Psyllid ID: psy5332

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-------
MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHELSHDALAC
ccEEEEEEEEcccccHHHHHHHHccccccccccccccccccccccccccccccEEEEEEEEEEccccccEEEEccccccccEEEEcccccccccccccccccccEEEEcccccEEEEEEEEEEcccccccccccccEEEEEEcccccccccccccccccccccccccccccccccccEEEcccEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccc
cccEEEEEEccccHHHHHHHHHHccccEcccccHHHHccccccccccccccccEEEEEEEEEEcccccccEcccccEccccEEEEccccccccccccccccccEEEEEEccccEEEEEEEEEccccHHHccccccEEEEEEEccccccccccccccHHcccHHcccccccccccccccccccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEEccEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHcHcc
MAIDWVQLEanstvlsdefiasriglipltsdevvdrilysrdctcvdfcsecsveftldvkcvddqtrhvttadlkstdarvvpvtsrnrdadmneygetDDILIVKLRKGQELRLRAYAKKgfgkehakwnptagvcfeydpdnsmrhtlfpkpdewpkseyseldetqheapynweakpnkyffnvesagalkpeniVIMGVTVLKQKLSNLQTQLAHDRVFYVIneapynweakpnkyffnvesagalkpeniVIMGVTVLKQKLSNLQTQLAHELSHDALAC
MAIDWVQLEanstvlsdefiasriglipltsdevVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRhvttadlkstdarvvpvtsrnrdadmneygetddiliVKLRKGQELRLRAYAkkgfgkehakwnptAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAhelshdalac
MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHELSHDALAC
**IDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLK****RVV*************YGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYD********************************YNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNL***************
MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVV*************YGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHEL*****AC
MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHELSHDALAC
MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHELSHDALAC
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MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHELSHDALAC
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 ?
Query287 2.2.26 [Sep-21-2011]
Q3T0Q3275 DNA-directed RNA polymera yes N/A 0.773 0.807 0.716 9e-97
P19387275 DNA-directed RNA polymera yes N/A 0.773 0.807 0.711 4e-96
P97760275 DNA-directed RNA polymera yes N/A 0.773 0.807 0.689 8e-92
Q54DH7302 DNA-directed RNA polymera yes N/A 0.749 0.711 0.402 7e-47
P16370318 DNA-directed RNA polymera yes N/A 0.770 0.694 0.401 7e-43
P37382297 DNA-directed RNA polymera yes N/A 0.745 0.720 0.380 1e-39
Q39211319 DNA-directed RNA polymera yes N/A 0.843 0.758 0.387 9e-39
Q39212319 DNA-directed RNA polymera no N/A 0.850 0.764 0.354 1e-33
P16925310 Conjugation stage-specifi N/A N/A 0.860 0.796 0.308 8e-23
Q2NFZ6270 DNA-directed RNA polymera yes N/A 0.693 0.737 0.291 5e-20
>sp|Q3T0Q3|RPB3_BOVIN DNA-directed RNA polymerase II subunit RPB3 OS=Bos taurus GN=POLR2C PE=2 SV=1 Back     alignment and function desciption
 Score =  353 bits (906), Expect = 9e-97,   Method: Compositional matrix adjust.
 Identities = 159/222 (71%), Positives = 195/222 (87%)

Query: 1   MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
           +AIDWVQ++ANS+VL DEFIA R+GLIPLTSD++VD++ YSRDCTC +FC ECSVEFTLD
Sbjct: 45  IAIDWVQIDANSSVLHDEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLD 104

Query: 61  VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 120
           V+C +DQTRHVT+ DL S   RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAY
Sbjct: 105 VRCNEDQTRHVTSRDLISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAY 164

Query: 121 AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEA 180
           AKKGFGKEHAKWNPTAGV FEYDPDN++RHT++PKP+EWPKSEYSELDE + +APY+   
Sbjct: 165 AKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNG 224

Query: 181 KPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHD 222
           KP ++++NVES G+L+PE IV+  ++ LK+KLS+LQTQL+H+
Sbjct: 225 KPERFYYNVESCGSLRPETIVLSALSGLKKKLSDLQTQLSHE 266
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. 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. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft.
Bos taurus (taxid: 9913)
>sp|P19387|RPB3_HUMAN DNA-directed RNA polymerase II subunit RPB3 OS=Homo sapiens GN=POLR2C PE=1 SV=2 Back     alignment and function description
>sp|P97760|RPB3_MOUSE DNA-directed RNA polymerase II subunit RPB3 OS=Mus musculus GN=Polr2c PE=2 SV=1 Back     alignment and function description
>sp|Q54DH7|RPB3_DICDI DNA-directed RNA polymerase II subunit rpb3 OS=Dictyostelium discoideum GN=polr2c PE=3 SV=1 Back     alignment and function description
>sp|P16370|RPB3_YEAST DNA-directed RNA polymerase II subunit RPB3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB3 PE=1 SV=2 Back     alignment and function description
>sp|P37382|RPB3_SCHPO DNA-directed RNA polymerase II subunit RPB3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb3 PE=1 SV=2 Back     alignment and function description
>sp|Q39211|RPB3A_ARATH DNA-directed RNA polymerase II subunit RPB3-A OS=Arabidopsis thaliana GN=RPB36A PE=2 SV=1 Back     alignment and function description
>sp|Q39212|RPB3B_ARATH DNA-directed RNA polymerase II subunit RPB3-B OS=Arabidopsis thaliana GN=RPB36B PE=1 SV=2 Back     alignment and function description
>sp|P16925|CNJC_TETTH Conjugation stage-specific protein OS=Tetrahymena thermophila GN=CNJC PE=2 SV=1 Back     alignment and function description
>sp|Q2NFZ6|RPOD_METST DNA-directed RNA polymerase subunit D OS=Methanosphaera stadtmanae (strain DSM 3091) GN=rpoD PE=3 SV=1 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query287
242011218275 DNA-directed RNA polymerase II 33 kDa po 0.773 0.807 0.837 1e-111
307202125276 DNA-directed RNA polymerase II subunit R 0.773 0.804 0.828 1e-111
340719719273 PREDICTED: DNA-directed RNA polymerase I 0.773 0.813 0.833 1e-111
350400985276 PREDICTED: DNA-directed RNA polymerase I 0.773 0.804 0.833 1e-111
383848177276 PREDICTED: DNA-directed RNA polymerase I 0.773 0.804 0.828 1e-111
66517558276 PREDICTED: DNA-directed RNA polymerase I 0.773 0.804 0.824 1e-110
156551093276 PREDICTED: DNA-directed RNA polymerase I 0.773 0.804 0.833 1e-110
307175611276 DNA-directed RNA polymerase II subunit R 0.773 0.804 0.810 1e-110
40645083275 homologue of DNA-directed RNA polymerase 0.773 0.807 0.824 1e-109
195579088275 GD23930 [Drosophila simulans] gi|1941914 0.773 0.807 0.816 1e-108
>gi|242011218|ref|XP_002426352.1| DNA-directed RNA polymerase II 33 kDa polypeptide, putative [Pediculus humanus corporis] gi|212510429|gb|EEB13614.1| DNA-directed RNA polymerase II 33 kDa polypeptide, putative [Pediculus humanus corporis] Back     alignment and taxonomy information
 Score =  408 bits (1048), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 186/222 (83%), Positives = 208/222 (93%)

Query: 1   MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
           MAIDWVQLEANSTVL+DEFI+ R+GLIPLTSDEVVDRI Y+RDCTC+DFC ECSVEFTLD
Sbjct: 45  MAIDWVQLEANSTVLADEFISHRVGLIPLTSDEVVDRIQYTRDCTCLDFCPECSVEFTLD 104

Query: 61  VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 120
           VKC DD TRHVTTADLKS+D RV+PVTSR+R+ D +EYGE D+ILIVKLRKGQEL+LRAY
Sbjct: 105 VKCTDDHTRHVTTADLKSSDPRVLPVTSRHREDDTSEYGEADEILIVKLRKGQELKLRAY 164

Query: 121 AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEA 180
           AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTL+PKPDEWPKSEY+ELD+TQ EAPYNWEA
Sbjct: 165 AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLYPKPDEWPKSEYTELDDTQCEAPYNWEA 224

Query: 181 KPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHD 222
           +PNK++FNVES GAL+PENIV+MGV VLK KLSNLQTQL+ +
Sbjct: 225 RPNKFYFNVESVGALRPENIVMMGVAVLKNKLSNLQTQLSQE 266

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|307202125|gb|EFN81625.1| DNA-directed RNA polymerase II subunit RPB3 [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|340719719|ref|XP_003398295.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Bombus terrestris] Back     alignment and taxonomy information
>gi|350400985|ref|XP_003486021.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|383848177|ref|XP_003699728.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|66517558|ref|XP_624836.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Apis mellifera] gi|380029804|ref|XP_003698555.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Apis florea] Back     alignment and taxonomy information
>gi|156551093|ref|XP_001603079.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|307175611|gb|EFN65520.1| DNA-directed RNA polymerase II subunit RPB3 [Camponotus floridanus] Back     alignment and taxonomy information
>gi|40645083|dbj|BAD06460.1| homologue of DNA-directed RNA polymerase II subunit [Antheraea pernyi] gi|40645085|dbj|BAD06461.1| homologue of DNA-directed RNA polymerase II subunit [Antheraea pernyi] Back     alignment and taxonomy information
>gi|195579088|ref|XP_002079394.1| GD23930 [Drosophila simulans] gi|194191403|gb|EDX04979.1| GD23930 [Drosophila simulans] 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 ?
Query287
FB|FBgn0026373275 RpII33 "RNA polymerase II 33kD 0.773 0.807 0.811 7.9e-101
UNIPROTKB|Q3T0Q3275 POLR2C "DNA-directed RNA polym 0.773 0.807 0.716 2.8e-89
UNIPROTKB|E2RQ42275 POLR2C "Uncharacterized protei 0.773 0.807 0.716 2.8e-89
RGD|1306935275 Polr2c "polymerase (RNA) II (D 0.773 0.807 0.716 2.8e-89
UNIPROTKB|I3LCH3275 POLR2C "Uncharacterized protei 0.773 0.807 0.711 9.6e-89
UNIPROTKB|P19387275 POLR2C "DNA-directed RNA polym 0.773 0.807 0.711 1.2e-88
UNIPROTKB|E1BV97275 POLR2C "Uncharacterized protei 0.773 0.807 0.702 8.6e-88
ZFIN|ZDB-GENE-030131-6609275 polr2c "polymerase (RNA) II (D 0.773 0.807 0.684 1.1e-85
MGI|MGI:109299275 Polr2c "polymerase (RNA) II (D 0.773 0.807 0.689 1.7e-84
UNIPROTKB|D4A8A8330 Polr2c "Protein Polr2c" [Rattu 0.641 0.557 0.75 1.1e-76
FB|FBgn0026373 RpII33 "RNA polymerase II 33kD subunit" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 1000 (357.1 bits), Expect = 7.9e-101, P = 7.9e-101
 Identities = 181/223 (81%), Positives = 210/223 (94%)

Query:     1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
             +AIDWVQLEANSTVLSDEF+A RIGLIPL SD+VV+R+ Y+RDC C+DFC ECSVEFTLD
Sbjct:    45 LAIDWVQLEANSTVLSDEFLAHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLD 104

Query:    61 VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGET-DDILIVKLRKGQELRLRA 119
             VKC ++QTRHVTTADLKS++A+V+PVTSRN+  + NEYGE+ D+ILI+KLRKGQEL+LRA
Sbjct:   105 VKCSEEQTRHVTTADLKSSNAKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELKLRA 164

Query:   120 YAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWE 179
             YAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTL+PKPDEWPKSE++EL++ Q+EAPYNWE
Sbjct:   165 YAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLYPKPDEWPKSEHTELEDDQYEAPYNWE 224

Query:   180 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHD 222
             AKPNK+FFNVESAGALKPENIV+MGV VLK KLSNLQTQL+H+
Sbjct:   225 AKPNKFFFNVESAGALKPENIVVMGVQVLKNKLSNLQTQLSHE 267
GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;NAS
GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISS;IDA
GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS
GO:0046983 "protein dimerization activity" evidence=IEA
GO:0034605 "cellular response to heat" evidence=IEP
GO:0005634 "nucleus" evidence=IDA
GO:0005703 "polytene chromosome puff" evidence=IDA
GO:0005737 "cytoplasm" evidence=IDA
GO:0005875 "microtubule associated complex" evidence=IDA
GO:0003677 "DNA binding" evidence=IDA
UNIPROTKB|Q3T0Q3 POLR2C "DNA-directed RNA polymerase II subunit RPB3" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RQ42 POLR2C "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
RGD|1306935 Polr2c "polymerase (RNA) II (DNA directed) polypeptide C" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|I3LCH3 POLR2C "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|P19387 POLR2C "DNA-directed RNA polymerase II subunit RPB3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E1BV97 POLR2C "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-6609 polr2c "polymerase (RNA) II (DNA directed) polypeptide C" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
MGI|MGI:109299 Polr2c "polymerase (RNA) II (DNA directed) polypeptide C" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|D4A8A8 Polr2c "Protein Polr2c" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q8ZYQ3RPOD_PYRAE2, ., 7, ., 7, ., 60.33330.68290.7538yesN/A
Q54DH7RPB3_DICDINo assigned EC number0.40230.74910.7119yesN/A
A4WNA4RPOD_PYRAR2, ., 7, ., 7, ., 60.32900.69330.7683yesN/A
P16370RPB3_YEASTNo assigned EC number0.40170.77000.6949yesN/A
Q8U0E4RPOD_PYRFU2, ., 7, ., 7, ., 60.30610.65850.7241yesN/A
B1YC30RPOD_PYRNV2, ., 7, ., 7, ., 60.33760.69680.7633yesN/A
P97760RPB3_MOUSENo assigned EC number0.68910.77350.8072yesN/A
A1RSE3RPOD_PYRIL2, ., 7, ., 7, ., 60.33890.68980.7557yesN/A
O59303RPOD_PYRHO2, ., 7, ., 7, ., 60.30610.65850.7297yesN/A
Q39211RPB3A_ARATHNo assigned EC number0.38790.84320.7586yesN/A
P37382RPB3_SCHPONo assigned EC number0.38030.74560.7205yesN/A
P19387RPB3_HUMANNo assigned EC number0.71170.77350.8072yesN/A
Q3T0Q3RPB3_BOVINNo assigned EC number0.71620.77350.8072yesN/A

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.7LOW CONFIDENCE prediction!
4th Layer2.7.7.6LOW CONFIDENCE prediction!

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 ?
Query287
cd07031265 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic 1e-123
smart00662224 smart00662, RPOLD, RNA polymerases D 9e-64
cd07030259 cd07030, RNAP_D, D subunit of Archaeal RNA polymer 9e-45
PRK00783263 PRK00783, PRK00783, DNA-directed RNA polymerase su 7e-41
cd07028212 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polym 2e-38
cd07032291 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryoti 3e-28
pfam01000117 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA 9e-28
COG0202317 COG0202, RpoA, DNA-directed RNA polymerase, alpha 2e-21
PRK14979195 PRK14979, PRK14979, DNA-directed RNA polymerase su 5e-11
cd07030259 cd07030, RNAP_D, D subunit of Archaeal RNA polymer 1e-04
pfam0119388 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 di 2e-04
cd07032291 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryoti 8e-04
pfam0119388 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 di 0.001
>gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information 
 Score =  353 bits (907), Expect = e-123
 Identities = 128/226 (56%), Positives = 167/226 (73%), Gaps = 5/226 (2%)

Query: 1   MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
           +AID V++E N++VL DEFIA R+GLIPLTSD+V + + YSRDC C +FC +CSVE TLD
Sbjct: 39  LAIDLVEIEENTSVLHDEFIAHRLGLIPLTSDDVDEFLYYSRDCDCDEFCDKCSVELTLD 98

Query: 61  VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 120
           VKC  DQTR VT+ DL S+  +V  V       D  + GE D ILIVKLRKGQEL+LR  
Sbjct: 99  VKCTGDQTREVTSRDLVSSGPKVNDVVPVPIRNDSEDNGEEDGILIVKLRKGQELKLRCI 158

Query: 121 AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPD----EWPKSEYSELDE-TQHEAP 175
           AKKG GKEHAKW+PTA V FEYDPDN++RHT +   +    EWPKSE + ++E  + +A 
Sbjct: 159 AKKGIGKEHAKWSPTAAVTFEYDPDNALRHTDYWYLEDEDKEWPKSENACIEEPPEKDAL 218

Query: 176 YNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 221
           ++ +AKP+K++FNVES GAL PE IV+ G+ +LK+KL++LQ QL+ 
Sbjct: 219 FDIDAKPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLSE 264

The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. Length = 265
>gnl|CDD|214766 smart00662, RPOLD, RNA polymerases D Back     alignment and domain information
>gnl|CDD|132908 cd07030, RNAP_D, D subunit of Archaeal RNA polymerase Back     alignment and domain information
>gnl|CDD|234837 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D; Provisional Back     alignment and domain information
>gnl|CDD|132906 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polymerase Back     alignment and domain information
>gnl|CDD|132910 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information
>gnl|CDD|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain Back     alignment and domain information
>gnl|CDD|223280 COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription] Back     alignment and domain information
>gnl|CDD|237878 PRK14979, PRK14979, DNA-directed RNA polymerase subunit D; Provisional Back     alignment and domain information
>gnl|CDD|132908 cd07030, RNAP_D, D subunit of Archaeal RNA polymerase Back     alignment and domain information
>gnl|CDD|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation domain Back     alignment and domain information
>gnl|CDD|132910 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information
>gnl|CDD|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 287
KOG1522|consensus285 100.0
cd07032291 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly 100.0
KOG1521|consensus338 100.0
cd07031265 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme 100.0
cd07028212 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The 100.0
PRK00783263 DNA-directed RNA polymerase subunit D; Provisional 100.0
cd07030259 RNAP_D D subunit of Archaeal RNA polymerase. The D 100.0
smart00662224 RPOLD RNA polymerases D. DNA-directed RNA polymera 100.0
PRK14979195 DNA-directed RNA polymerase subunit D; Provisional 100.0
PF01000112 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert dom 99.97
PRK05182310 DNA-directed RNA polymerase subunit alpha; Provisi 99.94
COG0202317 RpoA DNA-directed RNA polymerase, alpha subunit/40 99.94
cd06928215 RNAP_alpha_NTD N-terminal domain of the Alpha subu 99.92
TIGR02027297 rpoA DNA-directed RNA polymerase, alpha subunit, b 99.91
CHL00013327 rpoA RNA polymerase alpha subunit 99.74
cd07031265 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme 98.89
KOG1522|consensus285 98.87
cd0046086 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA pol 98.44
cd07032291 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly 98.36
PRK00783263 DNA-directed RNA polymerase subunit D; Provisional 98.3
cd07030259 RNAP_D D subunit of Archaeal RNA polymerase. The D 98.14
KOG1521|consensus338 97.9
cd0046086 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA pol 97.82
cd07028212 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The 97.8
PF0119366 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation 97.79
PF0119366 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation 97.66
PRK14979195 DNA-directed RNA polymerase subunit D; Provisional 97.6
COG0202317 RpoA DNA-directed RNA polymerase, alpha subunit/40 97.51
smart00662224 RPOLD RNA polymerases D. DNA-directed RNA polymera 97.5
TIGR02027297 rpoA DNA-directed RNA polymerase, alpha subunit, b 96.17
PRK05182310 DNA-directed RNA polymerase subunit alpha; Provisi 93.5
PF1365677 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisatio 92.95
PF1365677 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisatio 91.04
cd0702985 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA pol 90.13
cd0692783 RNAP_L L subunit of Archaeal RNA polymerase. The a 89.82
PRK0114685 DNA-directed RNA polymerase subunit L; Provisional 89.81
cd06928215 RNAP_alpha_NTD N-terminal domain of the Alpha subu 89.31
cd0692693 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA poly 88.56
cd0702783 RNAP_RPB11_like RPB11 subunit of RNA polymerase. T 88.15
cd0692693 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA poly 83.06
COG176199 RPB11 DNA-directed RNA polymerase, subunit L [Tran 81.51
cd0702985 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA pol 81.37
PRK0114685 DNA-directed RNA polymerase subunit L; Provisional 80.05
>KOG1522|consensus Back     alignment and domain information 
Probab=100.00  E-value=4e-68  Score=459.53  Aligned_cols=222  Identities=61%  Similarity=1.030  Sum_probs=202.5

Q ss_pred             CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeCCceeCC
Q psy5332           1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTD   80 (287)
Q Consensus         1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~d   80 (287)
                      +|||+|+|.-|||||+|||||||||||||.|+..+ .|+|.+||.|+++|++|||+|+|+++|++++.+.|||+||++.+
T Consensus        44 iAID~VeIe~NssVL~DEFiAHRLGLIPl~S~~~~-~l~ytrdC~C~~~C~eCSVef~L~~kc~~d~T~~VtsrDL~s~~  122 (285)
T KOG1522|consen   44 IAIDLVEIEVNSSVLPDEFIAHRLGLIPLISDRIV-ELQYTRDCECDEFCPECSVEFTLDVKCTDDQTRDVTSRDLVSLD  122 (285)
T ss_pred             eEEEEEEEecccccccHHHHHhhhcceeccchhhh-hhhhcccCchhccCCcceEEEEEeeeecccceeeeehHhhhccC
Confidence            69999999999999999999999999999999854 59999999999999999999999999999999999999999999


Q ss_pred             CeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCCCCC---
Q psy5332          81 ARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPD---  157 (287)
Q Consensus        81 ~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~~~~---  157 (287)
                      +.|.|+.+. .........-+++|+|+|||+||+|+|+|+|+||+||+||||||+++++|.|+|.+.++|+.+|..+   
T Consensus       123 ~~v~pv~~~-~~~~~~~~~e~~gilI~KLRkgQELkLra~akKGigKeHAKWsPta~V~FeYDPdn~lrhT~y~~e~~~~  201 (285)
T KOG1522|consen  123 PTVTPVDSN-RGSEIDDDSESKGILIVKLRKGQELKLRAIAKKGIGKEHAKWSPTAAVAFEYDPDNKLRHTLYWFEEDDL  201 (285)
T ss_pred             CcccccccC-CCCccccccccCCcEEEEeecCCceeeeeeecccccccccccCCcceEEEEECccHhhhccCCCccccch
Confidence            999999972 2333334455789999999999999999999999999999999999999999999999999999766   


Q ss_pred             -CCCCCccCccccc-ccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhcccc
Q psy5332         158 -EWPKSEYSELDET-QHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRV  224 (287)
Q Consensus       158 -~~~~~~~~~~~~~-~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e~~  224 (287)
                       +||++-..++++. ....+|+....+|+|+|+|||+|+++|..+|.+|+++|++|++.+...++.+.+
T Consensus       202 ~Ewp~sk~~e~~~~~~e~~pyd~~~kpd~F~~~VEs~Gal~~~~iVl~gi~iLk~Kl~~l~~~l~~~~q  270 (285)
T KOG1522|consen  202 IEWPKSKNSELEEDPEEGAPYDPEGKPDKFYFNVESVGALPPSQIVLMGIDILKEKLAALRLALSTEDQ  270 (285)
T ss_pred             hhCCcccccCCCCCccccCCCCccCCCceEEEEeEecCCCCHHHHHHHHHHHHHHHHHHHHhhhcccch
Confidence             9999988777665 456788888899999999999999999999999999999999999988876544

>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information
>KOG1521|consensus Back     alignment and domain information
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase Back     alignment and domain information
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional Back     alignment and domain information
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase Back     alignment and domain information
>smart00662 RPOLD RNA polymerases D Back     alignment and domain information
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional Back     alignment and domain information
>PF01000 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert domain; InterPro: IPR011262 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional Back     alignment and domain information
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription] Back     alignment and domain information
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase Back     alignment and domain information
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type Back     alignment and domain information
>CHL00013 rpoA RNA polymerase alpha subunit Back     alignment and domain information
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information
>KOG1522|consensus Back     alignment and domain information
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase Back     alignment and domain information
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional Back     alignment and domain information
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase Back     alignment and domain information
>KOG1521|consensus Back     alignment and domain information
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase Back     alignment and domain information
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase Back     alignment and domain information
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional Back     alignment and domain information
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription] Back     alignment and domain information
>smart00662 RPOLD RNA polymerases D Back     alignment and domain information
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type Back     alignment and domain information
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional Back     alignment and domain information
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K Back     alignment and domain information
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K Back     alignment and domain information
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase Back     alignment and domain information
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional Back     alignment and domain information
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase Back     alignment and domain information
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase Back     alignment and domain information
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription] Back     alignment and domain information
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information
>PRK01146 DNA-directed RNA polymerase subunit L; 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 ?
Query287
1i3q_C318 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 5e-44
3i4m_C324 8-oxoguanine Containing Rna Polymerase Ii Elongatio 5e-44
3how_C347 Complete Rna Polymerase Ii Elongation Complex Iii W 5e-44
3j0k_C268 Orientation Of Rna Polymerase Ii Within The Human V 4e-43
3h0g_C297 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 9e-41
2pa8_D265 X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE 2e-17
2waq_D265 The Complete Structure Of The Archaeal 13-Subunit D 3e-17
>pdb|1I3Q|C Chain C, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 318 Back     alignment and structure 
Iteration: 1

 Score =  174 bits (441), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 94/234 (40%), Positives = 147/234 (62%), Gaps = 13/234 (5%)
Query: 1   MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
           +AID V++E N+TVL+DEFIA R+GLIPL S ++ +++ YSRDC C D C +CSV  TL 
Sbjct: 44  LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDI-EQLEYSRDCFCEDHCDKCSVVLTLQ 102
Query: 61  VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 120
                + T +V + DL      V  +  RN    + +  E + +LI KLRKGQEL+L   
Sbjct: 103 AFGESESTTNVYSKDL----VIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCV 158
Query: 121 AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLF----PKPDEWPKSEYSELDETQHEA-P 175
           AKKG  KEHAKW P A + FEYDP N ++HT +        EWP+S+  E ++  +E  P
Sbjct: 159 AKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDP 218
Query: 176 YNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNL---QTQLAHDRVFY 226
           ++++A+ + ++ NVES G++  + +V+ G+  L++K++++    TQ+  D+V +
Sbjct: 219 FDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVNF 272
>pdb|3I4M|C Chain C, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex D Length = 324 Back     alignment and structure
>pdb|3HOW|C Chain C, Complete Rna Polymerase Ii Elongation Complex Iii With A T-U Mismatch And A Frayed Rna 3'-Uridine Length = 347 Back     alignment and structure
>pdb|3J0K|C Chain C, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 268 Back     alignment and structure
>pdb|3H0G|C Chain C, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 297 Back     alignment and structure
>pdb|2PA8|D Chain D, X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE SULFOLOBUS Solfataricus Rna Polymerase Length = 265 Back     alignment and structure
>pdb|2WAQ|D Chain D, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 265 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 ?
Query287
1twf_C318 B44.5, DNA-directed RNA polymerase II 45 kDa polyp 9e-53
3h0g_C297 DNA-directed RNA polymerase II subunit RPB3; trans 3e-50
2pa8_D265 DNA-directed RNA polymerase subunit D; ferredoxin- 1e-47
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-10
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-04
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ... Length = 318 Back     alignment and structure
 Score =  174 bits (440), Expect = 9e-53
 Identities = 89/226 (39%), Positives = 137/226 (60%), Gaps = 10/226 (4%)

Query: 1   MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
           +AID V++E N+TVL+DEFIA R+GLIPL S ++ +++ YSRDC C D C +CSV  TL 
Sbjct: 44  LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDI-EQLEYSRDCFCEDHCDKCSVVLTLQ 102

Query: 61  VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 120
                + T +V + DL         +  RN    + +  E + +LI KLRKGQEL+L   
Sbjct: 103 AFGESESTTNVYSKDLVIVS----NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCV 158

Query: 121 AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLF----PKPDEWPKSEYSELD-ETQHEAP 175
           AKKG  KEHAKW P A + FEYDP N ++HT +        EWP+S+  E +       P
Sbjct: 159 AKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDP 218

Query: 176 YNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 221
           ++++A+ + ++ NVES G++  + +V+ G+  L++K++++   L  
Sbjct: 219 FDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQ 264
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 297 Back     alignment and structure
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D Length = 265 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 ?
Query287
3h0g_C297 DNA-directed RNA polymerase II subunit RPB3; trans 100.0
1twf_C318 B44.5, DNA-directed RNA polymerase II 45 kDa polyp 100.0
2pa8_D265 DNA-directed RNA polymerase subunit D; ferredoxin- 100.0
2a6h_A315 DNA-directed RNA polymerase alpha chain; RNA polym 100.0
1bdf_A235 RNA polymerase alpha subunit; nucleotidyltransfera 100.0
3lu0_A329 DNA-directed RNA polymerase subunit alpha; E. coli 99.96
1twf_C318 B44.5, DNA-directed RNA polymerase II 45 kDa polyp 98.51
3h0g_C297 DNA-directed RNA polymerase II subunit RPB3; trans 98.5
2pa8_D265 DNA-directed RNA polymerase subunit D; ferredoxin- 97.9
1bdf_A235 RNA polymerase alpha subunit; nucleotidyltransfera 97.48
2a6h_A315 DNA-directed RNA polymerase alpha chain; RNA polym 97.24
2pa8_L92 DNA-directed RNA polymerase subunit L; ferredoxin- 92.91
2pa8_L92 DNA-directed RNA polymerase subunit L; ferredoxin- 92.29
3h0g_K123 DNA-directed RNA polymerase II subunit RPB11; tran 91.69
3h0g_K123 DNA-directed RNA polymerase II subunit RPB11; tran 91.49
1twf_K120 B13.6, DNA-directed RNA polymerase II 13.6 kDa pol 90.67
3lu0_A329 DNA-directed RNA polymerase subunit alpha; E. coli 90.1
1twf_K120 B13.6, DNA-directed RNA polymerase II 13.6 kDa pol 89.5
1xpp_A115 TA1416, DNA-directed RNA polymerase subunit L; str 88.31
1xpp_A115 TA1416, DNA-directed RNA polymerase subunit L; str 88.28
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
Probab=100.00  E-value=3.4e-59  Score=425.79  Aligned_cols=214  Identities=39%  Similarity=0.791  Sum_probs=186.8

Q ss_pred             CeeeEEEEeeCCCcchhhHhhhhcCccccccccccc----cceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeCCc
Q psy5332           1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVD----RILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL   76 (287)
Q Consensus         1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~----~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl   76 (287)
                      |||+.|+|++|||||+||+|||||||||+.+++..+    .|+|..+|.|.+.|+.|+++|+|+|+|+++.+++|||+||
T Consensus        43 ~AI~~V~I~~NtSvl~DE~laHrlglIP~v~edv~e~~~~~l~~k~~c~~~~~~~~~~v~l~L~v~g~~~~~~~Vta~Dl  122 (297)
T 3h0g_C           43 VAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDL  122 (297)
T ss_dssp             EEEEEEEEEEECSSSCHHHHHHHHHHSCBCCTTCSSCSSSCCCCSSSCSSSSSCGGGSCEEEEEECCCCSSCEEEEGGGC
T ss_pred             ceEEEEEEEeCCccccccceeeeeccCCcccccccccccceeEeccccccccCCCCceEEEEEEEEeccCCCceEEcccc
Confidence            699999999999999999999999999999986322    3899999999999999999999999999888999999999


Q ss_pred             eeCCCe--eeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCC
Q psy5332          77 KSTDAR--VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFP  154 (287)
Q Consensus        77 ~s~d~~--v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~  154 (287)
                      ++.+..  +.|+...         ++++||+|+||+|||+|+|+|+|+||+||+|||||||++|+|||+|.|+|++..+|
T Consensus       123 ~~~~~~~~~~pv~~~---------~~n~di~IakL~~gq~l~le~~a~kG~G~~HAKwsPv~~~~y~~~P~i~l~~~~~~  193 (297)
T 3h0g_C          123 VVSSNSSLGHPILAD---------PKSRGPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYW  193 (297)
T ss_dssp             BCCSCCSSCCBCCCS---------TTSCCSEEEEECSSCCEEEEEEEEEECGGGCTTSCCBCCCCCCSSSSCSSCCSCCC
T ss_pred             cccCccccccccccc---------CCCCCeEEEEECCCCEEEEEEEEECCEeccccccCcceEEEEEeccceEEcccccc
Confidence            987643  3344311         36799999999999999999999999999999999999999999999999987654


Q ss_pred             ----CCCCCCCCccCccccc-ccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhccc
Q psy5332         155 ----KPDEWPKSEYSELDET-QHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDR  223 (287)
Q Consensus       155 ----~~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e~  223 (287)
                          ..++||++++...+.. .+...|+....+|||+|+|||+|+++|+++|.+|+++|++|++.|.+.|+++.
T Consensus       194 ~e~~~~~~~P~~~~~~~~~~~~~~~~~~~~~~~dkfif~VET~Gsl~p~eiv~~A~~iL~~kl~~f~~~L~~~~  267 (297)
T 3h0g_C          194 FENDADAEWPKSKNADWEEPPREGEPFNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVRDLDEEQ  267 (297)
T ss_dssp             CSSCSTTTSCCCGGGTTCCCCSCCSCCCSSCCCCCEEEEEEBCSSSCTTTTTHHHHHHHHHHHHHHHHHHHCC-
T ss_pred             ccchhHhhCCccccceeeccccccccccccccCCEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence                3567899877654332 23456888899999999999999999999999999999999999999987653
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ... Back     alignment and structure
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D Back     alignment and structure
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3aoh_A* 3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* ... Back     alignment and structure
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1 Back     alignment and structure
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A Back     alignment and structure
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ... Back     alignment and structure
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D Back     alignment and structure
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1 Back     alignment and structure
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3aoh_A* 3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* ... Back     alignment and structure
>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L 2y0s_L Back     alignment and structure
>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L 2y0s_L Back     alignment and structure
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ... Back     alignment and structure
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A Back     alignment and structure
>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ... Back     alignment and structure
>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2 Back     alignment and structure
>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2 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 287
d1twfc2131 d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharo 1e-44
d1twfc1135 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (S 2e-32
>d1twfc2 d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 131 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Insert subdomain of RNA polymerase alpha subunit
superfamily: Insert subdomain of RNA polymerase alpha subunit
family: Insert subdomain of RNA polymerase alpha subunit
domain: RPB3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  145 bits (368), Expect = 1e-44
 Identities = 63/134 (47%), Positives = 84/134 (62%), Gaps = 5/134 (3%)

Query: 1   MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
           +AID V++E N+TVL+DEFIA R+GLIPL S ++ +++ YSRDC C D C +CSV  TL 
Sbjct: 3   LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDI-EQLEYSRDCFCEDHCDKCSVVLTLQ 61

Query: 61  VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 120
                + T +V + DL         +  RN    + +  E + +LI KLRKGQEL+L   
Sbjct: 62  AFGESESTTNVYSKDLVIVS----NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCV 117

Query: 121 AKKGFGKEHAKWNP 134
           AKKG  KEHAKW P
Sbjct: 118 AKKGIAKEHAKWGP 131
>d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 135 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 ?
Query287
d1twfc2131 RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1twfc1135 RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta 99.5
d1twfc1135 RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta 99.23
d1bdfa1105 RNA polymerase alpha {Escherichia coli [TaxId: 562 98.94
d1smya1106 RNA polymerase alpha {Thermus thermophilus [TaxId: 98.5
d1bdfa2126 RNA polymerase alpha subunit {Escherichia coli [Ta 98.17
d1smya2123 RNA polymerase alpha subunit {Thermus thermophilus 98.1
d1bdfa1105 RNA polymerase alpha {Escherichia coli [TaxId: 562 91.47
d1smya1106 RNA polymerase alpha {Thermus thermophilus [TaxId: 89.59
d1twfk_114 RPB11 {Baker's yeast (Saccharomyces cerevisiae) [T 85.1
d1xppa_99 DNA-directed RNA polymerase subunit L, RpoL {Therm 84.61
d1twfk_114 RPB11 {Baker's yeast (Saccharomyces cerevisiae) [T 81.45
d1xppa_99 DNA-directed RNA polymerase subunit L, RpoL {Therm 80.18
>d1twfc2 d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Insert subdomain of RNA polymerase alpha subunit
superfamily: Insert subdomain of RNA polymerase alpha subunit
family: Insert subdomain of RNA polymerase alpha subunit
domain: RPB3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=9.7e-46  Score=299.93  Aligned_cols=128  Identities=48%  Similarity=0.763  Sum_probs=110.1

Q ss_pred             CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeCCceeCC
Q psy5332           1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTD   80 (287)
Q Consensus         1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~d   80 (287)
                      ||||.|+|++|||+|+|||||||||||||.+++ .+.|.|.++|.|++.|+.|+|+|+|+|+|+++++..|||+||++.+
T Consensus         3 lAid~V~I~~NTS~l~DE~iaHRLglIPi~~~~-~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~Dl~~~~   81 (131)
T d1twfc2           3 LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS   81 (131)
T ss_dssp             EEEEEEEEEEECSSSCHHHHHHHHHTSCEEETT-GGGSCCTTTSSSSSCCTTTEEEEEEEEECCSSSCEEEEGGGEEECS
T ss_pred             EEEEEEEEEECCcccchHHHHHhhcCceeeccC-hhhccccccccccCCCCCceEEEEeEcccCCCCCceEEhhheEEcC
Confidence            799999999999999999999999999999876 4789999999999999999999999999999999999999998654


Q ss_pred             C-eeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecc
Q psy5332          81 A-RVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP  134 (287)
Q Consensus        81 ~-~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsP  134 (287)
                      . .+.+...     +......+++|+|+||+|||+|+|+|+|+||+||+||||||
T Consensus        82 ~~~~~~~~~-----~~~~~~~~~~IlI~kL~pGQ~i~l~a~a~kG~Gk~HAK~sP  131 (131)
T d1twfc2          82 NLMGRNIGH-----PIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGP  131 (131)
T ss_dssp             CCTTCSEEE-----ECCCSTTSCCSEEEEECTTCEEEEEEEEEEECTTTCGGGCC
T ss_pred             CccccccCC-----ccccCCcCCCCEEEEeCCCCEEEEEEEEEecccccCcEeCc
Confidence            2 1111110     00111346899999999999999999999999999999998
>d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1bdfa2 d.181.1.1 (A:53-178) RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1smya2 d.181.1.1 (A:50-172) RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1twfk_ d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1xppa_ d.74.3.2 (A:) DNA-directed RNA polymerase subunit L, RpoL {Thermoplasma acidophilum [TaxId: 2303]} Back     information, alignment and structure
>d1twfk_ d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1xppa_ d.74.3.2 (A:) DNA-directed RNA polymerase subunit L, RpoL {Thermoplasma acidophilum [TaxId: 2303]} Back     information, alignment and structure