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View Structure Prediction Details

Protein: RPO41
Organism: Saccharomyces cerevisiae
Length: 1351 amino acids
Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076



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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for RPO41.

Description E-value Query
Range		 Subject
Range
RPO41 - Mitochondrial RNA polymerase; single subunit enzyme similar to those of T3 and T7 bacteriophages; re...
RPOM_YEAST - DNA-directed RNA polymerase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ...
 0.0 [1..1351] [1..1351]
gi|4559304, gi|1... - gi|4559304|gb|AAD22976.1|AF127021_1 T7-like RNA polymerase [Zea mays], gi|162457737|ref|NP_001104931...
 0.0 [402..1249] [121..967]
gi|6958204 - gi|6958204|gb|AAF32492.1|AF091838_1 single-subunit RNA polymerase G [Triticum aestivum]
 0.0 [407..1249] [157..997]
gi|15823750 - gi|15823750|dbj|BAB69063.1| T7 bacteriophage-type single subunit RNA polymerase [Nicotiana sylvestri...
 0.0 [386..1249] [136..994]
RPOT1_ARATH - DNA-directed RNA polymerase 1, mitochondrial OS=Arabidopsis thaliana GN=RPOT1 PE=2 SV=1
 0.0 [376..1249] [85..968]
gi|1865721 - gi|1865721|emb|CAA69305.1| mitochondrial single-subunit DNA-dependent RNA polymerase [Chenopodium al...
 0.0 [384..1249] [121..980]

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Predicted Domain #1
Region A:
Residues: [1-379] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLRPAYKSLV KTSLLQRRLI SSKGSKLFKP SPDSTSTILI SEDPLVTGSS PTSSTTSGII  60
   61 SSNDFPLFNK NRKDAKSSIS YQWKNPSELE FDPFNKSHAS AVTSMTRTRD VMQLWSLLEA 120
  121 CLQSNLMKRA FSILESLYLV PEHKQRFIED YNMYLNSFSK NDPNFPILKM NEKLTNDLET 180
  181 SFKDVNYNDK TLAIMIHHAL NFHSTTSSML LKPIISAYLK MSVNGIREIF SCLDILTISD 240
  241 LNILMNDLKV ITPSQLPNSV RPILESLTLS PTPVNNIENE EGLNKVEAEN DSKLHKASNA 300
  301 SSDSIKKPSL DPLREVSFHG STEVLSKDAE KLIAVDTIGM RVIRHTLLGL SLTPEQKEQI 360
  361 SKFKFDANDN VLKMKPTKN

[Run NCBI BLAST on this sequence.]

Detection Method: deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2
Region A:
Residues: [380-423] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DDNNNSINFF EIYNSLPTLE EKKAFESALN IFNQDRQKVL ENRA

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [547-591] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RSEQVLKSES QAFRDVNKKS PEFKKLVQNA KSVFRSSQIE QSKIL

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [671-696] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QLLPMLVEPK PWVNWRSGGY HYTQST

[Run NCBI BLAST on this sequence.]

Region D:
Residues: [805-820] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YKLEIARAFL GEKLYF

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 1703.0103
Match: 1aroP_
Description: T7 RNA polymerase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
nucleotidyltransferase activity 7.61500320688433 bayes_pls_golite062009
DNA-directed RNA polymerase activity 7.08533444189463 bayes_pls_golite062009
RNA polymerase activity 7.08533444189463 bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups 5.40114148359009 bayes_pls_golite062009
transferase activity 4.7475061982508 bayes_pls_golite062009
DNA-directed DNA polymerase activity 3.58831088586896 bayes_pls_golite062009
DNA polymerase activity 3.3731931763308 bayes_pls_golite062009
binding 1.92492422240469 bayes_pls_golite062009
DNA binding 1.87721092677049 bayes_pls_golite062009
nucleic acid binding 1.64235873416087 bayes_pls_golite062009
chromatin binding 1.32386525961438 bayes_pls_golite062009
catalytic activity 1.04899053677564 bayes_pls_golite062009
protein binding 0.561579019896047 bayes_pls_golite062009
exonuclease activity 0.16454326755539 bayes_pls_golite062009
3'-5' exonuclease activity 0.0700154911930899 bayes_pls_golite062009
nuclease activity 0.0574785418962505 bayes_pls_golite062009

Predicted Domain #3
Region A:
Residues: [424-546] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TEAARERWKH DFEEAKARGD ISIEKNLNVK LWKWYNEMLP LVKEEINHCR SLLSEKLSDK  60
   61 KGLNKVDTNR LGYGPYLTLI DPGKMCVITI LELLKLNSTG GVIEGMRTAR AVISVGKAIE 120
  121 MEF

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [592-670] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 WPQSIRARIG SVLISMLIQV AKVSVQGVDP VTKAKVHGEA PAFAHGYQYH NGSKLGVLKI  60
   61 HKTLIRQLNG ERLIASVQP

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [697-733] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LLRTKDSPEQ VAYLKAASDN GDIDRVYDGL NVLGRTP

[Run NCBI BLAST on this sequence.]

Region D:
Residues: [769-804] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 APPKNSDPSI LRAWKLQVKT IANKFSSDRS NRCDTN

[Run NCBI BLAST on this sequence.]

Region E:
Residues: [821-840] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PHNLDFRGRA YPLSPHFNHL

[Run NCBI BLAST on this sequence.]

Region F:
Residues: [1124-1144] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EESKKQVETN LQTVFISDPF A

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 1703.0103
Match: 1aroP_
Description: T7 RNA polymerase
Matching Structure (courtesy of the PDB):

Predicted Domain #4
Region A:
Residues: [734-768] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 WTVNRKVFDV VSQVWNKGEG FLDIPGAQDE MVLPP

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [841-945] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GNDMSRGLLI FWHGKKLGPS GLKWLKIHLS NLFGFDKLPL KDRVAFTESH LQDIKDSAEN  60
   61 PLTGDRWWTT ADKPWQALAT CFELNEVMKM DNPEEFISHQ PVHQD

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [1167-1205] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ASHMLLSAAE CGKQGLDFAS VHDSYWTHAS DIDTMNVVL

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 1703.0103
Match: 1aroP_
Description: T7 RNA polymerase
Matching Structure (courtesy of the PDB):

Predicted Domain #5
Region A:
Residues: [946-1123] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GTCNGLQHYA ALGGDVEGAT QVNLVPSDKP QDVYAHVARL VQKRLEIAAE KGDENAKILK  60
   61 DKITRKVVKQ TVMTNVYGVT YVGATFQIAK QLSPIFDDRK ESLDFSKYLT KHVFSAIREL 120
  121 FHSAHLIQDW LGESAKRISK SIRLDVDEKS FKNGNKPDFM SSVIWTTPLG LPIVQPYR

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [1145-1166] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VNPVNARRQK AGLPPNFIHS LD

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [1206-1259] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 REQFIKLHEV DLVLRLKEEF DQRYKNYVKI GKLKRSTDLA QKIIRIRKDL SRKL

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 1703.0103
Match: 1aroP_
Description: T7 RNA polymerase
Matching Structure (courtesy of the PDB):

Predicted Domain #6
Region A:
Residues: [1260-1351] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GRSTTLADEI YFEKKRQELL NSPLIEDRNV GEKMVTTVSL FEDITDLDAL ELENGGDENS  60
   61 GMSVLLPLRL PEIPPKGDFD VTVLRNSQYF FS

[Run NCBI BLAST on this sequence.]

Detection Method: deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle