YRC Public Data Repository - Protein Structure Prediction

Protein:	VTS1
Organism:	Saccharomyces cerevisiae
Length:	523 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 VTS1.

Description	E-value	Query Range	Subject Range
gi\|7494259 - pir\|\|T18492 hypothetical protein C0805w - malaria parasite (Plasmodium falciparum) gi\|124505021, gi... - gi\|3758846\|emb\|CAB11131.1\| DNA-directed RNA polymerase II, putative [Plasmodium falciparum 3D7], gi\|...	1.0E-56	[136..462]	[2072..2393]
gi\|9943, gi\|66976 - gi\|9943\|emb\|CAA34560.1\| unnamed protein product [Plasmodium falciparum], pir\|\|RNZQ2L DNA-directed RN... RPB1_PLAFD - DNA-directed RNA polymerase II subunit RPB1 OS=Plasmodium falciparum (isolate CDC / Honduras) GN=RPI...	8.0E-55	[136..462]	[2074..2388]
VTS1 - Post-transcriptional gene regulator, flap-structured DNA-binding and RNA-binding protein; shows gene... VTS1_YEAST - Protein VTS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=VTS1 PE=1 SV=1 gi\|151945436 - gi\|151945436\|gb\|EDN63679.1\| VTi1-2 suppressor [Saccharomyces cerevisiae YJM789] gi\|190407652 - gi\|190407652\|gb\|EDV10919.1\| protein VTS1 [Saccharomyces cerevisiae RM11-1a]	6.0E-54	[1..523]	[1..523]
gi\|23491122 - gi\|23491122\|gb\|EAA22733.1\| RNA polymerase A/beta'/A'' subunit, putative [Plasmodium yoelii yoelii] gi\|83317456 - gi\|83317456\|ref\|XP_731168.1\| RNA polymerase A/beta'/A'' subunit [Plasmodium yoelii yoelii str. 17XNL...	5.0E-51	[122..473]	[1961..2281]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	4.0E-45	[158..406]	[1429..1689]
gi\|12642614 - gi\|12642614\|gb\|AAK00311.1\|AF315821_1 DNA-dependent RNA polymerase II largest subunit RPB1 [Monosiga ...	1.0E-43	[101..421]	[1414..1743]
gi\|40217297, gi\|... - gi\|4808164\|emb\|CAB42795.1\| largest subunit of the RNA polymerase II complex [Drosophila guanche], gi...	8.0E-43	[122..458]	[1498..1868]
gi\|4808166 - gi\|4808166\|emb\|CAB42797.1\| largest subunit of the RNA polymerase II complex [Drosophila pseudoobscur...	3.0E-42	[122..458]	[1420..1790]
gi\|14388553 - gi\|14388553\|dbj\|BAB60796.1\| hypothetical protein [Macaca fascicularis]	6.0E-42	[298..519]	[168..396]

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Predicted Domain #1

Region A:
Residues: [1-416]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKHPYEEFPT GSKSPYNMSR GAHPGAVLLS PQSSAINKNN PGSNSGNNQG NSSVTANVLS  60
   61 PQSHSMSLND MLDQQSFMLD TAGTRAQPLQ QQQQQQQQQQ QASLPSLNIQ TVSSTAAGSA 120
  121 IVSPMMQSPK ALQSTLSSTS MYLDSFQRSP NNILGIPSQS GSIPLPQSRQ SQQQSQSQKN 180
  181 DPNMGTNFSQ DINQLCSWIS MLNSSQQNTV MDNILSILND DVLKYTKLKI ETLTNTPFIS 240
  241 PPLPAIASPI PNRDDTQILN IDSVFSSSPI TNDPENTDNL LYQNWSPQPH SIPISQPIYD 300
  301 NITDASQRSK SAEPHVNSSP NLIPVQKQFN NGNSTKYKKL PSENPNYLSH SLSSSHSFFQ 360
  361 PKKRSNMGNE YNSHHHHSLH HPLHNTTSYF SNTSRPSGTD LNKSNQNVFN NTITHP

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [417-523]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NAGPTSATST STSSNGNTPL SSNSSMNPKS LTDPKLLKNI PMWLKSLRLH KYSDALSGTP  60
   61 WIELIYLDDE TLEKKGVLAL GARRKLLKAF GIVIDYKERD LIDRSAY

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [309-407]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SKSAEPHVNS SPNLIPVQKQ FNNGNSTKYK KLPSENPNYL SHSLSSSHSF FQPKKRSNMG  60
   61 NEYNSHHHHS LHHPLHNTTS YFSNTSRPSG TDLNKSNQN

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #4

Region A:
Residues: [408-523]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VFNNTITHPN AGPTSATSTS TSSNGNTPLS SNSSMNPKSL TDPKLLKNIP MWLKSLRLHK  60
   61 YSDALSGTPW IELIYLDDET LEKKGVLALG ARRKLLKAFG IVIDYKERDL IDRSAY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	28.0
Match:	2b6gA
Description:	RNA recognition by the Vts1 SAM domain
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