YRC Public Data Repository - Protein Structure Prediction

Protein:	RPO21
Organism:	Saccharomyces cerevisiae
Length:	1733 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 RPO21.

Description	E-value	Query Range	Subject Range
gi\|83767526, gi\|... - gi\|9955855\|dbj\|BAB12227.1\| RNA polymerase II largest subunit [Aspergillus oryzae], gi\|83767526\|dbj\|B... gi\|169770395 - gi\|169770395\|ref\|XP_001819667.1\| hypothetical protein [Aspergillus oryzae RIB40]	0.0	[6..1680]	[8..1746]
RPOC_BACSU - DNA-directed RNA polymerase subunit beta' OS=Bacillus subtilis GN=rpoC PE=3 SV=3	0.0	[10..1078]	[3..1049]
gi\|13310932 - gi\|13310932\|gb\|AAF36438.2\|AF126254_1 RNA polymerase II largest subunit [Leishmania donovani]	0.0	[7..1656]	[10..1665]
RPOC_BACAN - DNA-directed RNA polymerase subunit beta' OS=Bacillus anthracis GN=rpoC PE=3 SV=3 gi\|254733742 - gi\|254733742\|ref\|ZP_05191457.1\| DNA-directed RNA polymerase subunit beta' [Bacillus anthracis str. W... gi\|254739411 - gi\|254739411\|ref\|ZP_05197111.1\| DNA-directed RNA polymerase subunit beta' [Bacillus anthracis str. K... gi\|254751216 - gi\|254751216\|ref\|ZP_05203254.1\| DNA-directed RNA polymerase subunit beta' [Bacillus anthracis str. V... gi\|254756815 - gi\|254756815\|ref\|ZP_05208843.1\| DNA-directed RNA polymerase subunit beta' [Bacillus anthracis str. A... gi\|167642035, gi... - gi\|167642035\|ref\|ZP_02400264.1\| DNA-directed RNA polymerase, beta' subunit [Bacillus anthracis str. ... gi\|170666334, gi... - gi\|170689709\|ref\|ZP_02880885.1\| DNA-directed RNA polymerase, beta' subunit [Bacillus anthracis str. ... gi\|49183137, gi\|... - gi\|49183137\|ref\|YP_026389.1\| DNA-directed RNA polymerase subunit beta' [Bacillus anthracis str. Ster... gi\|65317560, gi\|... - gi\|65317560\|ref\|ZP_00390519.1\| COG0086: DNA-directed RNA polymerase, beta' subunit/160 kD subunit [B... gi\|227006019, gi... - gi\|227812776\|ref\|YP_002812785.1\| DNA-directed RNA polymerase, beta' subunit [Bacillus anthracis str.... gi\|229269269, gi... - gi\|229604861\|ref\|YP_002864754.1\| DNA-directed RNA polymerase, beta' subunit [Bacillus anthracis str.... gi\|254684393 - gi\|254684393\|ref\|ZP_05148253.1\| DNA-directed RNA polymerase subunit beta' [Bacillus anthracis str. C...	0.0	[10..1090]	[3..1037]
gi\|16505 - gi\|16505\|emb\|CAA37130.1\| RNA polymerase II [Arabidopsis thaliana]	0.0	[6..1646]	[7..1760]
gi\|238913733 - gi\|238913733\|ref\|ZP_04657570.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subsp... gi\|194404810, gi... - gi\|194446147\|ref\|YP_002043406.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica sub... gi\|195629010, gi... - gi\|195629010\|gb\|EDX48402.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica subsp. e... gi\|168264591, gi... - gi\|205346976\|gb\|EDZ33607.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica subsp. e... RPOC_SALCH - DNA-directed RNA polymerase subunit beta' OS=Salmonella choleraesuis GN=rpoC PE=3 SV=1 RPOC_SALTY - DNA-directed RNA polymerase subunit beta' OS=Salmonella typhimurium GN=rpoC PE=3 SV=1 lcl\|NC_016856.1_... - [gene=rpoC] [protein=DNA-directed RNA polymerase subunit beta'] [protein_id=YP_005240433.1] [locatio... gi\|224585696, gi... - gi\|224585696\|ref\|YP_002639495.1\| DNA-directed RNA polymerase beta' subunit [Salmonella enterica subs... gi\|213650889 - gi\|213650889\|ref\|ZP_03380942.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subsp... gi\|213582657 - gi\|213582657\|ref\|ZP_03364483.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subsp... RPOC_SALCH - DNA-directed RNA polymerase subunit beta' OS=Salmonella choleraesuis (strain SC-B67) GN=rpoC PE=3 SV... gi\|197264212, gi... - gi\|197264212\|ref\|ZP_03164286.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica subs... gi\|197215260, gi... - gi\|197251557\|ref\|YP_002149065.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica sub... RPOC_SALTY - DNA-directed RNA polymerase subunit beta' OS=Salmonella typhimurium GN=rpoC PE=3 SV=1 gi\|194469670, gi... - gi\|194469670\|ref\|ZP_03075654.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica subs... gi\|194450168, gi... - gi\|194450168\|ref\|YP_002048141.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subs... gi\|213425738 - gi\|213425738\|ref\|ZP_03358488.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subsp... gi\|207859332, gi... - gi\|207859332\|ref\|YP_002245983.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subs... gi\|204319887, gi... - gi\|204931272\|ref\|ZP_03222032.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica subs... gi\|199603876, gi... - gi\|200386778\|ref\|ZP_03213390.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica subs... RPOC_SALTY - DNA-directed RNA polymerase subunit beta' OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 70... gi\|29139422, gi\|... - gi\|29143787\|ref\|NP_807129.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subsp. e... RPOC_SALTI - DNA-directed RNA polymerase subunit beta' OS=Salmonella typhi GN=rpoC PE=3 SV=1 RPOC_SALTI - DNA-directed RNA polymerase subunit beta' OS=Salmonella typhi GN=rpoC PE=3 SV=1 gi\|16762299 - gi\|16762299\|ref\|NP_457916.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subsp. e... RPOC_SALCH - DNA-directed RNA polymerase subunit beta' OS=Salmonella choleraesuis GN=rpoC PE=3 SV=1	0.0	[7..1489]	[10..1406]
gi\|7434739 - pir\|\|H71031 probable DNA-directed RNA polymerase subunit A' - Pyrococcus horikoshii gi\|14591328, gi\|... - gi\|3257973\|dbj\|BAA30656.1\| 907aa long hypothetical DNA-directed RNA polymerase subunit A' [Pyrococcu...	0.0	[11..899]	[5..906]
RPOC_BRUME - DNA-directed RNA polymerase subunit beta' OS=Brucella melitensis GN=rpoC PE=3 SV=1 RPOC_BRUME - DNA-directed RNA polymerase subunit beta' OS=Brucella melitensis biotype 1 (strain 16M / ATCC 23456 ...	0.0	[8..1469]	[12..1399]
gi\|9587193, gi\|9... - gi\|9587199\|gb\|AAF89203.1\|AF272653_1 RNA polymerase II largest subunit [Drosophila subobscura], gi\|95...	0.0	[1..1713]	[1..1816]
RpII215-PA - The gene RNA polymerase II 215kD subunit is referred to in FlyBase by the symbol Dmel\RpII215 (CG155...	0.0	[1..1685]	[1..1814]

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Predicted Domain #1

Region A:
Residues: [1-1555]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS  60
   61 IDRNLKCQTC QEGMNECPGH FGHIDLAKPV FHVGFIAKIK KVCECVCMHC GKLLLDEHNE 120
  121 LMRQALAIKD SKKRFAAIWT LCKTKMVCET DVPSEDDPTQ LVSRGGCGNT QPTIRKDGLK 180
  181 LVGSWKKDRA TGDADEPELR VLSTEEILNI FKHISVKDFT SLGFNEVFSR PEWMILTCLP 240
  241 VPPPPVRPSI SFNESQRGED DLTFKLADIL KANISLETLE HNGAPHHAIE EAESLLQFHV 300
  301 ATYMDNDIAG QPQALQKSGR PVKSIRARLK GKEGRIRGNL MGKRVDFSAR TVISGDPNLE 360
  361 LDQVGVPKSI AKTLTYPEVV TPYNIDRLTQ LVRNGPNEHP GAKYVIRDSG DRIDLRYSKR 420
  421 AGDIQLQYGW KVERHIMDND PVLFNRQPSL HKMSMMAHRV KVIPYSTFRL NLSVTSPYNA 480
  481 DFDGDEMNLH VPQSEETRAE LSQLCAVPLQ IVSPQSNKPC MGIVQDTLCG IRKLTLRDTF 540
  541 IELDQVLNML YWVPDWDGVI PTPAIIKPKP LWSGKQILSV AIPNGIHLQR FDEGTTLLSP 600
  601 KDNGMLIIDG QIIFGVVEKK TVGSSNGGLI HVVTREKGPQ VCAKLFGNIQ KVVNFWLLHN 660
  661 GFSTGIGDTI ADGPTMREIT ETIAEAKKKV LDVTKEAQAN LLTAKHGMTL RESFEDNVVR 720
  721 FLNEARDKAG RLAEVNLKDL NNVKQMVMAG SKGSFINIAQ MSACVGQQSV EGKRIAFGFV 780
  781 DRTLPHFSKD DYSPESKGFV ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR 840
  841 LVKALEDIMV HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGSD AAFEKRYRVD 900
  901 LLNTDHTLDP SLLESGSEIL GDLKLQVLLD EEYKQLVKDR KFLREVFVDG EANWPLPVNI 960
  961 RRIIQNAQQT FHIDHTKPSD LTIKDIVLGV KDLQENLLVL RGKNEIIQNA QRDAVTLFCC1020
 1021 LLRSRLATRR VLQEYRLTKQ AFDWVLSNIE AQFLRSVVHP GEMVGVLAAQ SIGEPATQMT1080
 1081 LNTFHFAGVA SKKVTSGVPR LKEILNVAKN MKTPSLTVYL EPGHAADQEQ AKLIRSAIEH1140
 1141 TTLKSVTIAS EIYYDPDPRS TVIPEDEEII QLHFSLLDEE AEQSFDQQSP WLLRLELDRA1200
 1201 AMNDKDLTMG QVGERIKQTF KNDLFVIWSE DNDEKLIIRC RVVRPKSLDA ETEAEEDHML1260
 1261 KKIENTMLEN ITLRGVENIE RVVMMKYDRK VPSPTGEYVK EPEWVLETDG VNLSEVMTVP1320
 1321 GIDPTRIYTN SFIDIMEVLG IEAGRAALYK EVYNVIASDG SYVNYRHMAL LVDVMTTQGG1380
 1381 LTSVTRHGFN RSNTGALMRC SFEETVEILF EAGASAELDD CRGVSENVIL GQMAPIGTGA1440
 1441 FDVMIDEESL VKYMPEQKIT EIEDGQDGGV TPYSNESGLV NADLDVKDEL MFSPLVDSGS1500
 1501 NDAMAGGFTA YGGADYGEAT SPFGAYGEAP TSPGFGVSSP GFSPTSPTYS PTSPA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11000.0
Match:	1k83A_
Description:	RBP1
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [1556-1733]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT  60
   61 SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPAYSPTS PSYSPTSPSY 120
  121 SPTSPSYSPT SPSYSPTSPN YSPTSPSYSP TSPGYSPGSP AYSPKQDEQK HNENENSR

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	14.21
Match:	1m2vB
Description:	Sec24
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits