 4e-26
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 1e-85
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 2e-24
4ayb_A 880 DNA-directed RNA polymerase; transferase, multi-su 3e-77
4ayb_A880 DNA-directed RNA polymerase; transferase, multi-su 3e-24
3qqc_A436 DNA-directed RNA polymerase subunit B, DNA-direct 5e-66
3qqc_A436 DNA-directed RNA polymerase subunit B, DNA-direct 1e-14
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 7e-11
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-07
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 3e-10
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 9e-10
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 4e-09
>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 =  304 bits (780), Expect = 5e-90
 Identities = 116/489 (23%), Positives = 189/489 (38%), Gaps = 83/489 (16%)

Query: 129 YTDQEVKQLSVVKVFSPITFNSLGHT-IPGGLYDLAMGPISERGDPCTTCGNNYTKCKGH 187
            + +E++ +SV K+  P T +  G     GGL D  +G I +R   C TCG     C GH
Sbjct: 24  LSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTI-DRQFKCQTCGETMADCPGH 82

Query: 188 IGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKD 247
            GHIEL  PV +  F   ++ +L+  C+ C K+ I +++                     
Sbjct: 83  FGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPK------------------- 123

Query: 248 LEETLFNEENLRLHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRH 307
                FN+      P   +  V +     +     +CD     G +         + +  
Sbjct: 124 -----FNDTQRYRDPKNRLNAVWN-----VCKTKMVCDTGLSAGSDN------FDLSNPS 167

Query: 308 VKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSNQIIRKREQGYVMAS 367
                  C      I     ++  S+K  KD  D                  E+  +   
Sbjct: 168 ANMGHGGCGAAQPTIRKDGLRLWGSWKRGKDESDL----------------PEKRLLSPL 211

Query: 368 EVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPL-SMEQMPPV 426
           EV   F  + + +       +  L   ++    D M I  L VPP ++RP  S++     
Sbjct: 212 EVHTIFTHISSED-------LAHLGLNEQYARPDWMIITVLPVPPPSVRPSISVDGTSRG 264

Query: 427 EHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYN 486
           E         I+ +  +++                            + +      LQ++
Sbjct: 265 EDDLTHKLSDIIKANANVRRCEQEGAP-------------------AHIVSEYEQLLQFH 305

Query: 487 VDLLMD---AKLNINKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYL 543
           V   MD   A            +  ++  L GK G +R N+MGKRV+F+ R+VIT DP L
Sbjct: 306 VATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNL 365

Query: 544 NIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQ 603
           ++D +GVP   AKTLTYP  VTP+N+  L+++V NGP+ +PGA  I  + G  + +   +
Sbjct: 366 SLDELGVPRSIAKTLTYPETVTPYNIYQLQELVRNGPDEHPGAKYIIRDTGERIDLRYHK 425

Query: 604 AVQRESLAK 612
                 L  
Sbjct: 426 RAGDIPLRY 434
>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
>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
>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
>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
>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
>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
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524 Back     alignment and structure
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Length = 1265 Back     alignment and structure
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Length = 1407 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query621
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 100.0
4ayb_A 880 DNA-directed RNA polymerase; transferase, multi-su 100.0
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 100.0
3qqc_A436 DNA-directed RNA polymerase subunit B, DNA-direct 100.0
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 100.0
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 100.0
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 100.0
4ayb_A880 DNA-directed RNA polymerase; transferase, multi-su 100.0
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 99.98
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 99.97
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 99.9
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 99.89
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 99.84
>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=2.8e-90  Score=839.79  Aligned_cols=409  Identities=26%  Similarity=0.411  Sum_probs=337.0

Q ss_pred             hhcccccCcceEEEecCChHHHHhhcccccccccccCCC-CCccccCccCCCCCccccCCCccCCCCCCccccCCccccc
Q psy16766        113 IITRQEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSL-GHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHI  191 (621)
Q Consensus       113 ~~~~p~~~~~g~ef~~~s~eei~~lSv~~I~~~~~~d~~-g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfGhI  191 (621)
                      ....|.++|.+++|+++|||||+++||++|+++.+||.. |+|+.|||+|+|||+ .++...|.|||++..+||||||||
T Consensus         8 ~s~~~~~~i~~i~Fg~~S~eeI~~~Sv~~I~~~~~~d~~~~~P~~~Gl~D~rlG~-~~~~~~C~TCg~~~~~CpGHFGHI   86 (1752)
T 3h0g_A            8 PSSVPLRRVEEVQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGT-IDRQFKCQTCGETMADCPGHFGHI   86 (1752)
T ss_dssp             CCSSCCCCCCCBEECCCCHHHHHHHCCCCCCCTTCTTCSSSSSCCSSSSSSSCCC-SSSSCCCTTSCCSSSSCCCCCEEC
T ss_pred             CCcCcceeeeeEEEecCCHHHHHHhCeeEEecccccccccCCCCCCCCcCccccC-CCCCCCCCCCCCCCCcCCCcceee
Confidence            345678899999999999999999999999999999987 699999999999999 788999999999999999999999


Q ss_pred             CCCcccccchhhHhHHHHHhhccccccCcccCcchHHHHHHHHhhccc-cchHHHHhHHHhhhhccccCcChHHHHHHHH
Q psy16766        192 ELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDA-GYVTQAKDLEETLFNEENLRLHPAQLVQLVD  270 (621)
Q Consensus       192 ~L~~Pv~hp~f~~~v~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkll~~-G~l~~a~~L~~~~~~~~~~~~~~~~~~~~~~  270 (621)
                      ||+.|||||+||+.+++||+|+|++|||+++++.+.+ |..++++.+. ..+.+.++++.....|+.....++       
T Consensus        87 ELa~PVfHpgF~~~I~kILr~vC~~C~klll~~~~~~-f~~~lrlrd~k~r~~~V~~~ck~k~~Ce~~~~~~~-------  158 (1752)
T 3h0g_A           87 ELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPK-FNDTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGS-------  158 (1752)
T ss_dssp             CCCSCBCCHHHHHHHHHHSSSSCTTTCCCSCCSCSHH-HHHHHHSSCTTTTHHHHHHHHHHCCCCCSSTTCCS-------
T ss_pred             ecccceEeehhhHHHHHHHHHHHHHhcccccccccHH-HHHHHHccCHHHHHHHHHHHhccccccCCCCcccc-------
Confidence            9999999999999999999999999999999988765 7777776542 234444544433222211100000       


Q ss_pred             HHHHHHHhhccccccCCCCcchHHHHHHHHHHHHhhhcCCCCCCCCCCCceeecccceEEEEeeccccccchhhhhhhcc
Q psy16766        271 SHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNK  350 (621)
Q Consensus       271 ~~~~~~~~~~~~~~~~~~~k~~~~~r~~i~~~~~~~~~~kkC~~C~~~~p~irk~~~~~i~~~~~~~~~~~~~~d~~~e~  350 (621)
                                   ......               +....++|+|||+.+|.|||++.+++..|+..++     ++     
T Consensus       159 -------------~~~~~~---------------~~~~~~~~~gCG~~qP~IRKeglkl~~~~k~~k~-----~~-----  200 (1752)
T 3h0g_A          159 -------------DNFDLS---------------NPSANMGHGGCGAAQPTIRKDGLRLWGSWKRGKD-----ES-----  200 (1752)
T ss_dssp             -------------SCCCSS---------------CCCCCCSSCSSCCCCCCCEEETTEEECCBCCSSS-----SC-----
T ss_pred             -------------cchhcc---------------cccccccCCCcCCcCCcEEeeccEEEEEEccccc-----cc-----
Confidence                         000000               0003457999999999999999866554542210     00     


Q ss_pred             cchhhhhhccccccCHHHHHHHHhhcchhhHHHHhhhcccCCCcccCCCCceEEEEeeecCCCCCccccccCCC-ccccc
Q psy16766        351 SSNQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQMP-PVEHS  429 (621)
Q Consensus       351 ~~~~~~~~~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~~~~~~~~d~ffl~~lpVpP~~~RP~~~~~~~-~~ed~  429 (621)
                         + .  ..+++|+|.+|+++|++||++|+++|++..       ...+||||||++|||||+++||++.++|+ ..|||
T Consensus       201 ---~-~--~~k~~LtP~eVl~ifk~IsdeD~~lLGl~~-------~~~rPewmiL~vLPVpPp~vRPsv~ldg~~~~edD  267 (1752)
T 3h0g_A          201 ---D-L--PEKRLLSPLEVHTIFTHISSEDLAHLGLNE-------QYARPDWMIITVLPVPPPSVRPSISVDGTSRGEDD  267 (1752)
T ss_dssp             ---B-C--SSCCCCCHHHHHHHHHHSCHHHHHHSSCCS-------SSCCGGGSSBSSCEECCGGGSCCCCCSSSCCCCCT
T ss_pred             ---c-c--ccceecCHHHHHHHHHhcCHHHHHHhCCCc-------cCCChhheEeeccccCCCCccCceEcCCCccCCCh
Confidence               0 0  235689999999999999999999998521       13479999999999999999999999875 89999


Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHHHHHHHHHHHhhcccccCCCCC-----CCC
Q psy16766        430 RNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTT-----GAH  504 (621)
Q Consensus       430 ~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w~~LQ~~V~~~~d~~~~~~~~~-----~~k  504 (621)
                      +|.+|++||+.|+.|++.+..   +.                ....+.+.|..||.+|++||||+  ..+.+     .++
T Consensus       268 Lt~~l~~II~~N~~Lk~~~~~---ga----------------p~~~~~~~~~~LQ~~v~~~~dn~--~~~~~~~~~~~~r  326 (1752)
T 3h0g_A          268 LTHKLSDIIKANANVRRCEQE---GA----------------PAHIVSEYEQLLQFHVATYMDNE--IAGQPQALQKSGR  326 (1752)
T ss_dssp             TTTHHHHHHHHHHHHHGGGGC---CS----------------SSTTHHHHHHHHHHHHHHTTCTT--CSSCCCCCSSSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHh---cc----------------hhHHHHHHHHHHHHHHHHhhcCC--CCCCccccccCCC
Confidence            999999999999999875421   11                12246678999999999999999  54432     235


Q ss_pred             CccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccchHHHHhhCCcCcccCHHHHHHHHHHHHcCCCCCC
Q psy16766        505 QIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYP  584 (621)
Q Consensus       505 ~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT~PE~VT~~Ni~~Lr~lV~NGp~~~P  584 (621)
                      +.+||+|||||||||||+|||||||||||||||+|||||++||||||..||++|||||+||+|||++||+||.|||++||
T Consensus       327 p~k~~~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~evGvP~~~A~~Lt~Pe~vt~~ni~~l~~lv~nG~~~~p  406 (1752)
T 3h0g_A          327 PLKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQELVRNGPDEHP  406 (1752)
T ss_dssp             CCCCHHHHHTCSSSSSTTTTSSCCCSSEEEEEEEEETTSCTTBCBCCHHHHTSCCCCCBCCTTTHHHHHHHHHHCTTSSS
T ss_pred             CCcchHhhhhcccccccccccccccCCccceeecCCCCcccceeeChHHHHHhcCCCccccHHHHHHHHHHHHcCCcccc
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cceEEEcCCCcEEEeCCC
Q psy16766        585 GANMIQNEDGSVVRISSS  602 (621)
Q Consensus       585 GA~~i~~~~G~~~~L~~~  602 (621)
                      ||++|++++|.+++|++.
T Consensus       407 ga~~v~~~~~~~~~l~~~  424 (1752)
T 3h0g_A          407 GAKYIIRDTGERIDLRYH  424 (1752)
T ss_dssp             CEEEEECTTCCBCCTTTT
T ss_pred             CceeeecCCCcEeechhh
Confidence            999999999999998875
>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
>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
>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
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Back     alignment and structure
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Back     alignment and structure
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Back     alignment and structure
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Back     alignment and structure
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Back     alignment and structure

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 621
d1twfa_ 1449 e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c 5e-72
d1twfa_ 1449 e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c 1e-13
d1smyd_ 1504 e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t 4e-33
d1smyd_ 1504 e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t 7e-10
>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 =  250 bits (639), Expect = 5e-72
 Identities = 112/481 (23%), Positives = 183/481 (38%), Gaps = 87/481 (18%)

Query: 124 LKLKYYTDQEVKQLSVVKVFSPITFNSLGHTI-PGGLYDLAMGPISERGDPCTTCGNNYT 182
           ++   ++ +EV+ +SV K+  P T +        GGL D  +G I +R   C TC     
Sbjct: 16  VQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSI-DRNLKCQTCQEGMN 74

Query: 183 KCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYV 242
           +C GH GHI+L  PV +  F   ++ + +  C  C K+       LL  +   +  A  +
Sbjct: 75  ECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKL-------LLDEHNELMRQALAI 127

Query: 243 TQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQ 302
             +K     ++                       L     +C+  D    ++        
Sbjct: 128 KDSKKRFAAIWT----------------------LCKTKMVCE-TDVPSEDDPTQ----- 159

Query: 303 VLSRHVKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSNQIIRKREQG 362
                       C      I     K++ S+K D+   D                + E  
Sbjct: 160 ------LVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGD--------------ADEPELR 199

Query: 363 YVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPL-SME 421
            +   E+   FK +   +          L   +     + M +  L VPP  +RP  S  
Sbjct: 200 VLSTEEILNIFKHISVKD-------FTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFN 252

Query: 422 QMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWH 481
           +    E         IL +  SL+                           ++ ++ +  
Sbjct: 253 ESQRGEDDLTFKLADILKANISLE-------------------TLEHNGAPHHAIEEAES 293

Query: 482 ELQYNVDLLMD---AKLNINKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVIT 538
            LQ++V   MD   A            +  ++  L GK G IR N+MGKRV+F+ R+VI+
Sbjct: 294 LLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVIS 353

Query: 539 PDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVR 598
            DP L +D +GVP   AKTLTYP  VTP+N+  L ++V NGPN +PGA  +  + G  + 
Sbjct: 354 GDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRID 413

Query: 599 I 599
           +
Sbjct: 414 L 414
>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 ?
Query621
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 99.96
d1smyd_ 1504 RNA-polymerase beta-prime {Thermus thermophilus [T 99.91
>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=8.2e-81  Score=763.63  Aligned_cols=408  Identities=26%  Similarity=0.420  Sum_probs=326.9

Q ss_pred             hhhhcccccCcceEEEecCChHHHHhhcccccccccccCCC-CCccccCccCCCCCccccCCCccCCCCCCccccCCccc
Q psy16766        111 EKIITRQEVVPEILKLKYYTDQEVKQLSVVKVFSPITFNSL-GHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIG  189 (621)
Q Consensus       111 ~~~~~~p~~~~~g~ef~~~s~eei~~lSv~~I~~~~~~d~~-g~Pi~ggl~D~~lG~~~~~~~~C~tC~~~~~~C~GhfG  189 (621)
                      ......|+++|++++|+++|||||+++|+++|++|.+||.. ++|..|||+|++||+ .+....|.||++...+||||||
T Consensus         3 ~~~~~~p~~~i~~i~f~~~s~eeIr~~S~~ei~~~~~~~~~~~~p~~~Gl~d~rlG~-~~~~~~C~tC~~~~~~CpGHfG   81 (1449)
T d1twfa_           3 QQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGS-IDRNLKCQTCQEGMNECPGHFG   81 (1449)
T ss_dssp             CSCCCSCBCCCCEEECCBCCHHHHHHTCCCCCCCSCCSCTTSCCSCCSSSSCSSSCC-CTTCCCSSSCCCCTTSCCCCCC
T ss_pred             CCCCcCccceeceEEEEecCHHHHHHhcceEEcCCCcccCCCCCCCCCCCcchhhCC-CCCcCCCCCCCCCCcCCCCCCE
Confidence            34557899999999999999999999999999999999886 569999999999999 7888999999999999999999


Q ss_pred             ccCCCcccccchhhHhHHHHHhhccccccCcccCcchHHHHHHHHhhccccchHHHHhHHHhhhhccccCcChHHHHHHH
Q psy16766        190 HIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEETLFNEENLRLHPAQLVQLV  269 (621)
Q Consensus       190 hI~L~~Pv~hp~f~~~v~~lL~~iC~~C~~l~~~~~~~~~~~~~Lkll~~G~l~~a~~L~~~~~~~~~~~~~~~~~~~~~  269 (621)
                      ||+|+.|||||+||+.++++|+++|++||+++++..... +...+...+....                           
T Consensus        82 hIeL~~PV~h~~f~~~~~~~L~~~C~~C~~l~l~~~~~~-~~~~~~~~~~~~~---------------------------  133 (1449)
T d1twfa_          82 HIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNEL-MRQALAIKDSKKR---------------------------  133 (1449)
T ss_dssp             CEEEEEEEECGGGHHHHHHHHHHBCTTTCCBSCCTTSHH-HHHHHTCCSHHHH---------------------------
T ss_pred             eeEecccchhHHHHHHHHHHHHHhhhccCCEeecccHHH-HHHHHhhcchhhh---------------------------
Confidence            999999999999999999999999999999999876543 2233332221100                           


Q ss_pred             HHHHHHHHhhccccccCCCCcchHHHHHHHHHHHHhhhcCCCCCCCCCCCceeecccceEEEEeeccccccchhhhhhhc
Q psy16766        270 DSHVQSILAHGTKICDINDYKGGEELRSAFVAQVLSRHVKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLN  349 (621)
Q Consensus       270 ~~~~~~~~~~~~~~~~~~~~k~~~~~r~~i~~~~~~~~~~kkC~~C~~~~p~irk~~~~~i~~~~~~~~~~~~~~d~~~e  349 (621)
                      ...+....+.. ......... ...          .. ....|++|++.++.+++.....++.+....  ..        
T Consensus       134 ~~~~~~~~~~~-~~~~~~~~~-~~~----------~~-~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~--~~--------  190 (1449)
T d1twfa_         134 FAAIWTLCKTK-MVCETDVPS-EDD----------PT-QLVSRGGCGNTQPTIRKDGLKLVGSWKKDR--AT--------  190 (1449)
T ss_dssp             HHHHHHHHTTC-CBCCSEECC-SSC----------TT-SCEECCSCCCBCCCCEECSSCEEEEECSSS--SC--------
T ss_pred             hHHHHHHhhhh-eeccccccc-hhh----------hh-hhhhcCCCCcCChhhhhhhHHHHHHHHHhh--hc--------
Confidence            00001111110 000000000 000          00 345799999999999999877766543221  00        


Q ss_pred             ccchhhhhhccccccCHHHHHHHHhhcchhhHHHHhhhcccCCCcccCCCCceEEEEeeecCCCCCccccccCCC-cccc
Q psy16766        350 KSSNQIIRKREQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPLSMEQMP-PVEH  428 (621)
Q Consensus       350 ~~~~~~~~~~~~~~l~p~ev~~~lk~i~~~d~~~L~~l~~~~~~~~~~~~~d~ffl~~lpVpP~~~RP~~~~~~~-~~ed  428 (621)
                          .........+++|.+++++|++||++|..+|++.     +  ...+|+||||++|||||+++||++.++|+ ..+|
T Consensus       191 ----~~~~~~~~~~l~~~~~~~i~~~i~~~~~~~l~~~-----~--~~~~p~~~~l~~lpV~P~~~RP~~~~~~~~~~~~  259 (1449)
T d1twfa_         191 ----GDADEPELRVLSTEEILNIFKHISVKDFTSLGFN-----E--VFSRPEWMILTCLPVPPPPVRPSISFNESQRGED  259 (1449)
T ss_dssp             ----TTSCSCEEEEECHHHHHHHHTTSCHHHHHHTTCB-----T--TTBCGGGGEEEEECCCCTTTSCCCCCSSSCCCCC
T ss_pred             ----ccccchhheeCCHHHHHHHHHhCCHhHHHHhCCC-----c--CCCChHHEEeeeeecCCCCcCCceEeCCCcccCC
Confidence                0011122357999999999999999999988741     1  13478999999999999999999988775 7799


Q ss_pred             chhHHHHHHHHHHHHHHHHHHHhhhhchhhhhHHHhhcccCCchhhHHHHHHHHHHHHHHHhhcccccCCCC-----CCC
Q psy16766        429 SRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKT-----TGA  503 (621)
Q Consensus       429 ~~t~~l~~Il~~N~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~~~w~~LQ~~V~~~~d~~~~~~~~-----~~~  503 (621)
                      |+|.+|++||+.|+.|++.+..   +                .....+.+.|..||.+|+.||||+  ..+.     ..+
T Consensus       260 dlt~~~~~Ii~~n~~l~~~~~~---~----------------~~~~~~~~~~~~LQ~~v~~~~dn~--~~~~~~~~~~~~  318 (1449)
T d1twfa_         260 DLTFKLADILKANISLETLEHN---G----------------APHHAIEEAESLLQFHVATYMDND--IAGQPQALQKSG  318 (1449)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSS---C----------------CCHHHHHHHHHHHHHHHHHHHCCC--SSCCCCCSSCTT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHc---C----------------CcHHHHHHHHHHHHHHHHHhcccc--ccCCchhccccC
Confidence            9999999999999999976521   1                122356789999999999999998  4432     124


Q ss_pred             CCccchHHhhccCccccccccCCCccCcccceeecCCCCCccccccchHHHHhhCCcCcccCHHHHHHHHHHHHcCCCCC
Q psy16766        504 HQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVY  583 (621)
Q Consensus       504 k~~~gi~q~L~gKeG~fR~nlmGKRVnfsaRSVIsPDP~l~idevGvP~~fAk~LT~PE~VT~~Ni~~Lr~lV~NGp~~~  583 (621)
                      ++.+||+|+|+||+||||+|||||||||||||||||||+|++||||||..||++|||||+||+||+++|+++|+|||++|
T Consensus       319 ~~~k~i~~~L~gK~GrfR~nl~GKRVd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~~n~~~l~~~v~ng~~~~  398 (1449)
T d1twfa_         319 RPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEH  398 (1449)
T ss_dssp             CCCCCSTTSCTTTTTTSSGGGTTCSCCSEEEEEEEECTTSCTTEEEEEHHHHTTCEEEEECCTTTHHHHHHHHHHTTTSS
T ss_pred             CCccchhhHhccchhhhhhhccccccccccceeeccCCccceeecccHHHHHhhCCCCeeecHHHHHHHHHHHHcCCccC
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcceEEEcCCCcEEEeCCC
Q psy16766        584 PGANMIQNEDGSVVRISSS  602 (621)
Q Consensus       584 PGA~~i~~~~G~~~~L~~~  602 (621)
                      |||++++.++|.++.|+..
T Consensus       399 pga~~~~~~~g~~~~l~~~  417 (1449)
T d1twfa_         399 PGAKYVIRDSGDRIDLRYS  417 (1449)
T ss_dssp             SCEEEEECTTCCEEETTSC
T ss_pred             CcccceecccCceEEEecc
Confidence            9999999999999998765
>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