Citrus Sinensis ID: 016812

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380--
MAEREETEKKKEAESFSIWDLPDVPQKLPPHIEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS
ccHHHHHHHHHHHcccccccccccccccccHHHHcccEEEEcccccccccccccccccccccccccccHHHHHccccEEEEEEcccEEEEEEEcccHHHHHHHHHHHHHcccEEEEEEEEEEEccccccHHHHHHHHccccEEEccccccccccccccccccEEEEEEEEEEEccccEEEEEccccccccccccccccccccccccccccEEccccccccccccccccccccccccEEEEcccccEEEEEEEEEEcccccccccccEEEEEEEEcccEEEEccccHHHHHHHHHHccccEEEcccccccccccEEccccccHHHHHHHHHcccccccEEEEEEccEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHc
ccccccccccHccccccccccccccccccccHHHHccEEEEcccccccccccccccccccccccccccHHHHHHccEEEEEEcccccEEEEEEcccHHHHHHHHHHHHHHcccEEEEEEEEEccccHHHHHHHHHHccccEccccHHHccccccccccccccEEEEEEEEEEccccccccccHHHHcccccccccHHHHcccccccccccEEcccccccHHccccccccccccccEEEEEEccccEEEEEEEEEcccccccccccccEEEEEEcccEEEEEccccHHHHHHHHHHccccEEEEEccccccEEEEEEccccccccHHHHHccHHHcccEEEcEcccEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHcc
MAEREETEKKkeaesfsiwdlpdvpqklpphiefqrtrvqcnldapihtenvmysgayasmgvdnslqldhFCNNFRVEVIRLtkddmefdLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLglipiivdprlfeymsendtsneknTIVFKLHVLCerggprltvktnelkwlpngselpletkpdsnpsskprtytsfsssqdllpefsnnpirpmlditiarlgpgqeieLEAHAVKGIgkthakwspVATAWYRMLPeivlledvededaeklvktcpvnvfdiedigsgkkratvaqpraCTLCRECLRCGEEWEKRVSIRRVKDHFIFtiestgalspetLFTEAVKILEDKCERVITELS
maereetekkkeaesfsiwdlpdvpQKLPPHIEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCErggprltvktnelkwlpngselpletkpdsnpssKPRTYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDaeklvktcpvnvfdiedigsgkkratvaqpractlcreclrcgeewekrvsirrVKDHFIFtiestgalspetlFTEAVKILEDKCERVITELS
MaereetekkkeaeSFSIWDLPDVPQKLPPHIEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPeivlledvededaeklvKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS
****************SIWDLPDVPQKLPPHIEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWL****************************************IRPMLDITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVL************VKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVI****
***************************************QCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELP*ETKPDSNPSSKPRTYTS**********FSNNPIRPMLDITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS
**************SFSIWDLPDVPQKLPPHIEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPL*********************QDLLPEFSNNPIRPMLDITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGS*********PRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS
****************SIWDLPDVPQKLPPHIEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS
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MAEREETEKKKEAESFSIWDLPDVPQKLPPHIEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS
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 ?
Query382 2.2.26 [Sep-21-2011]
Q32L22346 DNA-directed RNA polymera yes no 0.871 0.962 0.470 3e-79
O15160346 DNA-directed RNA polymera yes no 0.827 0.913 0.476 5e-78
P52432346 DNA-directed RNA polymera yes no 0.863 0.953 0.466 6e-78
Q54SN4345 DNA-directed RNA polymera yes no 0.832 0.921 0.423 2e-74
O94616348 DNA-directed RNA polymera yes no 0.837 0.919 0.403 9e-67
P07703335 DNA-directed RNA polymera yes no 0.774 0.883 0.405 2e-57
Q54DH7302 DNA-directed RNA polymera no no 0.698 0.884 0.340 1e-38
P16925310 Conjugation stage-specifi N/A no 0.719 0.887 0.322 3e-32
Q39211319 DNA-directed RNA polymera no no 0.706 0.846 0.341 1e-31
Q2NFZ6270 DNA-directed RNA polymera yes no 0.641 0.907 0.332 3e-31
>sp|Q32L22|RPAC1_BOVIN DNA-directed RNA polymerases I and III subunit RPAC1 OS=Bos taurus GN=POLR1C PE=2 SV=1 Back     alignment and function desciption
 Score =  295 bits (756), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 165/351 (47%), Positives = 224/351 (63%), Gaps = 18/351 (5%)

Query: 32  IEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRVEVIRLTKDDMEFD 91
           +E  RTRV        +     + G Y+  G D++   D F  NFRV+V+ + ++ +EFD
Sbjct: 7   VEEMRTRVVLGEFGVRNVHTTDFPGNYS--GYDDAWDQDRFEKNFRVDVVHMDENSLEFD 64

Query: 92  LIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEY 151
           ++GIDAAIANAFRRIL+AE+PTMA+EKVL+ NNTS++QDE+LAHRLGLIPI  DPRLFEY
Sbjct: 65  MVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRLGLIPIHADPRLFEY 124

Query: 152 MSENDTSN-EKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPR 210
            ++ D    E +T+ F+L V C R  P     +++          P E   +    ++  
Sbjct: 125 RNQGDEGGTEIDTLQFRLQVRCTR-NPHAAKDSSD----------PNELYVNHRVYTRHM 173

Query: 211 TYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATA 270
           T+    +  DL PE +  P+    DI IA+L PGQEI+L  H VKGIGK HAK+SPVATA
Sbjct: 174 TWVPLGNQADLFPEGAIRPVHD--DILIAQLRPGQEIDLLMHCVKGIGKDHAKFSPVATA 231

Query: 271 WYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRC 330
            YR+LP+I LLE VE E AE+L +     V ++++I  GKK A VA PR  T  RE  R 
Sbjct: 232 SYRLLPDITLLEPVEGEAAEELSRCFSPGVIEVQEI-QGKKVARVANPRLDTFSREVFR- 289

Query: 331 GEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITEL 381
            E+ +K V + RV+DHFIF++ESTG L P+ L +EA+K+L  KC+R + EL
Sbjct: 290 NEKLKKVVRLARVRDHFIFSVESTGVLPPDVLVSEAIKVLMGKCQRFLDEL 340
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1 is part of the Pol core element with the central large cleft and probably a clamp element that moves to open and close the cleft.
Bos taurus (taxid: 9913)
>sp|O15160|RPAC1_HUMAN DNA-directed RNA polymerases I and III subunit RPAC1 OS=Homo sapiens GN=POLR1C PE=1 SV=1 Back     alignment and function description
>sp|P52432|RPAC1_MOUSE DNA-directed RNA polymerases I and III subunit RPAC1 OS=Mus musculus GN=Polr1c PE=1 SV=3 Back     alignment and function description
>sp|Q54SN4|RPAC1_DICDI DNA-directed RNA polymerases I and III subunit rpac1 OS=Dictyostelium discoideum GN=polr1c PE=3 SV=1 Back     alignment and function description
>sp|O94616|RPAC1_SCHPO DNA-directed RNA polymerases I and III subunit RPAC1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc40 PE=3 SV=1 Back     alignment and function description
>sp|P07703|RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPC40 PE=1 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|P16925|CNJC_TETTH Conjugation stage-specific protein OS=Tetrahymena thermophila GN=CNJC PE=2 SV=1 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|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 ?
Query382
225461965372 PREDICTED: DNA-directed RNA polymerases 0.947 0.973 0.795 1e-164
255563568374 DNA-directed RNA polymerase I/III subuni 0.939 0.959 0.777 1e-159
363807500388 uncharacterized protein LOC100786622 [Gl 0.950 0.935 0.752 1e-156
356527169393 PREDICTED: DNA-directed RNA polymerases 0.950 0.923 0.75 1e-156
224061238390 predicted protein [Populus trichocarpa] 0.955 0.935 0.726 1e-155
15219773385 RNA polymerase I subunit 43 [Arabidopsis 0.973 0.966 0.707 1e-155
297840495385 ATRPAC43 [Arabidopsis lyrata subsp. lyra 0.973 0.966 0.704 1e-154
449461051391 PREDICTED: DNA-directed RNA polymerases 0.989 0.966 0.719 1e-151
297837401376 ATRPAC42 [Arabidopsis lyrata subsp. lyra 0.963 0.978 0.687 1e-144
357460223399 DNA-directed RNA polymerase subunit D [M 0.945 0.904 0.675 1e-144
>gi|225461965|ref|XP_002270559.1| PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC1 [Vitis vinifera] gi|296089944|emb|CBI39763.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  585 bits (1508), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 291/366 (79%), Positives = 328/366 (89%), Gaps = 4/366 (1%)

Query: 20  DLPDVPQ-KLPPHIEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRV 78
           D+PDVP+ +LPPHIE QRTRV CN DAP HTENV YSGAY+SMGVDNSL++D FCNNFRV
Sbjct: 8   DMPDVPKGQLPPHIELQRTRVLCNFDAPTHTENVQYSGAYSSMGVDNSLRMDQFCNNFRV 67

Query: 79  EVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLG 138
           EVIRL++DDMEFD+IGID +IANAFRRILIAELPTMAIEKVLIANNTS++QDEVLAHRLG
Sbjct: 68  EVIRLSEDDMEFDMIGIDPSIANAFRRILIAELPTMAIEKVLIANNTSIVQDEVLAHRLG 127

Query: 139 LIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLE 198
           LIPI  DPRLF+ +SENDT NEKNTIVF LHV CERGGPRLTVK+NELKWLP+GSE PL 
Sbjct: 128 LIPINADPRLFDDLSENDTPNEKNTIVFNLHVRCERGGPRLTVKSNELKWLPHGSEFPLA 187

Query: 199 TK-PDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPML-DITIARLGPGQEIELEAHAVKG 256
           T+   S+ +SKP+TYTSFS SQD LPEFS+  I P   DI IA+LGPGQEIELEAHAVKG
Sbjct: 188 TENTTSSSTSKPKTYTSFSCSQDSLPEFSDKSIGPKHPDIIIAKLGPGQEIELEAHAVKG 247

Query: 257 IGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVA 316
           +GKTHAKWSPVATAWYRMLPE+VLL+++EDE AE+LVK CPVNVFDIEDI  GKK+ATVA
Sbjct: 248 MGKTHAKWSPVATAWYRMLPEVVLLQEIEDEKAEELVKKCPVNVFDIEDIAKGKKKATVA 307

Query: 317 QPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCER 376
           +PRACTLCREC+R G++W+K V+IRRVK+HFIFTIESTGAL PE LF EAVK+LEDKCER
Sbjct: 308 RPRACTLCRECIR-GDDWDKHVAIRRVKNHFIFTIESTGALPPEVLFNEAVKVLEDKCER 366

Query: 377 VITELS 382
           VITELS
Sbjct: 367 VITELS 372

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255563568|ref|XP_002522786.1| DNA-directed RNA polymerase I/III subunits, putative [Ricinus communis] gi|223538024|gb|EEF39637.1| DNA-directed RNA polymerase I/III subunits, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|363807500|ref|NP_001242652.1| uncharacterized protein LOC100786622 [Glycine max] gi|255637183|gb|ACU18922.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|356527169|ref|XP_003532185.1| PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC1-like [Glycine max] Back     alignment and taxonomy information
>gi|224061238|ref|XP_002300385.1| predicted protein [Populus trichocarpa] gi|222847643|gb|EEE85190.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|15219773|ref|NP_176261.1| RNA polymerase I subunit 43 [Arabidopsis thaliana] gi|14423464|gb|AAK62414.1|AF386969_1 RNA polymerase subunit (isoform B) [Arabidopsis thaliana] gi|514324|gb|AAB00529.1| RNA polymerase subunit [Arabidopsis thaliana] gi|2462755|gb|AAB71974.1| RNA polymerase subunit (isoform B) [Arabidopsis thaliana] gi|24899667|gb|AAN65048.1| RNA polymerase subunit (isoform B) [Arabidopsis thaliana] gi|332195585|gb|AEE33706.1| RNA polymerase I subunit 43 [Arabidopsis thaliana] gi|1586550|prf||2204246B RNA polymerase Back     alignment and taxonomy information
>gi|297840495|ref|XP_002888129.1| ATRPAC43 [Arabidopsis lyrata subsp. lyrata] gi|297333970|gb|EFH64388.1| ATRPAC43 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|449461051|ref|XP_004148257.1| PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC1-like [Cucumis sativus] gi|449522768|ref|XP_004168398.1| PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297837401|ref|XP_002886582.1| ATRPAC42 [Arabidopsis lyrata subsp. lyrata] gi|297332423|gb|EFH62841.1| ATRPAC42 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|357460223|ref|XP_003600393.1| DNA-directed RNA polymerase subunit D [Medicago truncatula] gi|355489441|gb|AES70644.1| DNA-directed RNA polymerase subunit D [Medicago truncatula] 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 ?
Query382
TAIR|locus:2036494385 RPAC43 "RNA polymerase I subun 0.955 0.948 0.685 1.1e-133
TAIR|locus:2025855375 ATRPAC42 [Arabidopsis thaliana 0.939 0.957 0.654 6.5e-122
DICTYBASE|DDB_G0282339345 rpa5 "RNA polymerase III subun 0.460 0.510 0.430 9.8e-70
UNIPROTKB|Q32L22346 POLR1C "DNA-directed RNA polym 0.871 0.962 0.444 2.1e-68
UNIPROTKB|E2RH57346 POLR1C "Uncharacterized protei 0.827 0.913 0.458 5.6e-68
MGI|MGI:103288346 Polr1c "polymerase (RNA) I pol 0.871 0.962 0.444 7.2e-68
UNIPROTKB|O15160346 POLR1C "DNA-directed RNA polym 0.827 0.913 0.455 1.2e-67
UNIPROTKB|Q5RJK9346 Polr1c "Protein Polr1c" [Rattu 0.871 0.962 0.438 4.5e-66
UNIPROTKB|F1RRJ4351 POLR1C "Uncharacterized protei 0.827 0.900 0.452 9.4e-66
UNIPROTKB|E1C548346 POLR1C "Uncharacterized protei 0.827 0.913 0.452 3.3e-63
TAIR|locus:2036494 RPAC43 "RNA polymerase I subunit 43" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1310 (466.2 bits), Expect = 1.1e-133, P = 1.1e-133
 Identities = 253/369 (68%), Positives = 293/369 (79%)

Query:    15 SFSIWDLPDVPQKLPPHIEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCN 74
             +F+I+DLPDVP  LPPH+E QRTRV C  D+ IH   + +SGAY+SMGVDNS++L++F  
Sbjct:    20 NFNIFDLPDVPTGLPPHLELQRTRVVCKKDSNIHPTAITFSGAYSSMGVDNSVRLENFSE 79

Query:    75 NFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLA 134
             +F+V+VI LT+ DM FD+IG+ A IANAFRRIL+AELP+MAIEKV +ANNTSVIQDEVLA
Sbjct:    80 DFKVDVISLTETDMVFDMIGVHAGIANAFRRILLAELPSMAIEKVYVANNTSVIQDEVLA 139

Query:   135 HRLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSE 194
             HRLGLIPI  DPRLFEY+SEND  NEKNTIVFKLHV C +G PR  V T+ELKWLPNGSE
Sbjct:   140 HRLGLIPIAADPRLFEYLSENDQPNEKNTIVFKLHVKCLKGDPRRKVLTSELKWLPNGSE 199

Query:   195 LPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPML-DITIARLGPGQEIELEAHA 253
             L    K     ++ P+TYTSF+ SQD  PEF+ NPIRP L DI IA+LGPGQEIELEAHA
Sbjct:   200 L---IKESGGSTTTPKTYTSFNHSQDSFPEFAENPIRPTLKDILIAKLGPGQEIELEAHA 256

Query:   254 VKGIGKTHAKWSPVATAWYRMLPXXXXXXXXXXXXXXXXXKTCPVNVFDIEDIGSGKKRA 313
             VKGIGKTHAKWSPVATAWYRMLP                 K CP  VFDIED+G G+KRA
Sbjct:   257 VKGIGKTHAKWSPVATAWYRMLPEVVLLKEFEGKHAEELVKVCPKKVFDIEDMGQGRKRA 316

Query:   314 TVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDK 373
             TVA+PR C+LCREC+R G EWE +V +RRVK+HFIFTIESTG+  PE LF EAVKILEDK
Sbjct:   317 TVARPRDCSLCRECIRDGVEWEDQVDLRRVKNHFIFTIESTGSQPPEVLFNEAVKILEDK 376

Query:   374 CERVITELS 382
             CERVI+ELS
Sbjct:   377 CERVISELS 385
GO:0003677 "DNA binding" evidence=IEA;ISS
GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS
GO:0046983 "protein dimerization activity" evidence=IEA
GO:0006626 "protein targeting to mitochondrion" evidence=RCA
TAIR|locus:2025855 ATRPAC42 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0282339 rpa5 "RNA polymerase III subunit" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|Q32L22 POLR1C "DNA-directed RNA polymerases I and III subunit RPAC1" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RH57 POLR1C "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:103288 Polr1c "polymerase (RNA) I polypeptide C" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|O15160 POLR1C "DNA-directed RNA polymerases I and III subunit RPAC1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q5RJK9 Polr1c "Protein Polr1c" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1RRJ4 POLR1C "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|E1C548 POLR1C "Uncharacterized protein" [Gallus gallus (taxid:9031)] 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) ?
Q32L22RPAC1_BOVINNo assigned EC number0.47000.87170.9624yesno
P52432RPAC1_MOUSENo assigned EC number0.46610.86380.9537yesno
Q54SN4RPAC1_DICDINo assigned EC number0.42370.83240.9217yesno
O94616RPAC1_SCHPONo assigned EC number0.40370.83760.9195yesno
O15160RPAC1_HUMANNo assigned EC number0.47610.82720.9132yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.70.691
4th Layer2.7.7.6LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
eugene3.00012667
hypothetical protein (390 aa)
(Populus trichocarpa)
Predicted Functional Partners:
estExt_Genewise1_v1.C_LG_XIV2383
CTP synthase (EC-6.3.4.2) (562 aa)
   • •  0.906
gw1.X.1387.1
CTP synthase (EC-6.3.4.2) (589 aa)
   • •  0.906
estExt_Genewise1_v1.C_LG_III0729
CTP synthase (EC-6.3.4.2) (596 aa)
   • •  0.906
gw1.I.8101.1
CTP synthase (EC-6.3.4.2) (591 aa)
   • •  0.906
fgenesh4_pm.C_LG_VIII000317
CTP synthase (EC-6.3.4.2) (605 aa)
   • •  0.905
gw1.I.2477.1
hypothetical protein (950 aa)
   • •  0.901
gw1.XIII.2192.1
polyribonucleotide nucleotidyltransferase (EC-2.7.7.8) (853 aa)
     •  0.899
gw1.XII.1350.1
hypothetical protein (612 aa)
     •  0.899
gw1.IX.2629.1
pyruvate kinase (EC-2.7.1.40) (481 aa)
     •  0.899
gw1.II.1445.1
SubName- Full=Putative uncharacterized protein; (164 aa)
     •  0.899

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query382
cd07032291 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryoti 1e-152
smart00662224 smart00662, RPOLD, RNA polymerases D 1e-76
PRK00783263 PRK00783, PRK00783, DNA-directed RNA polymerase su 3e-63
cd07030259 cd07030, RNAP_D, D subunit of Archaeal RNA polymer 2e-59
cd07031265 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic 9e-59
cd07028212 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polym 6e-49
COG0202317 COG0202, RpoA, DNA-directed RNA polymerase, alpha 1e-39
PRK14979195 PRK14979, PRK14979, DNA-directed RNA polymerase su 7e-22
pfam01000117 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA 1e-09
pfam0119388 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 di 2e-08
pfam0119388 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 di 9e-08
cd07028212 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polym 1e-05
>gnl|CDD|132910 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information 
 Score =  430 bits (1108), Expect = e-152
 Identities = 171/320 (53%), Positives = 216/320 (67%), Gaps = 44/320 (13%)

Query: 76  FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAH 135
           F++E+I L+ +++EFDLIG+DA+IANAFRRIL+AE+PTMAIEKV I NNTSVIQDEVLAH
Sbjct: 1   FKIEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAH 60

Query: 136 RLGLIPIIVDPRLFEYMSE-NDTSNEKNTIVFKLHVLCERGGPR-------------LTV 181
           RLGLIPI  DPRLFEY  + +D   E+NT+VF+L V C R                   V
Sbjct: 61  RLGLIPIKADPRLFEYREDSDDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKV 120

Query: 182 KTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPML-DITIAR 240
            + +LKW+P GS+                              F++NPIRP+  DI IA+
Sbjct: 121 YSGDLKWVPIGSQEKR---------------------------FADNPIRPVHPDILIAK 153

Query: 241 LGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNV 300
           L PGQEI+LE H VKGIGK HAK+SPVATA YR+LPEI LL+ +  EDAEKL K  P  V
Sbjct: 154 LRPGQEIDLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKPITGEDAEKLQKCFPPGV 213

Query: 301 FDIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPE 360
            DIE++  GKK+A VA PR  TL RE L   EE++ +V + RV+DHFIF+IESTGAL P+
Sbjct: 214 IDIEEVK-GKKKAVVANPRKDTLSREVL-RHEEFKDKVELGRVRDHFIFSIESTGALPPD 271

Query: 361 TLFTEAVKILEDKCERVITE 380
            LF EA+KIL++KC +++ E
Sbjct: 272 VLFLEAIKILKEKCRKLLEE 291

The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III 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 I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. 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. The homology of AC40 to RPB3 suggests a similar function. The AC40 subunit is likely to associate with the RPB11 counterpart, AC19, to form a heterodimer, which stabilizes the association of the two largest subunits of RNAP I and RNAP III. Length = 291
>gnl|CDD|214766 smart00662, RPOLD, RNA polymerases D Back     alignment and domain information
>gnl|CDD|234837 PRK00783, PRK00783, 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|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information
>gnl|CDD|132906 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polymerase 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|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain 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|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation domain Back     alignment and domain information
>gnl|CDD|132906 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polymerase Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 382
KOG1521338 consensus RNA polymerase I and III, subunit RPA40/ 100.0
cd07032291 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly 100.0
cd07031265 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme 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
KOG1522285 consensus RNA polymerase II, subunit POLR2C/RPB3 [ 100.0
cd07028212 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The 100.0
smart00662224 RPOLD RNA polymerases D. DNA-directed RNA polymera 100.0
PRK14979195 DNA-directed RNA polymerase subunit D; Provisional 100.0
COG0202317 RpoA DNA-directed RNA polymerase, alpha subunit/40 100.0
cd06928215 RNAP_alpha_NTD N-terminal domain of the Alpha subu 100.0
PRK05182310 DNA-directed RNA polymerase subunit alpha; Provisi 100.0
TIGR02027297 rpoA DNA-directed RNA polymerase, alpha subunit, b 99.97
PF01000112 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert dom 99.94
CHL00013 327 rpoA RNA polymerase alpha subunit 99.92
PF0119366 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation 99.35
COG0202317 RpoA DNA-directed RNA polymerase, alpha subunit/40 98.98
cd0046086 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA pol 98.93
PRK0114685 DNA-directed RNA polymerase subunit L; Provisional 94.64
PF1365677 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisatio 93.19
cd0692783 RNAP_L L subunit of Archaeal RNA polymerase. The a 92.74
cd0702783 RNAP_RPB11_like RPB11 subunit of RNA polymerase. T 91.72
cd0702985 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA pol 90.21
COG176199 RPB11 DNA-directed RNA polymerase, subunit L [Tran 89.92
cd0692783 RNAP_L L subunit of Archaeal RNA polymerase. The a 89.22
PRK0114685 DNA-directed RNA polymerase subunit L; Provisional 88.92
cd0692693 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA poly 88.68
cd0702783 RNAP_RPB11_like RPB11 subunit of RNA polymerase. T 87.57
cd0692693 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA poly 82.18
>KOG1521 consensus RNA polymerase I and III, subunit RPA40/RPC40 [Transcription] Back     alignment and domain information 
Probab=100.00  E-value=5.4e-116  Score=834.50  Aligned_cols=323  Identities=59%  Similarity=0.922  Sum_probs=310.4

Q ss_pred             CcchhhccCeEEeccCCCccccccccCCCCcCCCCCcccchhhccCCceEEEEEecCceEEEEEEccChhhHHHHHHHHH
Q 016812           29 PPHIEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILI  108 (382)
Q Consensus        29 ~~~~~~~r~~v~~~~~~~~~~~~~~~~g~~~~~~~d~~~~~~~f~~~~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILl  108 (382)
                      |+|++.+|++|++++++|+|++|+||||.|.  ++||.|++++|+++|+|.|.+++++.|+|+|+|+|++||||||||||
T Consensus         1 ~~~~~~~~~~v~~~~~~v~~~~s~dfpg~Y~--~~d~~~~~~~f~~~~~V~iv~~~~~~leFDligIda~IANAfRRILi   78 (338)
T KOG1521|consen    1 SAHLERMSTRVVLKEERVTNTTSTDFPGDYV--SEDDQWDLENFKDNFKVDIVSLDEETLEFDLIGIDASIANAFRRILI   78 (338)
T ss_pred             ChhhhhhcceeeeccccccccccccCCcchh--cccccccHHHhhhceEEEEEeccCcceeEEEeeccHHHHHHHHHHHH
Confidence            6789999999999999999999999999999  78899999999999999999999999999999999999999999999


Q ss_pred             hhCCcceEEEEEEeeCcccccccceeeecccCCCccCCceeeeecccCCCCCC-ceEEEEEEEEeecCCC----------
Q 016812          109 AELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSENDTSNEK-NTIVFKLHVLCERGGP----------  177 (382)
Q Consensus       109 sEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~d~~~~~~~~~~d~~~~~-~tv~~~L~v~c~~~~~----------  177 (382)
                      |||||||||+|||+||||||||||||||||||||.+||++|+|..+.++..+. +|++|+|+|+|++|+.          
T Consensus        79 aEVPtmAiEkVyi~nNTSViqDEvLaHRlGLvPl~aDPrlFe~~~e~d~~~e~~ntlvF~L~VkC~~n~~a~~~~sdpk~  158 (338)
T KOG1521|consen   79 AEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLVPLRADPRLFEYRSENDEDDEKENTLVFKLNVKCTKNPNAKKDSSDPKE  158 (338)
T ss_pred             hhcchhheeeeEEecCccccHHHHHHHhhcCcccccCcchhhccccCCCccCccceEEEEEEeeccCCCCcccCCCChhH
Confidence            99999999999999999999999999999999999999999999987776666 9999999999999842          


Q ss_pred             ---cceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccccCC-eEEEEeCCCceEEEEEEE
Q 016812          178 ---RLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHA  253 (382)
Q Consensus       178 ---~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~i~~v~~-IlIakL~pGQeI~le~~a  253 (382)
                         |+.|||+|++|.|.|.|.+.                           |++++++|+++ |+||||||||+|+|+|||
T Consensus       159 Ly~ns~vyS~~~~w~P~g~Q~~~---------------------------f~e~~i~~~~~DILiAkLrPGQEI~le~ha  211 (338)
T KOG1521|consen  159 LYNNSEVYSRDLTWKPKGYQAEI---------------------------FAENPIRPVHDDILIAKLRPGQEIELEAHA  211 (338)
T ss_pred             hccCcEEecCcceeccccchhhh---------------------------cccCCccccCcceEEEecCCCCEeeeeeee
Confidence               78999999999999988743                           78999999999 999999999999999999


Q ss_pred             EecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCceEEeccCCCCceeEEEecCccccccccceecCcc
Q 016812          254 VKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRCGEE  333 (382)
Q Consensus       254 ~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gvi~id~~~~g~~~~~V~~~r~~t~~rec~r~~~~  333 (382)
                      +|||||+||||||||||||||||.|.|++++.|++|++|++|||+|||+|++.+ ++++|+|++||+||+||||+| |++
T Consensus       212 vkGIGkdHAKfSPVaTAsYRLlP~I~l~~ei~ge~A~~lqkcfs~gVi~iee~~-~kk~A~Vad~R~dT~sRe~~R-~ee  289 (338)
T KOG1521|consen  212 VKGIGKDHAKFSPVATASYRLLPTIVLLAEIEGEDAERLQKCFSPGVIDIEEMG-GKKRAYVADPRKDTCSREVLR-HEE  289 (338)
T ss_pred             ecccCcccccccCcccceeeccceeEecCcccchhHHHHHhhCCCCeEeeecCC-CceEEEecCcccchhhHHHhc-cHH
Confidence            999999999999999999999999999999999999999999999999999875 478999999999999999999 999


Q ss_pred             cccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHhhC
Q 016812          334 WEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS  382 (382)
Q Consensus       334 ~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~L~  382 (382)
                      |+++|++++++|||||+|||+|+|+|+.+|.+|+++|+.||+.+.++++
T Consensus       290 ~~d~V~LgrvrdHfIFsvestgal~p~~lf~eavkvle~Kc~al~~~~~  338 (338)
T KOG1521|consen  290 LKDKVQLGRVRDHFIFSVESTGALKPEVLFEEAVKVLEEKCRALRDEIE  338 (338)
T ss_pred             hhhheeeccccceEEEEeecccCCCchhhHHHHHHHHHHHHHHHhhccC
Confidence            9999999999999999999999999999999999999999999998764

>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II 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
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription] Back     alignment and domain information
>cd07028 RNAP_RPB3_like RPB3 subunit of 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
>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
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional Back     alignment and domain information
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type 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
>CHL00013 rpoA RNA polymerase alpha subunit 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
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription] Back     alignment and domain information
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase Back     alignment and domain information
>PRK01146 DNA-directed RNA polymerase subunit L; 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
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase Back     alignment and domain information
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase 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
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription] 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
>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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query382
2waq_D265 The Complete Structure Of The Archaeal 13-Subunit D 4e-22
2pa8_D265 X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE 5e-22
3j0k_C268 Orientation Of Rna Polymerase Ii Within The Human V 9e-19
3how_C347 Complete Rna Polymerase Ii Elongation Complex Iii W 1e-18
1i3q_C318 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 1e-18
3i4m_C324 8-oxoguanine Containing Rna Polymerase Ii Elongatio 1e-18
3h0g_C297 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 1e-15
>pdb|2WAQ|D Chain D, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 265 Back     alignment and structure 
Iteration: 1

 Score =  102 bits (253), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 91/298 (30%), Positives = 127/298 (42%), Gaps = 50/298 (16%)
Query: 83  LTKDDMEFDLI--GIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLI 140
           L KDD   DL+  G      NA RR  +  +P M+I+ V    N S + DE+LAHRL LI
Sbjct: 6   LHKDDKRIDLVFEGYPLEFVNAIRRAAMLYVPVMSIDDVYFIENNSPLYDEILAHRLALI 65
Query: 141 PIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETK 200
           P   +  L  Y    +  +            CE+   ++ ++   L              
Sbjct: 66  PFTSEEALDTYRWPEECIDCTEN--------CEKCYTKIYIEAEAL-------------- 103
Query: 201 PDSNPSSKPRT-YTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELEAHAVKGIGK 259
                 ++P+  Y+    S+D  P  S  PI    DI I  LG  Q+I LEA    G GK
Sbjct: 104 ------NEPKMLYSKDIKSED--P--SIVPISG--DIPIVLLGANQKISLEARLRLGYGK 151
Query: 260 THAKWSPVATAWYRMLPXXXXXXXXXXXXXXXXXKTCPVNVFDIEDIGSGKKRATVAQPR 319
            HAK+ PV+ A  R  P                   CP  VF+++D      + +V    
Sbjct: 152 EHAKFIPVSLAIVRYYPKVEILGNCEKGAT-----VCPEGVFELKD-----GKLSVKNEL 201
Query: 320 ACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERV 377
           ACTLC ECLR        + I  V+D +I  +ES G+L PE +  EA K +  K E +
Sbjct: 202 ACTLCEECLR---YCNGLIRISSVEDKYILELESVGSLKPERILLEAGKSIIRKIEEL 256
>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|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|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|1I3Q|C Chain C, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 318 Back     alignment and structure
>pdb|3I4M|C Chain C, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex D Length = 324 Back     alignment and structure
>pdb|3H0G|C Chain C, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 297 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 ?
Query382
2pa8_D265 DNA-directed RNA polymerase subunit D; ferredoxin- 9e-64
3h0g_C297 DNA-directed RNA polymerase II subunit RPB3; trans 1e-59
1twf_C318 B44.5, DNA-directed RNA polymerase II 45 kDa polyp 5e-56
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 8e-06
>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
 Score =  203 bits (518), Expect = 9e-64
 Identities = 85/311 (27%), Positives = 126/311 (40%), Gaps = 56/311 (18%)

Query: 77  RVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHR 136
            + ++      ++    G      NA RR  +  +P MA++ V    N S + DE+LAHR
Sbjct: 2   SINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHR 61

Query: 137 LGLIPIIVDPRLFEY-----MSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPN 191
           L LIP + +  L  Y       E   + EK      +            + + ++K    
Sbjct: 62  LALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYIEAEAPNEP--RMIYSKDIKSEDP 119

Query: 192 GSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELEA 251
                                             S  PI    DI I  LG  Q+I LEA
Sbjct: 120 ----------------------------------SVVPISG--DIPIVLLGTNQKISLEA 143

Query: 252 HAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKK 311
               G GK HAK+ PV+ +  R  P++ +L +      EK V  CP  VF+++D      
Sbjct: 144 RLRLGYGKEHAKFIPVSLSVVRYYPKVEILAN-----CEKAVNVCPEGVFELKD-----G 193

Query: 312 RATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILE 371
           + +V    +CTLC ECLR        + I  V+D +I  IES G+L PE +  EA K + 
Sbjct: 194 KLSVKNELSCTLCEECLR---YCNGSIRISFVEDKYILEIESVGSLKPERILLEAGKSII 250

Query: 372 DKCERVITELS 382
            K E +  +L 
Sbjct: 251 RKIEELEKKLV 261
>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
>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
>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 ?
Query382
2pa8_D265 DNA-directed RNA polymerase subunit D; ferredoxin- 100.0
1twf_C318 B44.5, DNA-directed RNA polymerase II 45 kDa polyp 100.0
3h0g_C297 DNA-directed RNA polymerase II subunit RPB3; trans 100.0
1bdf_A235 RNA polymerase alpha subunit; nucleotidyltransfera 100.0
2a6h_A315 DNA-directed RNA polymerase alpha chain; RNA polym 100.0
3lu0_A329 DNA-directed RNA polymerase subunit alpha; E. coli 100.0
2pa8_L92 DNA-directed RNA polymerase subunit L; ferredoxin- 94.39
1xpp_A115 TA1416, DNA-directed RNA polymerase subunit L; str 93.86
2pa8_L92 DNA-directed RNA polymerase subunit L; ferredoxin- 92.25
3h0g_K123 DNA-directed RNA polymerase II subunit RPB11; tran 91.04
1twf_K120 B13.6, DNA-directed RNA polymerase II 13.6 kDa pol 90.96
1twf_K120 B13.6, DNA-directed RNA polymerase II 13.6 kDa pol 89.52
1xpp_A115 TA1416, DNA-directed RNA polymerase subunit L; str 87.32
>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
Probab=100.00  E-value=4.7e-69  Score=516.93  Aligned_cols=255  Identities=31%  Similarity=0.516  Sum_probs=229.9

Q ss_pred             ceEEEEEecCceEEEEEEccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCccC--Cceeeeec
Q 016812           76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVD--PRLFEYMS  153 (382)
Q Consensus        76 ~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~d--~~~~~~~~  153 (382)
                      |+|++.++++++++|+|+|++++|||||||||||||||+||+.|+|++|||+|+||+|||||||||+..+  ++.+.|+.
T Consensus         1 ~~i~i~~~~~~~~~f~l~g~~~t~~NalRRills~vp~~AI~~V~i~~Ntsvl~DE~v~Hr~~~Ip~~~edv~k~~~~~~   80 (265)
T 2pa8_D            1 MSINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPE   80 (265)
T ss_dssp             -CEEEEEECSSEEEEEEESSCHHHHHHHHHHHHHSCCEEEEEEEEEEEECSSSCHHHHHHHHTTSCBCCTTHHHHSCCGG
T ss_pred             CeEEEEEcCCCEEEEEEeCCCHHHHHHHHHHHHHcCccceEEEEEEEeCCCccccHHHHHhhcCCcCcccCchhhccccc
Confidence            5789999999999999999999999999999999999999999999999999999999999999999876  68888876


Q ss_pred             cc---CCCCCCceEEEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCc
Q 016812          154 EN---DTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPI  230 (382)
Q Consensus       154 ~~---d~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~i  230 (382)
                      .|   +..|+.|+++|+|+++|+++  +..|||+||++.                                     ++++
T Consensus        81 ~~~~~~~~~~~~~~~~~l~~~~~~g--~~~V~a~Di~~~-------------------------------------~~~v  121 (265)
T 2pa8_D           81 ECIECTENCEKCYTKIYIEAEAPNE--PRMIYSKDIKSE-------------------------------------DPSV  121 (265)
T ss_dssp             GCTTCCSSCTTTEEEEEEEEECCSS--CEEEEGGGCEES-------------------------------------STTC
T ss_pred             cccccccCCCCcEEEEEEEEEecCC--CcEEEhhhcccC-------------------------------------CCCc
Confidence            54   45677899999999999543  489999999962                                     2358


Q ss_pred             cccCC-eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCceEEeccCCCC
Q 016812          231 RPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSG  309 (382)
Q Consensus       231 ~~v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gvi~id~~~~g  309 (382)
                      +|+|| |+||||++||+|+|+|+|.||+||+||||+|+++++||++|.|.+.     ..+.++++.||.|+|.+++.   
T Consensus       122 ~~~~~~i~I~~L~~g~~l~~e~~~~~G~G~~~ak~~pv~t~~yr~~p~I~i~-----~~C~~C~~~CP~g~I~id~~---  193 (265)
T 2pa8_D          122 VPISGDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEIL-----ANCEKAVNVCPEGVFELKDG---  193 (265)
T ss_dssp             CBSCSCCEEEEECTTCEEEEEEEEEEECTTTCGGGCCEEEEEEEEEEEEEEC-----SCCTTHHHHCTTCCEEEETT---
T ss_pred             eecCCCcEEEEeCCCCEEEEEEEEecCccccccCcccceeeeeccccchhhh-----hhHHHHHHhCcccCeEecCC---
Confidence            89999 9999999999999999999999999999999999999999999987     34667888999999999852   


Q ss_pred             ceeEEEecCccccccccceecCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHhhC
Q 016812          310 KKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS  382 (382)
Q Consensus       310 ~~~~~V~~~r~~t~~rec~r~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~L~  382 (382)
                        ..++.++++|++|++|++ ..  ++.|.+.+++|+|+|+|||+|+++|++++.+|+++|++||+.|++.|+
T Consensus       194 --~~v~~d~~~C~~C~~C~~-vC--p~aI~~~~~~d~~i~~VEt~Gsl~Pee~v~~A~~iL~~~~~~~~~~l~  261 (265)
T 2pa8_D          194 --KLSVKNELSCTLCEECLR-YC--NGSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRKIEELEKKLV  261 (265)
T ss_dssp             --EEEESCGGGCCCCCHHHH-HH--TTSEEEEEEEEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --eeEEeccccCCCchHHHH-hC--CCceEEEecCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              266789999999999998 21  268999999999999999999999999999999999999999998773
>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
>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
>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
>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
>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
>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
>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
>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

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 382
d1twfc2131 d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharo 3e-35
d1twfc1135 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (S 3e-14
d1twfc1135 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (S 9e-12
>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 =  123 bits (311), Expect = 3e-35
 Identities = 45/158 (28%), Positives = 68/158 (43%), Gaps = 30/158 (18%)

Query: 112 PTMAIEKVLIANNTSVIQDEVLAHRLGLIPI-IVDPRLFEY--MSENDTSNEKNTIVFKL 168
           PT+AI+ V +  NT+V+ DE +AHRLGLIP+  +D    EY      +   +K ++V  L
Sbjct: 1   PTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTL 60

Query: 169 HVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNN 228
               E       V + +L  + N        +   +P  + +                  
Sbjct: 61  QAFGESESTT-NVYSKDLVIVSNLMG-----RNIGHPIIQDKEGN--------------- 99

Query: 229 PIRPMLDITIARLGPGQEIELEAHAVKGIGKTHAKWSP 266
                  + I +L  GQE++L   A KGI K HAKW P
Sbjct: 100 ------GVLICKLRKGQELKLTCVAKKGIAKEHAKWGP 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
>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 ?
Query382
d1twfc2131 RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1twfc1135 RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta 99.9
d1bdfa2126 RNA polymerase alpha subunit {Escherichia coli [Ta 98.81
d1smya2123 RNA polymerase alpha subunit {Thermus thermophilus 98.72
d1bdfa1105 RNA polymerase alpha {Escherichia coli [TaxId: 562 98.53
d1smya1106 RNA polymerase alpha {Thermus thermophilus [TaxId: 97.75
d1bdfa1105 RNA polymerase alpha {Escherichia coli [TaxId: 562 97.08
d1xppa_99 DNA-directed RNA polymerase subunit L, RpoL {Therm 94.53
d1smya1106 RNA polymerase alpha {Thermus thermophilus [TaxId: 93.83
>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=4.5e-40  Score=283.14  Aligned_cols=127  Identities=35%  Similarity=0.516  Sum_probs=105.8

Q ss_pred             CcceEEEEEEeeCcccccccceeeecccCCCcc-CCceeeeecc--cCCCCCCceEEEEEEEEeecCCCcceEEcCCcee
Q 016812          112 PTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIV-DPRLFEYMSE--NDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKW  188 (382)
Q Consensus       112 PT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~-d~~~~~~~~~--~d~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~  188 (382)
                      ||||||.|+|++|||+++||+||||||||||.+ +++.+.|...  |+..|+.|+++|+|+|+|+.+. ...|||+||+|
T Consensus         1 PtlAid~V~I~~NTS~l~DE~iaHRLglIPi~~~~~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~-~~~V~s~Dl~~   79 (131)
T d1twfc2           1 PTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESES-TTNVYSKDLVI   79 (131)
T ss_dssp             CEEEEEEEEEEEECSSSCHHHHHHHHHTSCEEETTGGGSCCTTTSSSSSCCTTTEEEEEEEEECCSSS-CEEEEGGGEEE
T ss_pred             CeEEEEEEEEEECCcccchHHHHHhhcCceeeccChhhccccccccccCCCCCceEEEEeEcccCCCC-CceEEhhheEE
Confidence            999999999999999999999999999999975 5677777654  4457889999999999998655 58999999999


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccccCC-eEEEEeCCCceEEEEEEEEecccccccccCc
Q 016812          189 LPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSP  266 (382)
Q Consensus       189 ~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~i~~v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsP  266 (382)
                      .+.+.+...                           +......+.++ |+|+||+|||+|+|+|+|+||+||+||||||
T Consensus        80 ~~~~~~~~~---------------------------~~~~~~~~~~~~IlI~kL~pGQ~i~l~a~a~kG~Gk~HAK~sP  131 (131)
T d1twfc2          80 VSNLMGRNI---------------------------GHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGP  131 (131)
T ss_dssp             CSCCTTCSE---------------------------EEECCCSTTSCCSEEEEECTTCEEEEEEEEEEECTTTCGGGCC
T ss_pred             cCCcccccc---------------------------CCccccCCcCCCCEEEEeCCCCEEEEEEEEEecccccCcEeCc
Confidence            765443211                           00112334566 9999999999999999999999999999998
>d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]} 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
>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure