Citrus Sinensis ID: 020983

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-------32
MDGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEADDQFGELGAHMRGG
cccHHHccccEEEEEEEcccEEEEEEEcccHHHHHHHHHHHHHcccEEEEEEEEEEEccccccHHHHHHHHcccEEEEccccccccccccccccccccccccEEEEEEEEcccccccccEEccccEEccccEEcccccccccccccccccccEEEEcccccEEEEEEEEEEccccccccccccEEEEEEEEccEEEccHHHHcccHHHHHHHHHccccccEEccccccEEEEEccccccccHHHHHHHHHccccccEEEEEEccEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccc
ccHHHHHcccEEEEEEccccEEEEEEEcccHHHHHHHHHHHHHHcccEEEEEEEEEccccHHHHHHHHHHccccEcccccHHHHccccccccccccccccccEEEEEEEEEEcccccccccccccccccccEEEcccccccccccccccccEEEEEEccccEEEEEEEEEccccccccccccEEEEEEEEcccEEEccccccccccHHHHHHHHHccccEEEEcccccEEEEEccccccccHHHHccHHHccccccEEEEEcccEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccc
mdgasyqrfpkvKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVnssvlndefiahrlglipltseramsmrfsrdcdacdgdgqcefcsvefhlrakchsdqtldvtskdlyssdhsvvpvdfvdpagydstdqqRGIIIVKLRRGQELRLRAIARKGigkdhakwspaatvtfmyepeihinedLMESLsleekqswvessptkvfdidpntgqvyvvdaeaytyddEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAvrlsedtvEADDQFGelgahmrgg
mdgasyqrfpkvkirelkddyakfelrdtDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVdpagydstdqqrgiiivklrrgqelRLRAIarkgigkdhakwspaATVTFMYEPEIHINEDLMESLSLEEKQSWVESsptkvfdidpntgQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDtveaddqfgelgahmrgg
MDGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEADDQFGELGAHMRGG
************KIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLME*********WV****TKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRL*********************
****SY*RFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDP*****TDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV***********************
MDGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLS***********PTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEADDQFGELGAHMRGG
MDGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVE***************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MDGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEADDQFGELGAHMRGG
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 ?
Query319 2.2.26 [Sep-21-2011]
Q39211319 DNA-directed RNA polymera yes no 1.0 1.0 0.827 1e-156
Q39212319 DNA-directed RNA polymera no no 1.0 1.0 0.768 1e-144
Q54DH7302 DNA-directed RNA polymera yes no 0.887 0.937 0.496 2e-75
Q3T0Q3275 DNA-directed RNA polymera yes no 0.780 0.905 0.423 6e-52
P16925310 Conjugation stage-specifi N/A no 0.884 0.909 0.383 2e-51
P19387275 DNA-directed RNA polymera yes no 0.780 0.905 0.419 2e-51
P97760275 DNA-directed RNA polymera yes no 0.780 0.905 0.409 7e-48
P16370318 DNA-directed RNA polymera yes no 0.818 0.820 0.384 1e-45
P37382297 DNA-directed RNA polymera yes no 0.761 0.818 0.352 5e-42
O94616348 DNA-directed RNA polymera no no 0.887 0.813 0.310 1e-32
>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 desciption
 Score =  550 bits (1416), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 264/319 (82%), Positives = 292/319 (91%)

Query: 1   MDGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSS 60
           MDGA+YQRFPK+KIRELKDDYAKFELR+TD SMANALRRVMI+EVPT+AIDLVEIEVNSS
Sbjct: 1   MDGATYQRFPKIKIRELKDDYAKFELRETDVSMANALRRVMISEVPTVAIDLVEIEVNSS 60

Query: 61  VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDV 120
           VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEF L +KC +DQTLDV
Sbjct: 61  VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFRLSSKCVTDQTLDV 120

Query: 121 TSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKW 180
           TS+DLYS+D +V PVDF   +    + + +GIIIVKLRRGQEL+LRAIARKGIGKDHAKW
Sbjct: 121 TSRDLYSADPTVTPVDFTIDSSVSDSSEHKGIIIVKLRRGQELKLRAIARKGIGKDHAKW 180

Query: 181 SPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTY 240
           SPAATVTFMYEP+I INED+M++LS EEK   +ESSPTKVF +DP T QV VVD EAYTY
Sbjct: 181 SPAATVTFMYEPDIIINEDMMDTLSDEEKIDLIESSPTKVFGMDPVTRQVVVVDPEAYTY 240

Query: 241 DDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSE 300
           D+EVIKKAEAMGKPGL+EI  K+DSFIFTVESTGA+KASQLVLNAI++LKQKLDAVRLS+
Sbjct: 241 DEEVIKKAEAMGKPGLIEISPKDDSFIFTVESTGAVKASQLVLNAIDLLKQKLDAVRLSD 300

Query: 301 DTVEADDQFGELGAHMRGG 319
           DTVEADDQFGELGAHMRGG
Sbjct: 301 DTVEADDQFGELGAHMRGG 319
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.
Arabidopsis thaliana (taxid: 3702)
>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|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|Q3T0Q3|RPB3_BOVIN DNA-directed RNA polymerase II subunit RPB3 OS=Bos taurus GN=POLR2C PE=2 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|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|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|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

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 ?
Query319
255555327318 DNA-directed RNA polymerase II subunit, 0.996 1.0 0.921 1e-172
147838054318 hypothetical protein VITISV_019338 [Viti 0.996 1.0 0.912 1e-170
225428887318 PREDICTED: DNA-directed RNA polymerase I 0.996 1.0 0.909 1e-170
356576253320 PREDICTED: DNA-directed RNA polymerase I 0.993 0.990 0.886 1e-165
356521566319 PREDICTED: DNA-directed RNA polymerase I 0.990 0.990 0.886 1e-164
449442251320 PREDICTED: DNA-directed RNA polymerase I 1.0 0.996 0.881 1e-164
224105591346 predicted protein [Populus trichocarpa] 0.993 0.916 0.872 1e-162
357475219318 DNA-directed RNA polymerase II subunit R 0.993 0.996 0.856 1e-159
388505946318 unknown [Medicago truncatula] 0.993 0.996 0.853 1e-157
297832026319 RBP36A [Arabidopsis lyrata subsp. lyrata 0.996 0.996 0.840 1e-155
>gi|255555327|ref|XP_002518700.1| DNA-directed RNA polymerase II subunit, putative [Ricinus communis] gi|223542081|gb|EEF43625.1| DNA-directed RNA polymerase II subunit, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  609 bits (1570), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 294/319 (92%), Positives = 309/319 (96%), Gaps = 1/319 (0%)

Query: 1   MDGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSS 60
           M+GASYQRFP++KIRELKDDY KFELRDTDASMANALRRVMIAEVPT+AIDLVEIEVNSS
Sbjct: 1   MEGASYQRFPRIKIRELKDDYCKFELRDTDASMANALRRVMIAEVPTVAIDLVEIEVNSS 60

Query: 61  VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDV 120
           VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQC++CSVEFHLRAKC +DQTLDV
Sbjct: 61  VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCDYCSVEFHLRAKCITDQTLDV 120

Query: 121 TSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKW 180
           TSKDLYSSDH+VVPVDF D +GYDS+ +QRGIIIVKLRRGQELRLRAIARKGIGKDHAKW
Sbjct: 121 TSKDLYSSDHTVVPVDFSDSSGYDSS-EQRGIIIVKLRRGQELRLRAIARKGIGKDHAKW 179

Query: 181 SPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTY 240
           SPAATVTFMYEP+IHINEDLMESLSLEEKQSWVESSPTKVFDIDPNT QV VVD EAYTY
Sbjct: 180 SPAATVTFMYEPDIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTQQVVVVDPEAYTY 239

Query: 241 DDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSE 300
           D+EVIKKAE+MGKPGLV I AKEDSFIFTVESTGAIKASQLVLNAIE+LKQKLDAVRLSE
Sbjct: 240 DEEVIKKAESMGKPGLVNIQAKEDSFIFTVESTGAIKASQLVLNAIEILKQKLDAVRLSE 299

Query: 301 DTVEADDQFGELGAHMRGG 319
           DTVEADDQFGELGAHMRGG
Sbjct: 300 DTVEADDQFGELGAHMRGG 318

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|147838054|emb|CAN60923.1| hypothetical protein VITISV_019338 [Vitis vinifera] Back     alignment and taxonomy information
>gi|225428887|ref|XP_002285322.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-A [Vitis vinifera] Back     alignment and taxonomy information
>gi|356576253|ref|XP_003556247.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-A-like [Glycine max] Back     alignment and taxonomy information
>gi|356521566|ref|XP_003529425.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-A-like [Glycine max] Back     alignment and taxonomy information
>gi|449442251|ref|XP_004138895.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-A-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|224105591|ref|XP_002313865.1| predicted protein [Populus trichocarpa] gi|222850273|gb|EEE87820.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|357475219|ref|XP_003607895.1| DNA-directed RNA polymerase II subunit RPB3-A [Medicago truncatula] gi|85719360|gb|ABC75365.1| RNA polymerase, dimerisation [Medicago truncatula] gi|355508950|gb|AES90092.1| DNA-directed RNA polymerase II subunit RPB3-A [Medicago truncatula] Back     alignment and taxonomy information
>gi|388505946|gb|AFK41039.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|297832026|ref|XP_002883895.1| RBP36A [Arabidopsis lyrata subsp. lyrata] gi|297329735|gb|EFH60154.1| RBP36A [Arabidopsis lyrata subsp. lyrata] 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 ?
Query319
TAIR|locus:2047168319 NRPB3 [Arabidopsis thaliana (t 1.0 1.0 0.827 5.6e-139
TAIR|locus:2047198319 NRPE3B [Arabidopsis thaliana ( 1.0 1.0 0.768 4e-129
DICTYBASE|DDB_G0292244302 rpb3 "RNA polymerase II core s 0.887 0.937 0.496 4.9e-69
UNIPROTKB|E1BV97275 POLR2C "Uncharacterized protei 0.576 0.669 0.549 6.9e-53
UNIPROTKB|I3LCH3275 POLR2C "Uncharacterized protei 0.570 0.661 0.544 1.4e-52
UNIPROTKB|Q3T0Q3275 POLR2C "DNA-directed RNA polym 0.576 0.669 0.544 2.3e-52
UNIPROTKB|E2RQ42275 POLR2C "Uncharacterized protei 0.576 0.669 0.544 2.3e-52
FB|FBgn0026373275 RpII33 "RNA polymerase II 33kD 0.655 0.76 0.468 4.8e-52
RGD|1306935275 Polr2c "polymerase (RNA) II (D 0.576 0.669 0.539 6.1e-52
UNIPROTKB|P19387275 POLR2C "DNA-directed RNA polym 0.576 0.669 0.539 9.9e-52
TAIR|locus:2047168 NRPB3 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1360 (483.8 bits), Expect = 5.6e-139, P = 5.6e-139
 Identities = 264/319 (82%), Positives = 292/319 (91%)

Query:     1 MDGASYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSS 60
             MDGA+YQRFPK+KIRELKDDYAKFELR+TD SMANALRRVMI+EVPT+AIDLVEIEVNSS
Sbjct:     1 MDGATYQRFPKIKIRELKDDYAKFELRETDVSMANALRRVMISEVPTVAIDLVEIEVNSS 60

Query:    61 VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDV 120
             VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEF L +KC +DQTLDV
Sbjct:    61 VLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFRLSSKCVTDQTLDV 120

Query:   121 TSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKW 180
             TS+DLYS+D +V PVDF   +    + + +GIIIVKLRRGQEL+LRAIARKGIGKDHAKW
Sbjct:   121 TSRDLYSADPTVTPVDFTIDSSVSDSSEHKGIIIVKLRRGQELKLRAIARKGIGKDHAKW 180

Query:   181 SPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTY 240
             SPAATVTFMYEP+I INED+M++LS EEK   +ESSPTKVF +DP T QV VVD EAYTY
Sbjct:   181 SPAATVTFMYEPDIIINEDMMDTLSDEEKIDLIESSPTKVFGMDPVTRQVVVVDPEAYTY 240

Query:   241 DDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSE 300
             D+EVIKKAEAMGKPGL+EI  K+DSFIFTVESTGA+KASQLVLNAI++LKQKLDAVRLS+
Sbjct:   241 DEEVIKKAEAMGKPGLIEISPKDDSFIFTVESTGAVKASQLVLNAIDLLKQKLDAVRLSD 300

Query:   301 DTVEADDQFGELGAHMRGG 319
             DTVEADDQFGELGAHMRGG
Sbjct:   301 DTVEADDQFGELGAHMRGG 319
GO:0003677 "DNA binding" evidence=IEA;ISS
GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM;IDA
GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS
GO:0046983 "protein dimerization activity" evidence=IEA
GO:0005730 "nucleolus" evidence=IDA
GO:0005737 "cytoplasm" evidence=IDA
GO:0000418 "DNA-directed RNA polymerase IV complex" evidence=IPI
GO:0000419 "DNA-directed RNA polymerase V complex" evidence=IPI
GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IPI
TAIR|locus:2047198 NRPE3B [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0292244 rpb3 "RNA polymerase II core subunit" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|E1BV97 POLR2C "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|I3LCH3 POLR2C "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
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
FB|FBgn0026373 RpII33 "RNA polymerase II 33kD subunit" [Drosophila melanogaster (taxid:7227)] 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|P19387 POLR2C "DNA-directed RNA polymerase II subunit RPB3" [Homo sapiens (taxid:9606)] 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) ?
Q54DH7RPB3_DICDINo assigned EC number0.49650.88710.9370yesno
Q2NFZ6RPOD_METST2, ., 7, ., 7, ., 60.32400.81500.9629yesno
A5UN55RPOD_METS32, ., 7, ., 7, ., 60.31450.80560.9379yesno
P16370RPB3_YEASTNo assigned EC number0.38460.81810.8207yesno
Q39211RPB3A_ARATHNo assigned EC number0.82751.01.0yesno
Q39212RPB3B_ARATHNo assigned EC number0.76801.01.0nono

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 Layer2.7.70.766
4th Layer2.7.7.60.824

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00036639001
SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (318 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00002744001
SubName- Full=Chromosome chr1 scaffold_135, whole genome shotgun sequence; (78 aa)
•  •••• 0.991
GSVIVG00033123001
SubName- Full=Putative uncharacterized protein (Chromosome chr5 scaffold_64, whole genome shotg [...] (114 aa)
   •••• 0.958
GSVIVG00032808001
SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (116 aa)
   •••• 0.945
GSVIVG00016705001
SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (206 aa)
•  •••• 0.924
GSVIVG00024229001
SubName- Full=Putative uncharacterized protein (Chromosome chr6 scaffold_3, whole genome shotgu [...] (176 aa)
   •••• 0.922
GSVIVG00020457001
SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (208 aa)
•  • •  0.917
Ndpk
RecName- Full=Nucleoside diphosphate kinase; EC=2.7.4.6; (148 aa)
   • •• 0.908
GSVIVG00028076001
SubName- Full=Chromosome chr7 scaffold_42, whole genome shotgun sequence; (533 aa)
   • •  0.906
GSVIVG00002140001
SubName- Full=Chromosome chr19 scaffold_126, whole genome shotgun sequence; (528 aa)
   • •  0.905
GSVIVG00006748001
RecName- Full=Nucleoside diphosphate kinase; EC=2.7.4.6; (235 aa)
     •• 0.900

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 ?
Query319
cd07031265 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic 1e-130
smart00662224 smart00662, RPOLD, RNA polymerases D 2e-77
cd07032291 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryoti 4e-70
PRK00783263 PRK00783, PRK00783, DNA-directed RNA polymerase su 2e-69
cd07030259 cd07030, RNAP_D, D subunit of Archaeal RNA polymer 9e-66
cd07028212 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polym 1e-47
COG0202317 COG0202, RpoA, DNA-directed RNA polymerase, alpha 3e-37
pfam01000117 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA 9e-20
PRK14979195 PRK14979, PRK14979, DNA-directed RNA polymerase su 3e-19
pfam0119388 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 di 2e-09
pfam0119388 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 di 8e-06
cd07028212 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polym 0.001
>gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information 
 Score =  371 bits (956), Expect = e-130
 Identities = 140/295 (47%), Positives = 176/295 (59%), Gaps = 33/295 (11%)

Query: 10  PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAH 69
           P+V+I EL DD  KF L +TD S+AN+LRRVMIAEVPT+AIDLVEIE N+SVL+DEFIAH
Sbjct: 1   PRVEITELTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHDEFIAH 60

Query: 70  RLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
           RLGLIPLTS+      +      CD D  C+ CSVE  L  KC  DQT +VTS+DL SS 
Sbjct: 61  RLGLIPLTSDDVDEFLYYSRD--CDCDEFCDKCSVELTLDVKCTGDQTREVTSRDLVSS- 117

Query: 130 HSVVPVDFVDPAGYDSTD--QQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVT 187
              V      P   DS D  ++ GI+IVKLR+GQEL+LR IA+KGIGK+HAKWSP A VT
Sbjct: 118 GPKVNDVVPVPIRNDSEDNGEEDGILIVKLRKGQELKLRCIAKKGIGKEHAKWSPTAAVT 177

Query: 188 FMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKK 247
           F Y+P+  +       L  E+K+ W +S                     A   +      
Sbjct: 178 FEYDPDNALRHTDYWYLEDEDKE-WPKS-------------------ENACIEEPPE--- 214

Query: 248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDT 302
                K  L +I AK D F F VESTGA+   Q+VL+ +E+LK+KL  ++L    
Sbjct: 215 -----KDALFDIDAKPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLSE 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|132910 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III 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|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|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain Back     alignment and domain information
>gnl|CDD|237878 PRK14979, PRK14979, DNA-directed RNA polymerase subunit D; Provisional 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 319
cd07032291 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly 100.0
KOG1522285 consensus RNA polymerase II, subunit POLR2C/RPB3 [ 100.0
cd07031265 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme 100.0
KOG1521338 consensus RNA polymerase I and III, subunit RPA40/ 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
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
cd06928215 RNAP_alpha_NTD N-terminal domain of the Alpha subu 100.0
PRK05182310 DNA-directed RNA polymerase subunit alpha; Provisi 100.0
COG0202317 RpoA DNA-directed RNA polymerase, alpha subunit/40 100.0
TIGR02027297 rpoA DNA-directed RNA polymerase, alpha subunit, b 100.0
CHL00013327 rpoA RNA polymerase alpha subunit 99.96
PF01000112 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert dom 99.96
PF0119366 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation 99.47
COG0202317 RpoA DNA-directed RNA polymerase, alpha subunit/40 99.23
cd0046086 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA pol 99.04
PRK0114685 DNA-directed RNA polymerase subunit L; Provisional 95.86
cd0692783 RNAP_L L subunit of Archaeal RNA polymerase. The a 94.92
cd0702783 RNAP_RPB11_like RPB11 subunit of RNA polymerase. T 94.22
COG176199 RPB11 DNA-directed RNA polymerase, subunit L [Tran 94.02
PF1365677 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisatio 92.86
cd0692783 RNAP_L L subunit of Archaeal RNA polymerase. The a 91.84
PRK0114685 DNA-directed RNA polymerase subunit L; Provisional 91.56
cd0702783 RNAP_RPB11_like RPB11 subunit of RNA polymerase. T 91.38
cd0702985 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA pol 90.76
cd0692693 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA poly 89.97
cd0692693 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA poly 89.27
cd0702985 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA pol 83.72
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information 
Probab=100.00  E-value=1.3e-78  Score=568.45  Aligned_cols=270  Identities=38%  Similarity=0.556  Sum_probs=240.4

Q ss_pred             cEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccceeeeccC
Q 020983           11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDC   90 (319)
Q Consensus        11 ~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~~~~~~~c   90 (319)
                      +|+|+++++++++|.|.|+++||||||||+|||||||||||.|+|++|||+|+|||||||||||||.++ .+.|+|+.+|
T Consensus         2 ~i~i~~~~~~~~~f~l~~~d~s~ANAlRRimiaEVPt~AId~V~i~~NTSvl~DE~lAHRLGLIPL~~d-~~~~~~~~~~   80 (291)
T cd07032           2 KIEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLIPIKAD-PRLFEYREDS   80 (291)
T ss_pred             eEEEEECCCCEEEEEEecCCHHHHHHHHHHHHhcCcceeEEEEEEEECCccchhHHHHHhhcCceeecC-HHHccccccc
Confidence            689999999999999999999999999999999999999999999999999999999999999999996 4579999998


Q ss_pred             CCCCCCCCCCCceEEEEEEEEeccCCC--------------ceeeccCeeeCCCceeeccccCCCC--CCCCCCCCCeEE
Q 020983           91 DACDGDGQCEFCSVEFHLRAKCHSDQT--------------LDVTSKDLYSSDHSVVPVDFVDPAG--YDSTDQQRGIII  154 (319)
Q Consensus        91 ~~~~~~~~~~~c~v~~~L~v~~~~~~~--------------~~V~s~Dl~~~~~~~~Pv~~~~~~~--~~~~~~~~~I~I  154 (319)
                       +   +..|+.|+|+|+|+|+|+.++.              ..|||+||+     |.|.+.|....  ..-.+.+++|+|
T Consensus        81 -~---~~~~~~~~v~f~L~v~c~~~~~~~~~~~~~~~~~~~~~VyS~dl~-----~~p~g~q~~~~~~~~v~~v~~dI~I  151 (291)
T cd07032          81 -D---DEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKVYSGDLK-----WVPIGSQEKRFADNPIRPVHPDILI  151 (291)
T ss_pred             -c---cCCCCCcEEEEEEEEEccCCcccccccccccccccccEEECCCCE-----ecCCCccccccCCCCcEEeCCCcEE
Confidence             3   2479999999999999986542              467777775     77888765321  122577999999


Q ss_pred             EEeCCCCEEEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCC--CCceee
Q 020983          155 VKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPN--TGQVYV  232 (319)
Q Consensus       155 ~kL~~gq~I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~--~~~~~~  232 (319)
                      +||++||+|+|+|+|+||+||+|||||||++++|||+|.|+|+++.    +++++++|+++||.|||.+++.  ++++.+
T Consensus       152 ~kL~~gQ~l~le~~a~kG~Gk~HAKwsPv~ta~yr~~P~I~i~~~~----~~~~~~~~~~~cP~~Vf~i~~~~~~~~~~V  227 (291)
T cd07032         152 AKLRPGQEIDLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKPI----TGEDAEKLQKCFPPGVIDIEEVKGKKKAVV  227 (291)
T ss_pred             EEECCCCEEEEEEEEEcCcccccceecCceeEEEEecceEEEcCcC----CHHHHHHHHhhCCCccEEecccCCCceEEE
Confidence            9999999999999999999999999999999999999999998764    3577889999999999999752  347889


Q ss_pred             cCCccccchHHHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983          233 VDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR  297 (319)
Q Consensus       233 ~~~~~~~~~~e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~  297 (319)
                      .+++.|++|++|++.++.   .+.|++++++|||+|+|||+|+|+|+++|.+|+++|++|++.|.
T Consensus       228 ~~~~~ct~crec~~~~~~---~~~V~v~~~~d~fiF~VES~G~l~p~~i~~~Ai~iL~~K~~~l~  289 (291)
T cd07032         228 ANPRKDTLSREVLRHEEF---KDKVELGRVRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLL  289 (291)
T ss_pred             cccccCcccHhHhhhhcc---CCceeEEEeCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999987644   46799999999999999999999999999999999999998874

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 subun
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription] Back     alignment and domain information
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information
>KOG1521 consensus RNA polymerase I and III, subunit RPA40/RPC40 [Transcription] 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
>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
>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
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription] 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
>PF01000 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert domain; InterPro: IPR011262 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
>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
>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
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription] 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
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional 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
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query319
1i3q_C318 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 7e-47
3i4m_C324 8-oxoguanine Containing Rna Polymerase Ii Elongatio 7e-47
3how_C347 Complete Rna Polymerase Ii Elongation Complex Iii W 8e-47
3j0k_C268 Orientation Of Rna Polymerase Ii Within The Human V 2e-46
3h0g_C297 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 4e-43
2waq_D265 The Complete Structure Of The Archaeal 13-Subunit D 1e-24
2pa8_D265 X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE 1e-23
>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 =  184 bits (466), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 115/299 (38%), Positives = 167/299 (55%), Gaps = 38/299 (12%)
Query: 10  PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAH 69
           P+VKIRE   D   F L + D +MAN+LRRVMIAE+PT+AID VE+E N++VL DEFIAH
Sbjct: 6   PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 65
Query: 70  RLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
           RLGLIPL S     + +SRDC   D    C+ CSV   L+A   S+ T +V SKDL    
Sbjct: 66  RLGLIPLQSMDIEQLEYSRDCFCED---HCDKCSVVLTLQAFGESESTTNVYSKDLVIVS 122
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
           + ++  +   P   D   +  G++I KLR+GQEL+L  +A+KGI K+HAKW PAA + F 
Sbjct: 123 N-LMGRNIGHPIIQDK--EGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFE 179
Query: 190 YEP--EIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKK 247
           Y+P  ++   +   E  S +E   W +S   + ++  PN G  +   A+A          
Sbjct: 180 YDPWNKLKHTDYWYEQDSAKE---WPQSKNCE-YEDPPNEGDPFDYKAQA---------- 225
Query: 248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEAD 306
                           D+F   VES G+I   Q+V+  I+ L++K+ ++ L+   ++ D
Sbjct: 226 ----------------DTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQD 268
>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|2WAQ|D Chain D, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 265 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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query319
2pa8_D265 DNA-directed RNA polymerase subunit D; ferredoxin- 3e-65
1twf_C318 B44.5, DNA-directed RNA polymerase II 45 kDa polyp 7e-62
3h0g_C297 DNA-directed RNA polymerase II subunit RPB3; trans 5e-61
>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 =  205 bits (522), Expect = 3e-65
 Identities = 79/288 (27%), Positives = 133/288 (46%), Gaps = 33/288 (11%)

Query: 11  KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
            + +    D               NA+RR  +  VP +A+D V    N+S L DE +AHR
Sbjct: 2   SINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHR 61

Query: 71  LGLIPLTSERAM-SMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
           L LIP  SE A+ + R+  +C  C  +  CE C  + ++ A+   ++   + SKD+ S D
Sbjct: 62  LALIPFMSEEALDTYRWPEECIECTEN--CEKCYTKIYIEAEA-PNEPRMIYSKDIKSED 118

Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
            SVVP+                I IV L   Q++ L A  R G GK+HAK+ P +     
Sbjct: 119 PSVVPIS-------------GDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVR 165

Query: 190 YEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249
           Y P++ I  +          +  V   P  VF++    G++ V +  + T  +E ++   
Sbjct: 166 YYPKVEILAN---------CEKAVNVCPEGVFELKD--GKLSVKNELSCTLCEECLRYCN 214

Query: 250 AMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297
                G + I   ED +I  +ES G++K  +++L A + + +K++ + 
Sbjct: 215 -----GSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRKIEELE 257
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query319
2pa8_D265 DNA-directed RNA polymerase subunit D; ferredoxin- 100.0
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
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- 95.67
1xpp_A115 TA1416, DNA-directed RNA polymerase subunit L; str 95.14
3h0g_K123 DNA-directed RNA polymerase II subunit RPB11; tran 92.34
2pa8_L92 DNA-directed RNA polymerase subunit L; ferredoxin- 92.33
1twf_K120 B13.6, DNA-directed RNA polymerase II 13.6 kDa pol 92.14
1twf_K120 B13.6, DNA-directed RNA polymerase II 13.6 kDa pol 90.7
1xpp_A115 TA1416, DNA-directed RNA polymerase subunit L; str 86.4
3h0g_K123 DNA-directed RNA polymerase II subunit RPB11; tran 85.85
>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=7.2e-69  Score=499.42  Aligned_cols=255  Identities=29%  Similarity=0.458  Sum_probs=231.9

Q ss_pred             CcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceecc-ccceeeec
Q 020983           10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSER-AMSMRFSR   88 (319)
Q Consensus        10 ~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~-~~~~~~~~   88 (319)
                      ++|++.+.++++++|.++|+++|+||||||+|||||||+||+.|+|++|||+|+|||+||||||||+++++ .+.|.|+.
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            46899999999999999999999999999999999999999999999999999999999999999999997 45688888


Q ss_pred             cC-CCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEEEE
Q 020983           89 DC-DACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRA  167 (319)
Q Consensus        89 ~c-~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~le~  167 (319)
                      +| .|+   ++|+.|+++|+|+++| ++++++|||+||++.++.+             ++++|+|+|+||++||+|+|++
T Consensus        81 ~~~~~~---~~~~~~~~~~~l~~~~-~~g~~~V~a~Di~~~~~~v-------------~~~~~~i~I~~L~~g~~l~~e~  143 (265)
T 2pa8_D           81 ECIECT---ENCEKCYTKIYIEAEA-PNEPRMIYSKDIKSEDPSV-------------VPISGDIPIVLLGTNQKISLEA  143 (265)
T ss_dssp             GCTTCC---SSCTTTEEEEEEEEEC-CSSCEEEEGGGCEESSTTC-------------CBSCSCCEEEEECTTCEEEEEE
T ss_pred             cccccc---cCCCCcEEEEEEEEEe-cCCCcEEEhhhcccCCCCc-------------eecCCCcEEEEeCCCCEEEEEE
Confidence            88 554   3799999999999999 6799999999999755555             5667789999999999999999


Q ss_pred             EEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHHHHHH
Q 020983          168 IARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKK  247 (319)
Q Consensus       168 ~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~  247 (319)
                      +|+||+||+||||+|+++++|++.|.+.++ .        .+..|.+.||.+++.+|+.  ...+.+..+|++|.+|.+.
T Consensus       144 ~~~~G~G~~~ak~~pv~t~~yr~~p~I~i~-~--------~C~~C~~~CP~g~I~id~~--~~v~~d~~~C~~C~~C~~v  212 (265)
T 2pa8_D          144 RLRLGYGKEHAKFIPVSLSVVRYYPKVEIL-A--------NCEKAVNVCPEGVFELKDG--KLSVKNELSCTLCEECLRY  212 (265)
T ss_dssp             EEEEECTTTCGGGCCEEEEEEEEEEEEEEC-S--------CCTTHHHHCTTCCEEEETT--EEEESCGGGCCCCCHHHHH
T ss_pred             EEecCccccccCcccceeeeeccccchhhh-h--------hHHHHHHhCcccCeEecCC--eeEEeccccCCCchHHHHh
Confidence            999999999999999999999999999987 2        3567888999999999863  2446688999999999998


Q ss_pred             HhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983          248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR  297 (319)
Q Consensus       248 ~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~  297 (319)
                      +     +++|.+.+++++|+|+|||+|+++|++++.+|+++|++||+.|.
T Consensus       213 C-----p~aI~~~~~~d~~i~~VEt~Gsl~Pee~v~~A~~iL~~~~~~~~  257 (265)
T 2pa8_D          213 C-----NGSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRKIEELE  257 (265)
T ss_dssp             H-----TTSEEEEEEEEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             C-----CCceEEEecCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            7     35899999999999999999999999999999999999999987
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} 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
>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
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} 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
>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
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} 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 319
d1twfc2131 d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharo 3e-49
d1twfc1135 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (S 7e-14
d1twfc1135 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (S 8e-11
>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 =  158 bits (401), Expect = 3e-49
 Identities = 65/137 (47%), Positives = 86/137 (62%), Gaps = 6/137 (4%)

Query: 46  PTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVE 105
           PT+AID VE+E N++VL DEFIAHRLGLIPL S     + +SRDC   D    C+ CSV 
Sbjct: 1   PTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDH---CDKCSVV 57

Query: 106 FHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRL 165
             L+A   S+ T +V SKDL    + ++  +   P   D      G++I KLR+GQEL+L
Sbjct: 58  LTLQAFGESESTTNVYSKDLVIVSN-LMGRNIGHPIIQDKEG--NGVLICKLRKGQELKL 114

Query: 166 RAIARKGIGKDHAKWSP 182
             +A+KGI K+HAKW P
Sbjct: 115 TCVAKKGIAKEHAKWGP 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 ?
Query319
d1twfc2131 RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1twfc1135 RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta 99.83
d1bdfa2126 RNA polymerase alpha subunit {Escherichia coli [Ta 99.37
d1smya2123 RNA polymerase alpha subunit {Thermus thermophilus 99.28
d1bdfa1105 RNA polymerase alpha {Escherichia coli [TaxId: 562 98.9
d1smya1106 RNA polymerase alpha {Thermus thermophilus [TaxId: 98.43
d1bdfa1105 RNA polymerase alpha {Escherichia coli [TaxId: 562 97.28
d1smya1106 RNA polymerase alpha {Thermus thermophilus [TaxId: 95.75
d1xppa_99 DNA-directed RNA polymerase subunit L, RpoL {Therm 95.57
d1twfk_114 RPB11 {Baker's yeast (Saccharomyces cerevisiae) [T 82.26
>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=4.8e-41  Score=279.33  Aligned_cols=130  Identities=48%  Similarity=0.763  Sum_probs=111.5

Q ss_pred             CcceEEEEEEeeCcccccchhhhhhhcCCcceeccccceeeeccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCe
Q 020983           46 PTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDL  125 (319)
Q Consensus        46 Pt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~~~~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl  125 (319)
                      ||||||.|+|++|||+|+|||||||||||||.+.+.+.|.|.+.|.|.+   .|+.|++.|+|+|+|+++++..|||+||
T Consensus         1 PtlAid~V~I~~NTS~l~DE~iaHRLglIPi~~~~~~~~~~~~~~~~~~---~~~~~~v~~~L~v~~~~~~~~~V~s~Dl   77 (131)
T d1twfc2           1 PTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCED---HCDKCSVVLTLQAFGESESTTNVYSKDL   77 (131)
T ss_dssp             CEEEEEEEEEEEECSSSCHHHHHHHHHTSCEEETTGGGSCCTTTSSSSS---CCTTTEEEEEEEEECCSSSCEEEEGGGE
T ss_pred             CeEEEEEEEEEECCcccchHHHHHhhcCceeeccChhhccccccccccC---CCCCceEEEEeEcccCCCCCceEEhhhe
Confidence            8999999999999999999999999999999998887899999988753   7999999999999999899999999999


Q ss_pred             eeCCCc-eeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEEEEEEEecccccccccCc
Q 020983          126 YSSDHS-VVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSP  182 (319)
Q Consensus       126 ~~~~~~-~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~le~~a~kG~Gk~HAKw~P  182 (319)
                      +..+.. +.+...+...    ...+++|+|+||+|||+|+|+|+|+||+||+||||||
T Consensus        78 ~~~~~~~~~~~~~~~~~----~~~~~~IlI~kL~pGQ~i~l~a~a~kG~Gk~HAK~sP  131 (131)
T d1twfc2          78 VIVSNLMGRNIGHPIIQ----DKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGP  131 (131)
T ss_dssp             EECSCCTTCSEEEECCC----STTSCCSEEEEECTTCEEEEEEEEEEECTTTCGGGCC
T ss_pred             EEcCCccccccCCcccc----CCcCCCCEEEEeCCCCEEEEEEEEEecccccCcEeCc
Confidence            874321 1111111101    3456789999999999999999999999999999998
>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
>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]} 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