YRC Public Data Repository - Protein Structure Prediction

Protein:	ptr8
Organism:	Schizosaccharomyces pombe
Length:	804 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 ptr8.

Description	E-value	Query Range	Subject Range
RAD25_YEAST - DNA repair helicase RAD25 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SSL2 PE=1 SV=1 SSL2 - Component of the holoenzyme form of RNA polymerase transcription factor TFIIH, has DNA-dependent ATP...	429.0	[0..2]	[802..26]
gi\|44984827 - gi\|44984827\|gb\|AAS53651.1\| AFR280Wp [Ashbya gossypii ATCC 10895] gi\|45198798, gi\|... - gi\|45198798\|ref\|NP_985827.1\| AFR280Wp [Ashbya gossypii ATCC 10895], gi\|44984827\|gb\|AAS53651.1\| AFR28...	423.0	[0..4]	[804..39]
gi\|49643672 - gi\|49643672\|emb\|CAG99624.1\| KLLA0E13025p [Kluyveromyces lactis] gi\|49643672, gi\|... - gi\|50309063\|ref\|XP_454537.1\| unnamed protein product [Kluyveromyces lactis], gi\|49643672\|emb\|CAG9962...	420.0	[0..63]	[803..123]
orf19.2857, orf1... - orf19.2857 CGDID:CAL0005155 Assembly 19, Contig19-10161 (108434, 105903) CDS, reverse complemented, ... gi\|68480483, gi\|... - gi\|68480588\|ref\|XP_715788.1\| hypothetical protein CaO19.2857 [Candida albicans SC5314], gi\|68480483\|...	412.0	[0..6]	[804..2]
gi\|50422289, gi\|... - gi\|50422289\|ref\|XP_459707.1\| hypothetical protein DEHA0E09757g [Debaryomyces hansenii CBS767], gi\|49...	412.0	[0..6]	[804..33]
gi\|42554670, gi\|... - gi\|46125805\|ref\|XP_387456.1\| hypothetical protein FG07280.1 [Gibberella zeae PH-1], gi\|42554670\|gb\|E...	410.0	[0..24]	[804..35]
hay-PB, hay-PA - The gene haywire is referred to in FlyBase by the symbol Dmel\hay (CG8019, FBgn0001179). It is a pro...	409.0	[0..2]	[799..7]
gi\|49646637, gi\|... - gi\|50546603\|ref\|XP_500771.1\| YALI0B11726p [Yarrowia lipolytica], gi\|49646637\|emb\|CAG83021.1\| unnamed... gi\|49646637 - gi\|49646637\|emb\|CAG83021.1\| YALI0B11726p [Yarrowia lipolytica]	407.0	[0..64]	[803..77]

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Predicted Domain #1

Region A:
Residues: [1-82]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSLKRKNNAR EGTPDEDLEE YSDYSDVDNY GEEDDDSYKP APRIRINNNK TKAQTTTNSN  60
   61 EARQSGISAM FGQNDFSNLL GL

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [83-730]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KLDHTARPLW INPIDGRIIL EAFSPLAEQA IDFLVTISEP VSRPAFIHEY RITAYSLYAA  60
   61 VSVGLKTEDI IAVLDRLSKT PIPPSIVDFI RACTVSYGKV KLVLKKNRYF IESGDASVLR 120
  121 LLLRDPVIGP LRIDYSTQSS KQKSSKPSNE DNVEDKKDIT NDSSKETAEK SSSDELFSAV 180
  181 VGLQEEEDDE DAVHLFEIKH SSVETIKKRC AEIDYPLLEE YDFRNDNINP DLPIDLKPST 240
  241 QIRPYQEKSL SKMFGNGRAR SGIIVLPCGA GKTLVGITAA CTIKKSVIVL CTSSVSVMQW 300
  301 RQQFLQWSNI KPDHIAVFTA DHKERFHSEA GVVVSTYSMV ANTRNRSYDS QKMMDFLTGR 360
  361 EWGFILLDEV HVVPAAMFRR VVTTIAAHTK LGLTATLVRE DDKIDDLNFL IGPKMYEANW 420
  421 MDLAQKGHIA KVQCAEVWCA MTTEFYNEYL RENSRKRMLL YIMNPKKFQA CQFLIDYHEK 480
  481 RGDKIIVFSD NVYALRAYAI KLGKYFIYGG TPQQERMRIL ENFQYNELVN TIFLSKVGDT 540
  541 SIDLPEATCL IQISSHYGSR RQEAQRLGRI LRAKRRNDEG FNAFFYSLVS KDTQEMYYSS 600
  601 KRQAFLIDQG YAFKVITNLK GMENLPNLAY ASKAERLELL QEVLLQNE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	74.221849
Match:	2eyqA
Description:	Crystal structure of Escherichia coli transcription-repair coupling factor
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
general RNA polymerase II transcription factor activity	5.47805400577115	bayes_pls_golite062009
hydrogen ion transporting ATP synthase activity, rotational mechanism	4.24230705019135	bayes_pls_golite062009
dATP binding	3.90236137621968	bayes_pls_golite062009
hydrogen ion transmembrane transporter activity	3.27883517727923	bayes_pls_golite062009
monovalent inorganic cation transmembrane transporter activity	3.1445172484282	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	2.99059500119562	bayes_pls_golite062009
nucleoside-triphosphatase activity	2.95079405147356	bayes_pls_golite062009
adenyl deoxyribonucleotide binding	2.90098016780049	bayes_pls_golite062009
purine deoxyribonucleotide binding	2.90098016780049	bayes_pls_golite062009
pyrophosphatase activity	2.87427509025394	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	2.85499564954033	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	2.85178667290149	bayes_pls_golite062009
deoxyribonuclease activity	2.72222787956584	bayes_pls_golite062009
binding	2.64537357529343	bayes_pls_golite062009
endodeoxyribonuclease activity	2.60873257753475	bayes_pls_golite062009
transporter activity	2.58140740499725	bayes_pls_golite062009
hydrolase activity	2.55157966585974	bayes_pls_golite062009
nucleic acid binding	2.51683451033161	bayes_pls_golite062009
transmembrane transporter activity	2.39695871109024	bayes_pls_golite062009
ATPase activity	2.39535714892224	bayes_pls_golite062009
ATPase activity, coupled	2.18396165590908	bayes_pls_golite062009
DNA binding	2.12258000781149	bayes_pls_golite062009
transcription regulator activity	2.09345198747025	bayes_pls_golite062009
endonuclease activity	1.96689197136388	bayes_pls_golite062009
purine ribonucleotide binding	1.85943679361938	bayes_pls_golite062009
ribonucleotide binding	1.85937484083653	bayes_pls_golite062009
purine nucleotide binding	1.8521191028835	bayes_pls_golite062009
nucleotide binding	1.84603132945448	bayes_pls_golite062009
	1.75135117904448	bayes_pls_golite062009
helicase activity	1.70242731830224	bayes_pls_golite062009
ATP binding	1.5859264197035	bayes_pls_golite062009
adenyl ribonucleotide binding	1.55520429131224	bayes_pls_golite062009
adenyl nucleotide binding	1.53158018507951	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
substrate-specific transporter activity	1.29730375126024	bayes_pls_golite062009
structure-specific DNA binding	1.2539059700735	bayes_pls_golite062009
protein binding	1.22129154759482	bayes_pls_golite062009
kinase activity	1.21578538537164	bayes_pls_golite062009
DNA-dependent ATPase activity	1.2155186842031	bayes_pls_golite062009
ATP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
purine NTP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
ATP-dependent DNA helicase activity	1.18669029764243	bayes_pls_golite062009
protein kinase activity	1.12864835254143	bayes_pls_golite062009
double-stranded DNA binding	1.117585097627	bayes_pls_golite062009
transcription elongation regulator activity	1.11383295816593	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	0.906554174337376	bayes_pls_golite062009
transcription activator activity	0.889929694023098	bayes_pls_golite062009
transcription factor activity	0.887108427603557	bayes_pls_golite062009
motor activity	0.87979065815418	bayes_pls_golite062009
DNA helicase activity	0.72881469450553	bayes_pls_golite062009
RNA binding	0.715902454627085	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	0.579884353047732	bayes_pls_golite062009
single-stranded DNA binding	0.568457189190858	bayes_pls_golite062009
sequence-specific DNA binding	0.543891899378373	bayes_pls_golite062009
active transmembrane transporter activity	0.434775387083003	bayes_pls_golite062009
microtubule motor activity	0.35554075339843	bayes_pls_golite062009
ion transmembrane transporter activity	0.355466224802969	bayes_pls_golite062009
protein serine/threonine kinase activity	0.345873656782869	bayes_pls_golite062009
mismatched DNA binding	0.31144582840038	bayes_pls_golite062009
primary active transmembrane transporter activity	0.294474570607914	bayes_pls_golite062009
DNA strand annealing activity	0.283577486331079	bayes_pls_golite062009
P-P-bond-hydrolysis-driven transmembrane transporter activity	0.282352478532746	bayes_pls_golite062009
four-way junction helicase activity	0.26252931460003	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.243902356228423	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	0.220608508617331	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of substances	0.219533217661421	bayes_pls_golite062009
ATPase activity, coupled to movement of substances	0.219157471322311	bayes_pls_golite062009
exodeoxyribonuclease V activity	0.185603938981231	bayes_pls_golite062009
nucleotidyltransferase activity	0.181509771587324	bayes_pls_golite062009
protein transporter activity	0.178442534411253	bayes_pls_golite062009
transferase activity	0.168270793917772	bayes_pls_golite062009
guanyl nucleotide binding	0.132012746266431	bayes_pls_golite062009
guanyl ribonucleotide binding	0.121792392568515	bayes_pls_golite062009
GTP binding	0.119757493758508	bayes_pls_golite062009
GTPase activity	0.105546189348878	bayes_pls_golite062009
proton-transporting ATPase activity, rotational mechanism	0.0263010404932493	bayes_pls_golite062009
cation transmembrane transporter activity	0.0254369227200564	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [731-804]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EAADLDDGED TSFGSRSLSR APAKAKRSSG SLSTLAGADN MAYVEYNKSA NKQLKKDSKE  60
   61 HHALFRKHLY TKRR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	14.69897
Match:	1d2mA
Description:	Nucleotide excision repair enzyme UvrB
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: