YRC Public Data Repository - Protein Structure Prediction

Protein:	CSL4
Organism:	Saccharomyces cerevisiae
Length:	292 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 CSL4.

Description	E-value	Query Range	Subject Range
CSL4 - Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the n... CSL4_YEAST - Exosome complex component CSL4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CSL4 PE=1... gi\|151944314 - gi\|151944314\|gb\|EDN62592.1\| conserved protein [Saccharomyces cerevisiae YJM789]	0.0	[1..292]	[1..292]
gi\|85102296 - gi\|85102296\|ref\|XP_961311.1\| hypothetical protein NCU04155 [Neurospora crassa OR74A] gi\|32405764, gi\|... - gi\|32405764\|ref\|XP_323495.1\| hypothetical protein ( (AL513463) conserved hypothetical protein [Neuro...	1.0E-63	[1..292]	[1..214]
EXOSC1 - exosome component 1 gi\|114632191 - gi\|114632191\|ref\|XP_507960.2\| PREDICTED: similar to CGI-108 protein [Pan troglodytes] CCDS7459.1_1 - null gi\|208966238 - gi\|208966238\|dbj\|BAG73133.1\| exosome component 1 [synthetic construct] gi\|109090153 - gi\|109090153\|ref\|XP_001103710.1\| PREDICTED: exosome component 1 [Macaca mulatta]	1.0E-56	[75..290]	[10..187]
EXOS1_MOUSE - Exosome complex component CSL4 OS=Mus musculus GN=Exosc1 PE=1 SV=1	1.0E-55	[75..290]	[10..187]
gi\|18891956, gi\|... - gi\|18976424\|ref\|NP_577781.1\| exosome complex RNA-binding protein Csl4 [Pyrococcus furiosus DSM 3638]...	7.0E-52	[66..292]	[2..192]
gi\|14520270, gi\|... - gi\|5457485\|emb\|CAB48976.1\| RNA-binding protein, putative, containing S1 RNA binding domain [Pyrococc... gi\|7445291, gi\|5... - pir\|\|A75191 hypothetical protein PAB2314 - Pyrococcus abyssi (strain Orsay), gi\|5457485\|emb\|CAB48976...	8.0E-51	[67..292]	[5..194]
gi\|7429750 - pir\|\|H71222 hypothetical protein PH0043 - Pyrococcus horikoshii gi\|3256428, gi\|1... - gi\|3256428\|dbj\|BAA29111.1\| 200aa long hypothetical protein [Pyrococcus horikoshii OT3], gi\|14589998\|...	4.0E-49	[68..292]	[6..195]
Csl4-PA - The gene Csl4 is referred to in FlyBase by the symbol Dmel\Csl4 (CG6249, FBgn0032346). It is a prote... gi\|220948428, gi... - gi\|220957608\|gb\|ACL91347.1\| Csl4-PA [synthetic construct], gi\|220948428\|gb\|ACL86757.1\| Csl4-PA [synt...	4.0E-46	[67..290]	[5..193]
CSL4_SCHPO - Exosome complex component csl4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=csl4 PE=3 S... csl4 - exosome subunit Csl4	4.0E-44	[80..291]	[7..177]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	5.0E-44	[80..291]	[6..176]

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Predicted Domain #1

Region A:
Residues: [1-292]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MACNFQFPEI AYPGKLICPQ YGTENKDGED IIFNYVPGPG TKLIQYEHNG RTLEAITATL  60
   61 VGTVRCEEEK KTDQEEEREG TDQSTEEEKS VDASPNDVTR RTVKNILVSV LPGTEKGRKT 120
  121 NKYANNDFAN NLPKEGDIVL TRVTRLSLQR ANVEILAVED KPSPIDSGIG SNGSGIVAAG 180
  181 GGSGAATFSV SQASSDLGET FRGIIRSQDV RSTDRDRVKV IECFKPGDIV RAQVLSLGDG 240
  241 TNYYLTTARN DLGVVFARAA NGAGGLMYAT DWQMMTSPVT GATEKRKCAK PF

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	8.02
Match:	1e3hA
Description:	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
ribonuclease activity	7.42330864261751	bayes_pls_golite062009
exoribonuclease activity	6.76241588209982	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	6.73428326869965	bayes_pls_golite062009
3'-5'-exoribonuclease activity	5.13367897180134	bayes_pls_golite062009
3'-5' exonuclease activity	3.51306349336452	bayes_pls_golite062009
nucleic acid binding	3.194200758646	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	3.07263153665399	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	2.73968547121328	bayes_pls_golite062009
DNA binding	2.71213098011194	bayes_pls_golite062009
exonuclease activity	2.66053639652924	bayes_pls_golite062009
RNA binding	2.41160981373213	bayes_pls_golite062009
binding	2.24181355929217	bayes_pls_golite062009
structural constituent of ribosome	2.02605441840546	bayes_pls_golite062009
structure-specific DNA binding	1.81524862921454	bayes_pls_golite062009
structural molecule activity	1.81283970647925	bayes_pls_golite062009
single-stranded DNA binding	1.62996999055328	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	1.35850109411274	bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds	1.35845277283398	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	1.35845277283398	bayes_pls_golite062009
	1.2099360907571	bayes_pls_golite062009
exoribonuclease II activity	1.18248519339188	bayes_pls_golite062009
transcription regulator activity	0.996884322431837	bayes_pls_golite062009
hydrolase activity	0.724860465280978	bayes_pls_golite062009
nuclease activity	0.57381531077345	bayes_pls_golite062009
mRNA binding	0.4162128308402	bayes_pls_golite062009
ligase activity	0.346041081217685	bayes_pls_golite062009
sequence-specific DNA binding	0.32084431704638	bayes_pls_golite062009
transcription factor activity	0.298729064067577	bayes_pls_golite062009
translation regulator activity	0.22908707234671	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.179682348023561	bayes_pls_golite062009
aspartate-tRNA ligase activity	0.151650064901878	bayes_pls_golite062009
translation initiation factor activity	0.11625379846973	bayes_pls_golite062009
RNA polymerase activity	0.0740938021136293	bayes_pls_golite062009
DNA-directed RNA polymerase activity	0.0740938021136293	bayes_pls_golite062009

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: