YRC Public Data Repository - Protein Structure Prediction

Protein:	SLH1
Organism:	Saccharomyces cerevisiae
Length:	1967 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 SLH1.

Description	E-value	Query Range	Subject Range
CE21971 - status:Partially_confirmed UniProt:Q9U2G0 protein_id:CAB60351.1	0.0	[3..1965]	[175..2124]
gi\|14043179 - gi\|14043179\|gb\|AAH07577.1\| SNRNP200 protein [Homo sapiens]	0.0	[642..1965]	[1..1294]
MUG81_SCHPO - Putative helicase mug81 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mug81 PE=1 SV=1 mug81 - ATP-dependent RNA helicase Slh1	0.0	[19..1966]	[19..1932]
DEXHD_ARATH - DExH-box ATP-dependent RNA helicase DExH13 OS=Arabidopsis thaliana GN=At2g42270 PE=2 SV=1	0.0	[29..1965]	[201..2157]
SLH1 - Putative RNA helicase related to Ski2p, involved in translation inhibition of non-poly(A) mRNAs; req...	0.0	[1..1967]	[1..1967]

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Predicted Domain #1

Region A:
Residues: [1-255]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSTEYSADSS KSFMIAMQSM IDTSQTFNLD RSKISLPDFD DELKKVQKDE PNQRTELTVL  60
   61 SQDRNDWDDI FEEFKDISFA QLQSIIDSYK TKNAVAVYKK IGKLINEAET TLSSNVLLET 120
  121 VLQMVYKHQK QELEKELLDF LGTGNIDLVS LLLQHRRMIV ATPIETTILL IKNAVNSTPE 180
  181 FLTQQDIRNQ VLESAEDAKN RKLNPATKII KYPHVFRKYE AGSTTAMAFA GQKFTLPVGT 240
  241 TRMSYNTHEE IIIPA

[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: [256-492]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ADQASNKNYL YTKLLKISDL DHFCKTVFPY ETLNQIQSLV YPVAYKTNEN MLICAPTGAG  60
   61 KTDIALLTII NTIKQFSVVN GENEIDIQYD DFKVIYVAPL KALAAEIVDK FSKKLAPFNI 120
  121 QVRELTGDMQ LTKAEILATQ VIVTTPEKWD VVTRKANGDN DLVSKVKLLI IDEVHLLHED 180
  181 RGPVIETLVA RTLRQVESSQ SMIRIIGLSA TLPNFMDVAD FLGVNRQIGM FYFDQSF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	80.69897
Match:	1hv8A_
Description:	Putative DEAD box RNA helicase
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [493-695]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RPKPLEQQLL GCRGKAGSRQ SKENIDKVAY DKLSEMIQRG YQVMVFVHSR KETVKSARNF  60
   61 IKLAESNHEV DLFAPDPIEK DKYSRSLVKN RDKDMKEIFQ FGFGIHHAGM ARSDRNLTEK 120
  121 MFKDGAIKVL CCTATLAWGV NLPADCVIIK GTQVYDSKKG GFIDLGISDV IQIFGRGGRP 180
  181 GFGSANGTGI LCTSNDRLDH YVS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	80.69897
Match:	1hv8A_
Description:	Putative DEAD box RNA helicase
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [696-789]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LITQQHPIES RFGSKLVDNL NAEISLGSVT NVDEAIEWLG YTYMFVRMRK NPFTYGIDWE  60
   61 EIANDPQLYE RRRKMIVVAA RRLHALQMIV FDEV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	4.39794
Match:	1d2mA_
Description:	Nucleotide excision repair enzyme UvrB
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
	6.33745214454795	bayes_pls_golite062009
RNA-dependent ATPase activity	2.97534133779092	bayes_pls_golite062009
ATP-dependent RNA helicase activity	2.96650679245363	bayes_pls_golite062009
RNA helicase activity	2.83814950186361	bayes_pls_golite062009
structural molecule activity	2.81579918518889	bayes_pls_golite062009
binding	2.59063189683655	bayes_pls_golite062009
nucleic acid binding	1.89039798688851	bayes_pls_golite062009
helicase activity	1.52111969749634	bayes_pls_golite062009
ATP-dependent helicase activity	1.48276729246798	bayes_pls_golite062009
purine NTP-dependent helicase activity	1.48276729246798	bayes_pls_golite062009
protein binding	1.40069187357924	bayes_pls_golite062009
cytoskeletal protein binding	0.262645824445581	bayes_pls_golite062009
ligand-gated ion channel activity	0.0135923951994963	bayes_pls_golite062009
ligand-gated channel activity	0.0135923951994963	bayes_pls_golite062009

Predicted Domain #5

Region A:
Residues: [790-1074]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SMHFIAKDLG RVSSDFYLLN ESVEIFNQMC DPRATEADVL SMISMSSEFD GIKFREEESK  60
   61 ELKRLSDESV ECQIGSQLDT PQGKANVLLQ AYISQTRIFD SALSSDSNYV AQNSVRICRA 120
  121 LFLIGVNRRW GKFSNVMLNI CKSIEKRLWA FDHPLCQFDL PENIIRRIRD TKPSMEHLLE 180
  181 LEADELGELV HNKKAGSRLY KILSRFPKIN IEAEIFPITT NVMRIHIALG PDFVWDSRIH 240
  241 GDAQFFWVFV EESDKSQILH FEKFILNRRQ LNNQHEMDFM IPLSD

[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 functions:

Term	Confidence	Notes
	4.704140727858	bayes_pls_golite062009
structural constituent of ribosome	3.070470376968	bayes_pls_golite062009
binding	2.64537357529343	bayes_pls_golite062009
RNA binding	2.29590582680214	bayes_pls_golite062009
nucleic acid binding	2.11222585187695	bayes_pls_golite062009
structural molecule activity	2.08211451183607	bayes_pls_golite062009
DNA binding	1.7904783386531	bayes_pls_golite062009
transcription regulator activity	1.68903321260301	bayes_pls_golite062009
RNA helicase activity	1.42791449104435	bayes_pls_golite062009
RNA-dependent ATPase activity	1.39335733374328	bayes_pls_golite062009
ATP-dependent RNA helicase activity	1.36724390116598	bayes_pls_golite062009
snRNA binding	1.20045983086701	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
mRNA binding	0.76699944561918	bayes_pls_golite062009
helicase activity	0.6191010101321	bayes_pls_golite062009
transcription factor activity	0.603758349693077	bayes_pls_golite062009
purine nucleotide binding	0.569910969126728	bayes_pls_golite062009
purine ribonucleotide binding	0.568840867400671	bayes_pls_golite062009
ribonucleotide binding	0.568779924702229	bayes_pls_golite062009
nucleotide binding	0.564275755355315	bayes_pls_golite062009
purine NTP-dependent helicase activity	0.29664013896754	bayes_pls_golite062009
ATP-dependent helicase activity	0.29664013896754	bayes_pls_golite062009
translation regulator activity	0.29096092258568	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.274994961137851	bayes_pls_golite062009
ATP binding	0.1860481660648	bayes_pls_golite062009
protein binding	0.170837278876362	bayes_pls_golite062009
adenyl ribonucleotide binding	0.152859582615242	bayes_pls_golite062009
adenyl nucleotide binding	0.138615225841109	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.0530667986761242	bayes_pls_golite062009
pyrophosphatase activity	0.0482442222493492	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.028470639373934	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.0265151533232588	bayes_pls_golite062009

Predicted Domain #6

Region A:
Residues: [1075-1270]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PLPPQVVVKV VSDTWIGCES THAISFQHLI RPFNETLQTK LLKLRPLPTS ALQNPLIESI  60
   61 YPFKYFNPMQ TMTFYTLYNT NENAFVGSPT GSGKTIVAEL AIWHAFKTFP GKKIVYIAPM 120
  121 KALVRERVDD WRKKITPVTG DKVVELTGDS LPDPKDVHDA TIVITTPEKF DGISRNWQTR 180
  181 KFVQDVSLII MDEIHL

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	14.93
Match:	1gm5A
Description:	RecG, N-terminal domain; RecG "wedge" domain; RecG helicase domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
structural molecule activity	2.80935217964088	bayes_pls_golite062009
binding	2.65544526722793	bayes_pls_golite062009
protein binding	1.50286160643298	bayes_pls_golite062009
ligand-gated ion channel activity	0.423207248971435	bayes_pls_golite062009
ligand-gated channel activity	0.423207248971435	bayes_pls_golite062009
cytoskeletal protein binding	0.42238661903557	bayes_pls_golite062009

Predicted Domain #7

Region A:
Residues: [1271-1588]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LASDRGPILE MIVSRMNYIS SQTKQPVRLL GMSTAVSNAY DMAGWLGVKD HGLYNFPSSV  60
   61 RPVPLKMYID GFPDNLAFCP LMKTMNKPVF MAIKQHSPDK PALIFVASRR QTRLTALDLI 120
  121 HLCGMEDNPR RFLNIDDEEE LQYYLSQVTD DTLKLSLQFG IGLHHAGLVQ KDRSISHQLF 180
  181 QKNKIQILIA TSTLAWGVNL PAHLVIIKGT QFFDAKIEGY RDMDLTDILQ MMGRAGRPAY 240
  241 DTTGTAIVYT KESKKMFYKH FLNVGFPVES SLHKVLDDHL GAEITSGSIT NKQEALDFLS 300
  301 WTFLFRRAHH NPTYYGIE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.0
Match:	1d9xA_
Description:	Nucleotide excision repair enzyme UvrB
Matching Structure (courtesy of the PDB):

Predicted Domain #8

Region A:
Residues: [1589-1776]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DDTSTAGVSE HLSSLIDSTL ENLRESQCVL LHGDDIVATP FLSISSYYYI SHLTIRQLLK  60
   61 QIHDHATFQE VLRWLSLAVE YNELPVRGGE IIMNEEMSQQ SRYSVESTFT DEFELPMWDP 120
  121 HVKTFLLLQA HLSRVDLPIA DYIQDTVSVL DQSLRILQAY IDVASELGYF HTVLTMIKMM 180
  181 QCIKQGYW

[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 #9

Region A:
Residues: [1777-1856]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YEDDPVSVLP GLQLRRIKDY TFSEQGFIEM TPQQKKKKLL TLEEIGRFGY KKLLNVFDQL  60
   61 TFGMTESEDT KKRFVSVCQR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	2.522879
Match:	1jj2X_
Description:	Ribosomal protein L32e
Matching Structure (courtesy of the PDB):

Predicted Domain #10

Region A:
Residues: [1857-1967]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LPVLEGMKFE EQENNEVLTF YSKHLSSKHN NGFEVYCDKF PKIQKELWFL IGHKGDELLM  60
   61 IKRCQPKQMN KEVIIHCDLF IPEEIRGEEL QFSLINDALG LRYDMVHKLI S

[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.

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:

Predicted functions:

Predicted functions: