YRC Public Data Repository - Protein Structure Prediction

Protein:	RET1
Organism:	Saccharomyces cerevisiae
Length:	1149 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 RET1.

Description	E-value	Query Range	Subject Range
gi\|15920466, gi\|... - gi\|15920466\|ref\|NP_376135.1\| DNA-directed RNA polymerase subunit beta [Sulfolobus tokodaii str. 7], ...	0.0	[39..1145]	[3..1116]
gi\|14520830, gi\|... - gi\|5458046\|emb\|CAB49536.1\| rpoB DNA-directed RNA polymerase, subunit B (EC 2.7.7.6) [Pyrococcus abys... gi\|7434758, gi\|5... - pir\|\|A75182 DNA-directed RNA polymerase (EC 2.7.7.6) chain B PAB0423 - Pyrococcus abyssi (strain Ors...	0.0	[40..1143]	[10..1113]
gi\|6606109 - gi\|6606109\|gb\|AAF19067.1\|AF107795_1 DNA-dependent RNA polymerase II RPB140 [Trichophyton rubrum]	0.0	[78..1062]	[14..1109]
NRPB2_ARATH - DNA-directed RNA polymerase II subunit 2 OS=Arabidopsis thaliana GN=NRPB2 PE=1 SV=2	0.0	[27..1144]	[9..1179]
gi\|220943532 - gi\|220943532\|gb\|ACL84309.1\| RpIII128-PA [synthetic construct] RpIII128-PA - The gene RNA polymerase III 128kD subunit is referred to in FlyBase by the symbol Dmel\RpIII128 (CG8...	0.0	[18..1146]	[8..1137]
gi\|168277428 - gi\|168277428\|dbj\|BAG10692.1\| DNA-directed RNA polymerase II subunit RPB2 [synthetic construct] gi\|62660340, gi\|... - gi\|62660340\|ref\|XP_214021.3\| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa polypeptid... gi\|114594586 - gi\|114594586\|ref\|XP_517275.2\| PREDICTED: DNA directed RNA polymerase II polypeptide B isoform 2 [Pan... ENSCJAT00000008049 - null ENSMMUT000000196... - null, null POLR2B - polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	0.0	[26..1142]	[6..1172]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[26..1143]	[7..1175]
gi\|172211 - gi\|172211\|gb\|AAA68096.1\| RNA polymerase II 48 kd subunit [Saccharomyces cerevisiae]	0.0	[26..1144]	[13..1219]

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Predicted Domain #1

Region A:
Residues: [1-202]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVAATKRRKT HIHKHVKDEA FDDLLKPVYK GKKLTDEINT AQDKWHLLPA FLKVKGLVKQ  60
   61 HLDSFNYFVD TDLKKIIKAN QLILSDVDPE FYLKYVDIRV GKKSSSSTKD YLTPPHECRL 120
  121 RDMTYSAPIY VDIEYTRGRN IIMHKDVEIG RMPIMLRSNK CILYDADESK MAKLNECPLD 180
  181 PGGYFIVNGT EKVILVQEQL SK

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [369-526]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RDYVGNKRLE LAGQLISLLF EDLFKKFNND FKLSIDKVLK KPNRAMEYDA LLSINVHSNN  60
   61 ITSGLNRAIS TGNWSLKRFK MERAGVTHVL SRLSYISALG MMTRISSQFE KSRKVSGPRA 120
  121 LQPSQFGMLC TADTPEGEAC GLVKNLALMT HITTDDEE

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [573-682]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TQFRHLRRTG KVSEFISIYS NSHQMAVHIA TDGGRICRPL IIVSDGQSRV KDIHLRKLLD  60
   61 GELDFDDFLK LGLVEYLDVN EENDSYIALY EKDIVPSMTH LEIEPFTILG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11000.0
Match:	1k83B_
Description:	RBP2
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA-directed RNA polymerase activity	10.2021663255698	bayes_pls_golite062009
RNA polymerase activity	10.2021663255698	bayes_pls_golite062009
nucleotidyltransferase activity	7.6240729546188	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	6.31198922553685	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	5.44374972993429	bayes_pls_golite062009
transferase activity	4.83218811360621	bayes_pls_golite062009
transcription regulator activity	2.34884279395902	bayes_pls_golite062009
nucleic acid binding	2.33174616086951	bayes_pls_golite062009
DNA binding	2.27079409864244	bayes_pls_golite062009
binding	1.73416306650822	bayes_pls_golite062009
RNA polymerase II transcription mediator activity	1.53259746846673	bayes_pls_golite062009
catalytic activity	1.36406839864424	bayes_pls_golite062009
RNA binding	1.12618950637766	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.847783043631028	bayes_pls_golite062009
protein binding	0.45174975126993	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [203-368]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NRIIVEADEK KGIVQASVTS STHERKSKTY VITKNGKIYL KHNSIAEEIP IAIVLKACGI  60
   61 LSDLEIMQLV CGNDSSYQDI FAVNLEESSK LDIYTQQQAL EYIGAKVKTM RRQKLTILQE 120
  121 GIEAIATTVI AHLTVEALDF REKALYIAMM TRRVVMAMYN PKMIDD

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [527-572]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EPIKKLCYVL GVEDITLIDS ASLHLNYGVY LNGTLIGSIR FPTKFV

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [683-1060]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AVAGLIPYPH HNQSPRNTYQ CAMGKQAIGA IAYNQFKRID TLLYLMTYPQ QPMVKTKTIE  60
   61 LIDYDKLPAG QNATVAVMSY SGYDIEDALV LNKSSIDRGF GRCETRRKTT TVLKRYANHT 120
  121 QDIIGGMRVD ENGDPIWQHQ SLGPDGLGEV GMKVQSGQIY INKSVPTNSA DAPNPNNVNV 180
  181 QTQYREAPVI YRGPEPSHID QVMMSVSDND QALIKVLLRQ NRRPELGDKF SSRHGQKGVC 240
  241 GIIVKQEDMP FNDQGIVPDI IMNPHGFPSR MTVGKMIELI SGKAGVLNGT LEYGTCFGGS 300
  301 KLEDMSKILV DQGFNYSGKD MLYSGITGEC LQAYIFFGPI YYQKLKHMVL DKMHARARGP 360
  361 RAVLTRQPTE GRSRDGGL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11000.0
Match:	1k83B_
Description:	RBP2
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [1061-1149]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RLGEMERDCV IAYGASQLLL ERLMISSDAF EVDVCDKCGL MGYSGWCTTC KSAENIIKMT  60
   61 IPYAAKLLFQ ELLSMNIAPR LRLEDIFQQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11000.0
Match:	1k83B_
Description:	RBP2
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

Predicted functions: