Psyllid ID: psy3022

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-------26
MLALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETACNAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLYIILRPATHYQVELISGARRVASLRLFGQEPPFLY
cccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHcccccHHHHHHHHHHHHccEEcccccccccccccccccccccccccccccccccccccccccHHHHHHcccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHccccccccccEEEEEEccccccccccccccHHHHHccccccccccEEEEcccccHHcHHHHHHHHHHHccccHHHHHHHHccccccccEEEccHHHHHHHHHHccccccccc
cccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHccHHHEEEEcccccEEEEEEEEEEEccccccccEccccccccccccccccccccccccccEHHHHccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHcHHHHHHHHEHccccccccccEEEEEEEEcccccccccccccHHHHHHHHcccccccEEEEEccHHHccHHHHHHHHHHHHHHHHHHcEEEEEcccccccEccHHHcHHHHccccccccccccc
MLALKQTFENQVNRILNdardktggsakksLTEYNNLKAMVVAgskgsninISQVIACVGqqnvegkripfgfrkrtlphfikddygpesrgfvensylagltpsefffhamggreGLIDTAVKTAETacnakcapgeMVGALAaqslgepatqmtlntfhfagvssknvtlgvprlkeiiniskkpkapsltvFLTGQAARDAEKAKNVLCRLEHTTLRKVLYIILRPATHYQVELISGARRVASLRlfgqeppfly
MLALKQTFENQVnrilndardktggsakkslteyNNLKAMVVAGSKGSNINISQVIACVgqqnvegkripfgfrkrtlphfikddygpesRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETACNAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIiniskkpkapslTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLYIILRPATHYQVELISGARRVASLRLFGQEPPFLY
MLALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETACNAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLYIILRPATHYQVELISGARRVASLRLFGQEPPFLY
*********************************YNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETACNAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLYIILRPATHYQVELISGARRVASLRLF********
MLALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETACNAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLYIILRPATHYQVELISGARRVASLRLFGQEPPFLY
MLALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETACNAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLYIILRPATHYQVELISGARRVASLRLFGQEPPFLY
****KQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETACNAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLYIILRPATHYQVELISGARRVASLRLFGQEPPFLY
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MLALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETACNAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLYIILRPATHYQVELISGARRVASLRLFGQEPPFLY
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 ?
Query258 2.2.26 [Sep-21-2011]
P04052 1887 DNA-directed RNA polymera yes N/A 0.488 0.066 0.952 6e-68
P16356 1856 DNA-directed RNA polymera yes N/A 0.488 0.067 0.880 3e-63
P35074 1853 DNA-directed RNA polymera N/A N/A 0.488 0.067 0.880 4e-63
P24928 1970 DNA-directed RNA polymera yes N/A 0.488 0.063 0.888 4e-63
P08775 1970 DNA-directed RNA polymera yes N/A 0.488 0.063 0.888 5e-63
P18616 1839 DNA-directed RNA polymera yes N/A 0.484 0.067 0.816 3e-56
P35084 1727 DNA-directed RNA polymera yes N/A 0.476 0.071 0.813 2e-55
Q8SSC4 1599 DNA-directed RNA polymera yes N/A 0.492 0.079 0.734 4e-52
P36594 1752 DNA-directed RNA polymera yes N/A 0.496 0.073 0.734 7e-50
Q75A34 1745 DNA-directed RNA polymera yes N/A 0.496 0.073 0.726 1e-49
>sp|P04052|RPB1_DROME DNA-directed RNA polymerase II subunit RPB1 OS=Drosophila melanogaster GN=RpII215 PE=3 SV=4 Back     alignment and function desciption
 Score =  257 bits (656), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 120/126 (95%), Positives = 125/126 (99%)

Query: 4   LKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQN 63
           L+QTFEN+VNRILNDARDKTGGSAKKSLTEYNNLKAMVV+GSKGSNINISQVIACVGQQN
Sbjct: 725 LRQTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQN 784

Query: 64  VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAV 123
           VEGKRIP+GFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEF+FHAMGGREGLIDTAV
Sbjct: 785 VEGKRIPYGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAV 844

Query: 124 KTAETA 129
           KTAET 
Sbjct: 845 KTAETG 850
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.
Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6
>sp|P16356|RPB1_CAEEL DNA-directed RNA polymerase II subunit RPB1 OS=Caenorhabditis elegans GN=ama-1 PE=1 SV=3 Back     alignment and function description
>sp|P35074|RPB1_CAEBR DNA-directed RNA polymerase II subunit RPB1 OS=Caenorhabditis briggsae GN=rpb-1 PE=3 SV=2 Back     alignment and function description
>sp|P24928|RPB1_HUMAN DNA-directed RNA polymerase II subunit RPB1 OS=Homo sapiens GN=POLR2A PE=1 SV=2 Back     alignment and function description
>sp|P08775|RPB1_MOUSE DNA-directed RNA polymerase II subunit RPB1 OS=Mus musculus GN=Polr2a PE=1 SV=3 Back     alignment and function description
>sp|P18616|RPB1_ARATH DNA-directed RNA polymerase II subunit RPB1 OS=Arabidopsis thaliana GN=RPB205 PE=1 SV=3 Back     alignment and function description
>sp|P35084|RPB1_DICDI DNA-directed RNA polymerase II subunit rpb1 OS=Dictyostelium discoideum GN=polr2a PE=2 SV=2 Back     alignment and function description
>sp|Q8SSC4|RPB1_ENCCU DNA-directed RNA polymerase II subunit RPB1 OS=Encephalitozoon cuniculi (strain GB-M1) GN=RPB1 PE=3 SV=1 Back     alignment and function description
>sp|P36594|RPB1_SCHPO DNA-directed RNA polymerase II subunit rpb1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb1 PE=1 SV=1 Back     alignment and function description
>sp|Q75A34|RPB1_ASHGO DNA-directed RNA polymerase II subunit RPB1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=RPB1 PE=3 SV=2 Back     alignment and function description

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 ?
Query258
31127054 543 RNA polymerase II largest subunit [Triop 0.492 0.233 0.976 1e-67
31127026 445 RNA polymerase II largest subunit [Machi 0.492 0.285 0.976 1e-67
324120568 1792 RNA polymerase II largest subunit [Metyl 0.488 0.070 0.984 1e-67
324120510 1549 RNA polymerase II largest subunit [Pedet 0.488 0.081 0.984 1e-67
324120512 1882 RNA polymerase II largest subunit [Petro 0.488 0.066 0.984 2e-67
324120530 1697 RNA polymerase II largest subunit [Apost 0.488 0.074 0.984 2e-67
357628227 1895 largest subunit of the RNA polymerase II 0.488 0.066 0.976 2e-67
321464303 1895 hypothetical protein DAPPUDRAFT_306846 [ 0.488 0.066 0.976 2e-67
38232323 624 RNA polymerase II largest subunit [Neogo 0.492 0.203 0.968 2e-67
38232303 445 RNA polymerase II largest subunit [Lynce 0.492 0.285 0.976 3e-67
>gi|31127054|gb|AAC03142.2| RNA polymerase II largest subunit [Triops longicaudatus] Back     alignment and taxonomy information
 Score =  262 bits (670), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 124/127 (97%), Positives = 125/127 (98%)

Query: 3   ALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQ 62
            L+QTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQ
Sbjct: 192 TLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQ 251

Query: 63  NVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTA 122
           NVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTA
Sbjct: 252 NVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTA 311

Query: 123 VKTAETA 129
           VKTAET 
Sbjct: 312 VKTAETG 318

Source: Triops longicaudatus

Species: Triops longicaudatus

Genus: Triops

Family: Triopsidae

Order: Notostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|31127026|gb|AAF26640.2|AF138990_1 RNA polymerase II largest subunit [Machiloides banksi] Back     alignment and taxonomy information
>gi|324120568|dbj|BAJ78675.1| RNA polymerase II largest subunit [Metylophorus sp. E-43] Back     alignment and taxonomy information
>gi|324120510|dbj|BAJ78646.1| RNA polymerase II largest subunit [Pedetontus unimaculatus] Back     alignment and taxonomy information
>gi|324120512|dbj|BAJ78647.1| RNA polymerase II largest subunit [Petrobiellus takunagae] Back     alignment and taxonomy information
>gi|324120530|dbj|BAJ78656.1| RNA polymerase II largest subunit [Aposthonia japonica] Back     alignment and taxonomy information
>gi|357628227|gb|EHJ77617.1| largest subunit of the RNA polymerase II complex [Danaus plexippus] Back     alignment and taxonomy information
>gi|321464303|gb|EFX75312.1| hypothetical protein DAPPUDRAFT_306846 [Daphnia pulex] Back     alignment and taxonomy information
>gi|38232323|gb|AAR14997.1| RNA polymerase II largest subunit [Neogonodactylus oerstedii] Back     alignment and taxonomy information
>gi|38232303|gb|AAR14987.1| RNA polymerase II largest subunit [Lynceus sp. JCR-2003] 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 ?
Query258
FB|FBgn0003277 1887 RpII215 "RNA polymerase II 215 0.484 0.066 0.96 6.9e-102
ZFIN|ZDB-GENE-041008-78 1965 polr2a "polymerase (RNA) II (D 0.484 0.063 0.912 7.1e-96
UNIPROTKB|J9NW09 1789 POLR2A "DNA-directed RNA polym 0.484 0.069 0.896 7.5e-95
UNIPROTKB|F1PGS0 1969 POLR2A "DNA-directed RNA polym 0.484 0.063 0.896 1e-94
UNIPROTKB|G3MZY8 1970 POLR2A "DNA-directed RNA polym 0.484 0.063 0.896 1e-94
UNIPROTKB|P24928 1970 POLR2A "DNA-directed RNA polym 0.484 0.063 0.896 1e-94
MGI|MGI:98086 1970 Polr2a "polymerase (RNA) II (D 0.484 0.063 0.896 1e-94
RGD|1587326 1970 Polr2a "polymerase (RNA) II (D 0.484 0.063 0.896 1e-94
WB|WBGene00000123 1856 ama-1 [Caenorhabditis elegans 0.484 0.067 0.888 1.8e-92
UNIPROTKB|P16356 1856 ama-1 "DNA-directed RNA polyme 0.484 0.067 0.888 1.8e-92
FB|FBgn0003277 RpII215 "RNA polymerase II 215kD subunit" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 628 (226.1 bits), Expect = 6.9e-102, Sum P(2) = 6.9e-102
 Identities = 120/125 (96%), Positives = 125/125 (100%)

Query:     4 LKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQN 63
             L+QTFEN+VNRILNDARDKTGGSAKKSLTEYNNLKAMVV+GSKGSNINISQVIACVGQQN
Sbjct:   725 LRQTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQN 784

Query:    64 VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAV 123
             VEGKRIP+GFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEF+FHAMGGREGLIDTAV
Sbjct:   785 VEGKRIPYGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAV 844

Query:   124 KTAET 128
             KTAET
Sbjct:   845 KTAET 849
GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISS;NAS;IDA
GO:0005703 "polytene chromosome puff" evidence=IDA
GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS;NAS
GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;NAS
GO:0005634 "nucleus" evidence=IDA
GO:0003677 "DNA binding" evidence=IEA
GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IGI
GO:0005700 "polytene chromosome" evidence=IDA
ZFIN|ZDB-GENE-041008-78 polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|J9NW09 POLR2A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|F1PGS0 POLR2A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|G3MZY8 POLR2A "DNA-directed RNA polymerase" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|P24928 POLR2A "DNA-directed RNA polymerase II subunit RPB1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:98086 Polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1587326 Polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
WB|WBGene00000123 ama-1 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
UNIPROTKB|P16356 ama-1 "DNA-directed RNA polymerase II subunit RPB1" [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
P08775RPB1_MOUSE2, ., 7, ., 7, ., 60.88880.48830.0639yesN/A
Q75A34RPB1_ASHGO2, ., 7, ., 7, ., 60.72650.49610.0733yesN/A
P16356RPB1_CAEEL2, ., 7, ., 7, ., 60.88090.48830.0678yesN/A
P04050RPB1_YEAST2, ., 7, ., 7, ., 60.71870.49610.0738yesN/A
P04052RPB1_DROME2, ., 7, ., 7, ., 60.95230.48830.0667yesN/A
P18616RPB1_ARATH2, ., 7, ., 7, ., 60.8160.48440.0679yesN/A
P35084RPB1_DICDI2, ., 7, ., 7, ., 60.81300.47670.0712yesN/A
P24928RPB1_HUMAN2, ., 7, ., 7, ., 4, 80.88880.48830.0639yesN/A
Q58445RPOA1_METJA2, ., 7, ., 7, ., 60.50780.49610.0954yesN/A
P36594RPB1_SCHPO2, ., 7, ., 7, ., 60.73430.49610.0730yesN/A
Q8SSC4RPB1_ENCCU2, ., 7, ., 7, ., 60.73430.49220.0794yesN/A
Q5ZL98RPC1_CHICK2, ., 7, ., 7, ., 60.5360.42240.0784yesN/A

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 ?
Query258
cd02584 410 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of 1e-63
PRK08566882 PRK08566, PRK08566, DNA-directed RNA polymerase su 2e-52
TIGR02390867 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer 3e-47
pfam05000108 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, do 1e-44
pfam04998 447 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do 5e-41
COG0086808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 3e-38
cd02736 300 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) o 1e-34
cd06528 363 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Pol 1e-33
cd02735 309 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of 9e-33
PRK04309 383 PRK04309, PRK04309, DNA-directed RNA polymerase su 3e-32
TIGR02389 367 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymer 3e-32
PRK14977 1321 PRK14977, PRK14977, bifunctional DNA-directed RNA 3e-30
PRK14897 509 PRK14897, PRK14897, unknown domain/DNA-directed RN 3e-28
cd00630158 cd00630, RNAP_largest_subunit_C, Largest subunit o 2e-23
PRK14977 1321 PRK14977, PRK14977, bifunctional DNA-directed RNA 5e-22
PRK14898 858 PRK14898, PRK14898, DNA-directed RNA polymerase su 5e-16
pfam04998 447 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do 3e-15
TIGR02386 1140 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, 6e-12
cd02655204 cd02655, RNAP_beta'_C, Largest subunit (beta') of 4e-11
COG0086 808 COG0086, RpoC, DNA-directed RNA polymerase, beta' 3e-10
PRK00566 1156 PRK00566, PRK00566, DNA-directed RNA polymerase su 3e-10
PRK14906 1460 PRK14906, PRK14906, DNA-directed RNA polymerase su 6e-10
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 2e-08
PRK02597 1331 PRK02597, rpoC2, DNA-directed RNA polymerase subun 2e-08
CHL00117 1364 CHL00117, rpoC2, RNA polymerase beta'' subunit; Re 6e-08
TIGR02388 1227 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase 3e-07
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 6e-07
TIGR02386 1140 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, 4e-05
PRK14906 1460 PRK14906, PRK14906, DNA-directed RNA polymerase su 2e-04
PRK14898 858 PRK14898, PRK14898, DNA-directed RNA polymerase su 5e-04
>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain Back     alignment and domain information 
 Score =  203 bits (520), Expect = 1e-63
 Identities = 65/91 (71%), Positives = 75/91 (82%)

Query: 132 AKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPS 191
           +   PGEMVG +AAQS+GEPATQMTLNTFHFAGVS+KNVTLGVPRLKEIIN++K  K PS
Sbjct: 22  SLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTPS 81

Query: 192 LTVFLTGQAARDAEKAKNVLCRLEHTTLRKV 222
           LTV+L    A+D EKAK +  RLEHTTL+ V
Sbjct: 82  LTVYLEPGFAKDEEKAKKIQSRLEHTTLKDV 112

RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures. Length = 410
>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|218372 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, domain 4 Back     alignment and domain information
>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5 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|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain Back     alignment and domain information
>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP) Back     alignment and domain information
>gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain Back     alignment and domain information
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A''; Validated Back     alignment and domain information
>gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A'' Back     alignment and domain information
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional Back     alignment and domain information
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional Back     alignment and domain information
>gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase (RNAP), C-terminal domain 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|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; Provisional Back     alignment and domain information
>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5 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|132721 cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain Back     alignment and domain information
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>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|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta'; Provisional Back     alignment and domain information
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed Back     alignment and domain information
>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed 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|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form 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|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A''; 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 258
PRK14977 1321 bifunctional DNA-directed RNA polymerase A'/A'' su 100.0
KOG0261|consensus 1386 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
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 100.0
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 100.0
CHL00117 1364 rpoC2 RNA polymerase beta'' subunit; Reviewed 100.0
PRK02597 1331 rpoC2 DNA-directed RNA polymerase subunit beta'; P 100.0
TIGR02388 1227 rpoC2_cyan DNA-directed RNA polymerase, beta'' sub 100.0
PF04998277 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; Int 100.0
TIGR02390868 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit 100.0
PRK08566882 DNA-directed RNA polymerase subunit A'; Validated 100.0
cd02584 410 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryoti 99.98
TIGR02389 367 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit 99.97
cd02736 300 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryot 99.97
cd06528 363 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (R 99.97
PRK04309 383 DNA-directed RNA polymerase subunit A''; Validated 99.97
cd02735 309 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic 99.97
PRK14897 509 unknown domain/DNA-directed RNA polymerase subunit 99.97
PF05000108 RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; Int 99.93
cd02737 381 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher 99.91
COG0086808 RpoC DNA-directed RNA polymerase, beta' subunit/16 99.84
cd02655204 RNAP_beta'_C Largest subunit (beta') of Bacterial 99.71
PRK14898 858 DNA-directed RNA polymerase subunit A''; Provision 99.62
cd00630158 RNAP_largest_subunit_C Largest subunit of RNA poly 99.48
COG0086 808 RpoC DNA-directed RNA polymerase, beta' subunit/16 98.29
PRK14898 858 DNA-directed RNA polymerase subunit A''; Provision 98.08
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional Back     alignment and domain information 
Probab=100.00  E-value=2.5e-70  Score=579.00  Aligned_cols=230  Identities=39%  Similarity=0.678  Sum_probs=220.2

Q ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHhhcCCCcChhhHHHHHhhhcccccC--------CcccCCCC
Q psy3022           2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVE--------GKRIPFGF   73 (258)
Q Consensus         2 ~~~~~~~E~~v~~~l~~~~~~~~~~~~~~~~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~~~--------G~ri~~~~   73 (258)
                      ++.+|++|.+++++|+++|+++++.+.++++++|++++|+.||||||+.|++||++|||||.++        |+|||.+|
T Consensus       719 ~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~l~~Mv~SGAKGS~~Ni~Qi~~~lGQQ~ve~~~~~~~~G~Ri~~~~  798 (1321)
T PRK14977        719 MKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGRLHEGY  798 (1321)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHhhcccccCHHHHHHHHhccccccccccccccCCCCCCcCCC
Confidence            5788999999999999999999999999999999999999999999999999999999999999        99999999


Q ss_pred             CCCCCCCCcCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccCC-----------------------
Q psy3022          74 RKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETAC-----------------------  130 (258)
Q Consensus        74 ~~r~lp~f~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG~-----------------------  130 (258)
                      ++|+||||.++|.+|+++|||.|||++||+|.|||||||||||||+|||||||+|||                       
T Consensus       799 ~~RtLPhF~~~d~~p~a~GfV~nsFl~GL~P~EfFFHaM~GREGLiDTAVKTA~SGYLQRrLvk~lEDl~v~YD~TVR~s  878 (1321)
T PRK14977        799 KDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDP  878 (1321)
T ss_pred             CCCcCCCCCCCCCCcccccchhhhhcCCCCHHHHHHHhhcccccccccccccCcCchhHHHHHHHhcceEEecCCeEEeC
Confidence            999999999999999999999999999999999999999999999999999999991                       


Q ss_pred             -------------------------C------------------------------------------------------
Q psy3022         131 -------------------------N------------------------------------------------------  131 (258)
Q Consensus       131 -------------------------~------------------------------------------------------  131 (258)
                                               +                                                      
T Consensus       879 ~g~iiQF~YGeDG~d~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  958 (1321)
T PRK14977        879 HGHIIQFKFGEDGIDPQKLDHGEAFNLERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNANLPKLLADAIHGAELKEDE  958 (1321)
T ss_pred             CCCEEEEeecCCCcCHHHhccCCcccHHHHHHHhhhhccccCCCHHHHHHHHHHHHHhhhhhhHHHHHHHHHHcCCCHHH
Confidence                                     0                                                      


Q ss_pred             --------------CccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhccCCCCCeEEEEec
Q psy3022         132 --------------AKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLT  197 (258)
Q Consensus       132 --------------~~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~~~t~~~~v~L~  197 (258)
                                    ..++||||||++||||||||+|||||||||+||+++++||+|+|||+||++++++++||.|+++|.
T Consensus       959 ~~~~~~~~~~~~~~~~~~pGe~VG~iaAQSiGEP~TQmTLnTFH~AGv~~~nvt~GvpRl~Eii~a~k~~~tp~m~~~l~ 1038 (1321)
T PRK14977        959 LEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLD 1038 (1321)
T ss_pred             HHHHHHHHHHHHHhcccCCcccchhhhhhhccCceeeecccccccccccccCcccCccchHHhhhcccCCCCCeEEEEeC
Confidence                          027899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcchhcHHHHHHHhccccceeccceeE---EEEcCCC
Q psy3022         198 GQAARDAEKAKNVLCRLEHTTLRKVLY---IILRPAT  231 (258)
Q Consensus       198 ~~~~~~~~~a~~v~~~L~~~~l~~v~~---I~ydp~~  231 (258)
                      +++..+++.|+.++.+|++++|++++.   +.|||+.
T Consensus      1039 ~~~~~~~~~a~~v~~~ie~~~l~~~~~~~~i~~~~~~ 1075 (1321)
T PRK14977       1039 DECKEDIEKAIEIARNLKELKVRALIADSAIDNANEI 1075 (1321)
T ss_pred             CcccchHHHHHHHHhheeeeEHHHhhhheEeeccCCc
Confidence            987778899999999999999999987   7788764

>KOG0261|consensus 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
>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
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed Back     alignment and domain information
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional Back     alignment and domain information
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit Back     alignment and domain information
>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
>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
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain Back     alignment and domain information
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A'' Back     alignment and domain information
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain Back     alignment and domain information
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP) Back     alignment and domain information
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated Back     alignment and domain information
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain Back     alignment and domain information
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional 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
>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain Back     alignment and domain information
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain Back     alignment and domain information
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional Back     alignment and domain information
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain Back     alignment and domain information
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] Back     alignment and domain information
>PRK14898 DNA-directed RNA polymerase subunit A''; 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 ?
Query258
3h0g_A 1752 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 5e-51
3h0g_A 1752 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 2e-30
3j0k_A 1455 Orientation Of Rna Polymerase Ii Within The Human V 2e-50
3j0k_A 1455 Orientation Of Rna Polymerase Ii Within The Human V 1e-28
4a3c_A 1732 Rna Polymerase Ii Initial Transcribing Complex With 3e-50
4a3c_A 1732 Rna Polymerase Ii Initial Transcribing Complex With 1e-28
1i3q_A 1733 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 3e-50
1i3q_A 1733 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 2e-28
2waq_A880 The Complete Structure Of The Archaeal 13-Subunit D 2e-28
2pmz_A880 Archaeal Rna Polymerase From Sulfolobus Solfataricu 2e-28
3hkz_C 395 The X-Ray Crystal Structure Of Rna Polymerase From 1e-23
2pmz_C 392 Archaeal Rna Polymerase From Sulfolobus Solfataricu 1e-23
2y0s_C 395 Crystal Structure Of Sulfolobus Shibatae Rna Polyme 2e-23
2waq_C 395 The Complete Structure Of The Archaeal 13-Subunit D 2e-23
4gzy_D 1534 Crystal Structures Of Bacterial Rna Polymerase Paus 5e-09
1iw7_D 1524 Crystal Structure Of The Rna Polymerase Holoenzyme 5e-09
1l9u_D 1524 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 1e-08
2gho_D 1233 Recombinant Thermus Aquaticus Rna Polymerase For St 1e-08
1i6v_D 1264 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 1e-08
1hqm_D 1265 Crystal Structure Of Thermus Aquaticus Core Rna Pol 2e-08
3iyd_D 1413 Three-Dimensional Em Structure Of An Intact Activat 4e-05
3lu0_D 1407 Molecular Model Of Escherichia Coli Core Rna Polyme 4e-05
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 Back     alignment and structure 
Iteration: 1

 Score =  197 bits (500), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 94/128 (73%), Positives = 106/128 (82%)
Query: 2   LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQ 61
           + L+++FE +V+RILN ARD  G SA+ SL + NN+K MV AGSKGS INISQ+ ACVGQ
Sbjct: 714 MTLRESFEAKVSRILNQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQ 773
Query: 62  QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDT 121
           Q VEGKRIPFGF+ RTLPHF KDD  PESRGF+ENSYL GLTP EFFFHAM GREGLIDT
Sbjct: 774 QIVEGKRIPFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDT 833
Query: 122 AVKTAETA 129
           AVKTAET 
Sbjct: 834 AVKTAETG 841
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 Back     alignment and structure
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455 Back     alignment and structure
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455 Back     alignment and structure
>pdb|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|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 880 Back     alignment and structure
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 880 Back     alignment and structure
>pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea Length = 395 Back     alignment and structure
>pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 392 Back     alignment and structure
>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In P21 Space Group Length = 395 Back     alignment and structure
>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 395 Back     alignment and structure
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused Elongation Complexes Length = 1534 Back     alignment and structure
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1524 Back     alignment and structure
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1524 Back     alignment and structure
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For Structural Studies Length = 1233 Back     alignment and structure
>pdb|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|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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query258
4ayb_A880 DNA-directed RNA polymerase; transferase, multi-su 6e-81
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 2e-69
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 4e-43
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 7e-69
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 4e-41
4ayb_C 395 DNA-directed RNA polymerase; transferase, multi-su 7e-46
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 2e-11
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 2e-11
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 7e-04
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 3e-11
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 4e-04
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-05
>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
 Score =  259 bits (663), Expect = 6e-81
 Identities = 58/125 (46%), Positives = 83/125 (66%)

Query: 4   LKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQN 63
           L+++ EN +   L+  R   G  A K L  +N    M   G++GS +NI+Q+ A +GQQ+
Sbjct: 692 LEESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQS 751

Query: 64  VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAV 123
           V G+RI  G+  RTLPHF   D  PE+RGF+ +S+  GL P+E FFHA GGREGL+DTAV
Sbjct: 752 VRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAV 811

Query: 124 KTAET 128
           +T+++
Sbjct: 812 RTSQS 816
>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
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C Length = 395 Back     alignment and structure
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query258
3h0g_A 1752 DNA-directed RNA polymerase II subunit RPB1; trans 100.0
1twf_A 1733 B220, DNA-directed RNA polymerase II largest subun 100.0
3lu0_D 1407 DNA-directed RNA polymerase subunit beta'; E. coli 100.0
1hqm_D 1265 DNA-directed RNA polymerase; transferase, transcri 100.0
2a6h_D 1524 DNA-directed RNA polymerase beta' chain; RNA polym 100.0
4ayb_A880 DNA-directed RNA polymerase; transferase, multi-su 100.0
4ayb_C 395 DNA-directed RNA polymerase; transferase, multi-su 99.96
2auk_A190 DNA-directed RNA polymerase beta' chain; sandwich- 95.37
>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=9.5e-71  Score=593.22  Aligned_cols=233  Identities=67%  Similarity=0.989  Sum_probs=222.9

Q ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHhhcCCCcChhhHHHHHhhhcccccCCcccCCCCCCCCCCCC
Q psy3022           2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHF   81 (258)
Q Consensus         2 ~~~~~~~E~~v~~~l~~~~~~~~~~~~~~~~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~~~G~ri~~~~~~r~lp~f   81 (258)
                      ||++|++|.+|+++|+++++++++.++++++++|++++|+.||||||+.|++||+||||||.++|+|||++|.+|+||||
T Consensus       714 ~~~~e~~e~~v~~~l~~~~~~~~~~~~~~l~~~N~~~~M~~SGakGs~~ni~Q~~~~~Gqq~~~GkrIp~g~~~rtLP~f  793 (1752)
T 3h0g_A          714 MTLRESFEAKVSRILNQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPHF  793 (1752)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHHHHHHHHTTSCSSCTTTHHHHHCSSCCHHHHHHHHTCCCCCCSTTSSSCCCSTTSSSTTS
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHhhhccccCHHHHHHHHhccCCCccCCccCCCCCCCccCCCC
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccC--------------------------------
Q psy3022          82 IKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETA--------------------------------  129 (258)
Q Consensus        82 ~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG--------------------------------  129 (258)
                      .++|.+++++|||.|||++||+|.|||||||||||||+|||||||+||                                
T Consensus       794 ~k~d~~~~a~GfV~~sF~~GL~p~EfFfhtmggReGLiDTAvKTA~SGYLqRRLVk~leDv~V~YDgTVRns~g~ivQF~  873 (1752)
T 3h0g_A          794 PKDDDSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFA  873 (1752)
T ss_dssp             CSSCCSTTTSSCCSSCTTTCCCHHHHHHHHHHHTTTTTHHHHTTTHHHHHHHHHHHHHTTCEEETTTEEECTTSCEEESS
T ss_pred             CCCCCCcccCcchhhcccCCCCHHHHHHHhhhhhhhhhHhhhhcCcCchhHHHHHHHHhheEEeeCCeeEcCCCcEEEEe
Confidence            999999999999999999999999999999999999999999999999                                


Q ss_pred             ---------------C----------------C------------------------------------------C----
Q psy3022         130 ---------------C----------------N------------------------------------------A----  132 (258)
Q Consensus       130 ---------------~----------------~------------------------------------------~----  132 (258)
                                     +                .                                          +    
T Consensus       874 YGeDGlD~~~~e~q~~~~~~~s~~~f~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~E~~~l~~dr~~lr~~i~~~~  953 (1752)
T 3h0g_A          874 YGEDGLDATLVEYQVFDSLRLSTKQFEKKYRIDLMEDRSLSLYMENSIENDSSVQDLLDEEYTQLVADRELLCKFIFPKG  953 (1752)
T ss_dssp             SSSSCBCGGGEEEEECTTTSCCHHHHTTTSCCCTTTTCCGGGTSCSCCTTSCSSTHHHHHHHHHHHHHHTTSSSSSSSCS
T ss_pred             cCCCCcChHHhhccccccccCCHHHHHHHhcccccccccccHHHHHHhccCHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence                           0                0                                          0    


Q ss_pred             --------------------------------------------------------------------------------
Q psy3022         133 --------------------------------------------------------------------------------  132 (258)
Q Consensus       133 --------------------------------------------------------------------------------  132 (258)
                                                                                                      
T Consensus       954 ~~~~~lP~N~~R~i~~~~~~f~~~~~~~s~l~p~~~~~~v~~~~~~l~~~~g~d~l~~~~~~na~~l~~~~lr~~l~~k~ 1033 (1752)
T 3h0g_A          954 DARWPLPVNVQRIIQNALQIFHLEAKKPTDLLPSDIINGLNELIAKLTIFRGSDRITRDVQNNATLLFQILLRSKFAVKR 1033 (1752)
T ss_dssp             CCEEEEESCHHHHTTTTTTTSCCCTTSCCCCCHHHHHHHHHHHHTTCCCSCCCSTTTTHHHHTSSHHHHHHHTTSSSHHH
T ss_pred             cccccCCccHHHHHHHHHHhcCCCcCccCCCCHHHHHHHHHHHHHhhhcccCCcchhhhhhhchHHHHHHHHHhhhhhhh
Confidence                                                                                            


Q ss_pred             --------------------------ccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhccC
Q psy3022         133 --------------------------KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKK  186 (258)
Q Consensus       133 --------------------------~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~  186 (258)
                                                .|+|||+||+|||||||||+|||||||||+||++++|||+|||||+||||++|+
T Consensus      1034 ~~~~~~l~~~~~~~~~~~~~~~y~~a~v~pGe~VG~iaAQSIgEp~TQMTLnTFHfAGvas~NVTlGVPRLkEIInask~ 1113 (1752)
T 3h0g_A         1034 VIMEYRLNKVAFEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVAKN 1113 (1752)
T ss_dssp             HHHSSCCCHHHHHHHHHHHHHHHHTTBCCSSCCHHHHHHHHHHHHHHHHHHHTTSSCCCCCSSCCCSGGGHHHHHTTCSC
T ss_pred             hhhhcCcCHHHHHHHHHHHHHHHHHhccCcccchhhhhhcccCCchhhhhHHhhhhccccccccccCcccHHHHHhhhcC
Confidence                                      169999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEEecCcchhcHHHHHHHhccccceeccceeE---EEEcCCCcee
Q psy3022         187 PKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLY---IILRPATHYQ  234 (258)
Q Consensus       187 ~~t~~~~v~L~~~~~~~~~~a~~v~~~L~~~~l~~v~~---I~ydp~~~~~  234 (258)
                      +|||+|+++|.+++..++++|+.|+++|++++|++|++   |.|||+...+
T Consensus      1114 ikTP~mtv~L~~~~~~d~e~A~~v~~~ie~t~L~~v~~~~~i~~~p~~~~~ 1164 (1752)
T 3h0g_A         1114 IKTPSLTIYLMPWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDT 1164 (1752)
T ss_dssp             CSCCCCEECCCSSSCSSSTTTHHHHTTSSCCSSCSCCSCEEEECCCSTTCC
T ss_pred             CCCCeEEEEecCccccCHHHHHHHHHhhccEEHHHheeEEEEEEecCccce
Confidence            99999999999887778899999999999999999976   8999987654
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Back     alignment and structure
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Back     alignment and structure
>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
>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
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C Back     alignment and structure
>2auk_A DNA-directed RNA polymerase beta' chain; sandwich-barrel hybrid motif, transferase; 2.30A {Escherichia coli} 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 258
d1twfa_ 1449 e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c 7e-40
d1twfa_ 1449 e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c 1e-20
d1smyd_ 1504 e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t 5e-31
d1smyd_ 1504 e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t 2e-22
>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 =  144 bits (364), Expect = 7e-40
 Identities = 92/125 (73%), Positives = 106/125 (84%)

Query: 4   LKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQN 63
           L+++FE+ V R LN+ARDK G  A+ +L + NN+K MV+AGSKGS INI+Q+ ACVGQQ+
Sbjct: 709 LRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQS 768

Query: 64  VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAV 123
           VEGKRI FGF  RTLPHF KDDY PES+GFVENSYL GLTP EFFFHAMGGREGLIDTAV
Sbjct: 769 VEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAV 828

Query: 124 KTAET 128
           KTAET
Sbjct: 829 KTAET 833
>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 ?
Query258
d1twfa_ 1449 RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1smyd_ 1504 RNA-polymerase beta-prime {Thermus thermophilus [T 100.0
>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=5.5e-62  Score=519.20  Aligned_cols=232  Identities=66%  Similarity=0.995  Sum_probs=211.1

Q ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHhhcCCCcChhhHHHHHhhhcccccCCcccCCCCCCCCCCCC
Q psy3022           2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHF   81 (258)
Q Consensus         2 ~~~~~~~E~~v~~~l~~~~~~~~~~~~~~~~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~~~G~ri~~~~~~r~lp~f   81 (258)
                      ++.++++|.+++++|+++++++++++++.+.++|++++|+.||||||..|+.||+||+|||.+.|+|++.++.+|+||||
T Consensus       707 ~~~~~~~e~~v~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGakGs~~n~~Qi~g~~Gqq~~~g~ri~~~~~~r~lp~f  786 (1449)
T d1twfa_         707 MTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHF  786 (1449)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHTSSCCHHHHHHHHSCCEECCBTTBSCCCCBTTBSSTTS
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccchHhheeccccCCccchHHHHhhhhhhcccCccccccccccccccC
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccCC-------------------------------
Q psy3022          82 IKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETAC-------------------------------  130 (258)
Q Consensus        82 ~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG~-------------------------------  130 (258)
                      .+++.+|+++|||.+||++||+|.|||||||||||||+|||+|||+|||                               
T Consensus       787 ~~~~~~~~~~GfI~~sf~~GL~p~Eyf~h~~~gReGLiDTAvkTa~sGYl~RrLvk~ledv~v~yD~tvr~~~g~IiQf~  866 (1449)
T d1twfa_         787 SKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFI  866 (1449)
T ss_dssp             CTTCCSTTTTTEECSCTTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCEECTTSCEECTTCCEEESS
T ss_pred             CCCCCCccccCcccchhhhhhcchheeeeeccchhhhhhhcccccccHHHHHHHHHHhcCeEEEecCccCcCCceEEEEE
Confidence            9999999999999999999999999999999999999999999999990                               


Q ss_pred             -C------------------------------------------------------------------------------
Q psy3022         131 -N------------------------------------------------------------------------------  131 (258)
Q Consensus       131 -~------------------------------------------------------------------------------  131 (258)
                       +                                                                              
T Consensus       867 YGeDg~d~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~i~~~~~~~l~~~r~~l~~~~  946 (1449)
T d1twfa_         867 YGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVF  946 (1449)
T ss_dssp             GGGTTBCGGGEEEEECGGGSSCHHHHHHHHCCCTTCTTTSCCTTTBTTHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             EcCccccceEEEEeecceeccchHHhhhhhhhcccccccccChhHhhhhHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence             0                                                                              


Q ss_pred             --------------------------------------------------------------------------------
Q psy3022         132 --------------------------------------------------------------------------------  131 (258)
Q Consensus       132 --------------------------------------------------------------------------------  131 (258)
                                                                                                      
T Consensus       947 ~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 1026 (1449)
T d1twfa_         947 VDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLA 1026 (1449)
T ss_dssp             TTCCCEEEEESCHHHHHHHHHHHTTCCTTSCBCCCHHHHHHHHHHHHTTCCSCCCCSHHHHHHHHHTTHHHHHHHHHHSC
T ss_pred             cCccccccCcchHHHHHHhhhhhcccccCccccccHHHHHHHHHHHHhhhheecccchhhhhhcccccceeeeeeccccc
Confidence                                                                                            


Q ss_pred             ----------------------------CccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhh
Q psy3022         132 ----------------------------AKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINI  183 (258)
Q Consensus       132 ----------------------------~~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~  183 (258)
                                                  ..|+||||||++||||||||+|||||||||+||+++++||+|+|||+||+++
T Consensus      1027 ~~~~~~~~~l~~~~~~~~~~~~~~ky~~slv~pGEaVGiiAAQSIGEP~TQmTLnTFH~AG~~~~nvT~GiPRl~EIl~a 1106 (1449)
T d1twfa_        1027 TRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNV 1106 (1449)
T ss_dssp             HHHHHHTSCCCHHHHHHHHHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC----------CCSCCHHHHHHHHTTT
T ss_pred             hhhhhhhcccCHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhhccchhhhhhhhhhhcceeeecccccchhhhhheee
Confidence                                        0168999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCeEEEEecCcchhcHHHHHHHhccccceeccceeE---EEEcCCCce
Q psy3022         184 SKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLY---IILRPATHY  233 (258)
Q Consensus       184 ~~~~~t~~~~v~L~~~~~~~~~~a~~v~~~L~~~~l~~v~~---I~ydp~~~~  233 (258)
                      +++++||.++++|.+....+.++++.++..++.++++++..   +.|||++..
T Consensus      1107 sk~iktp~~~v~l~~~~~~~~~~~k~~~~~i~~~~l~~vv~~~~v~~~~~~~~ 1159 (1449)
T d1twfa_        1107 AKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRS 1159 (1449)
T ss_dssp             CSSCSSCEEEEEBCSSSSSCHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSS
T ss_pred             ecccCCcceeEEeccccchhHHHHHhhhheeeeeeccceeeeeEEEEcCCCce
Confidence            99999999999999887778899999999999999999987   889998754
>d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure