YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|7470855
Organism:	Synechocystis sp.
Length:	1261 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 gi|7470855.

Description	E-value	Query Range	Subject Range
gi\|24372448, gi\|... - gi\|24372448\|ref\|NP_716490.1\| sensory box histidine kinase/response regulator [Shewanella oneidensis ... SO0859 - sensory box histidine kinase/response regulator	503.0	[0..104]	[1257..602]
gi\|117921856, gi... - gi\|78684566\|ref\|ZP_00849349.1\| PAS [Shewanella sp. ANA-3], gi\|78507503\|gb\|EAP21013.1\| PAS [Shewanell...	503.0	[0..85]	[1257..583]
gi\|113890238, gi... - gi\|78690356\|ref\|ZP_00855004.1\| PAS [Shewanella sp. MR-7], gi\|78510268\|gb\|EAP23642.1\| PAS [Shewanella...	503.0	[0..104]	[1257..602]
gi\|82405384, gi\|... - gi\|82496616\|ref\|ZP_00882182.1\| PAS [Shewanella sp. MR-4], gi\|82405384\|gb\|EAP46058.1\| PAS [Shewanella...	500.0	[0..104]	[1257..602]
gi\|68516760, gi\|... - gi\|68545731\|ref\|ZP_00585281.1\| PAS [Shewanella amazonensis SB2B], gi\|68516760\|gb\|EAN40471.1\| PAS [Sh...	496.0	[0..107]	[1257..605]
gi\|238790320, gi... - gi\|77972593\|ref\|ZP_00828155.1\| COG2202: FOG: PAS/PAC domain [Yersinia frederiksenii ATCC 33641], gi\|...	490.0	[0..82]	[1257..314]
gi\|78366316, gi\|... - gi\|78366316\|ref\|ZP_00836597.1\| PAS [Shewanella sp. PV-4], gi\|78361632\|gb\|EAP03455.1\| PAS [Shewanella...	488.0	[0..107]	[1255..605]
gi\|71281538, gi\|... - gi\|71281538\|ref\|YP_270817.1\| sensory box histidine kinase/response regulator [Colwellia psychrerythr...	483.0	[0..264]	[1254..679]
gi\|117609989, gi... - gi\|69256468\|ref\|ZP_00606017.1\| PAS [Magnetococcus sp. MC-1], gi\|68247589\|gb\|EAN29674.1\| PAS [Magneto...	483.0	[0..111]	[1179..109]
gi\|77809063, gi\|... - gi\|77815974\|ref\|ZP_00815187.1\| PAS [Shewanella putrefaciens CN-32], gi\|77809063\|gb\|EAO93472.1\| PAS [...	479.0	[0..107]	[1257..605]

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Predicted Domain #1

Region A:
Residues: [1-140]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MFWQPVSPLN ADQLNYQGSY DPKLVLLSVA IAIFTAYMAF LMASSALSLP GRWSRKIALA  60
   61 LSGTVMGLGI WAMHFIGMLG FELPCPISYD PLITFISVIP AIAASIYALN FLSFQAPTAK 120
  121 NLMVGAIWFG LGIGTMHYSG

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	24.055517
Match:	PF03707.7
Description:	No description for PF03707.7 was found.

Shown below are all of our structure 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: [141-242]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAALELHGNI YYELPLFVLS LVIAVMLAFV ALLFRFHSAK IFHTTHGPAL GSSALVMGLS  60
   61 TSGMHYTAMT ATHFICRPWG EFFIQGIDIQ EVAIAVTISI TL

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	22.251812
Match:	PF03707.7
Description:	No description for PF03707.7 was found.

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [243-434]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LTGGVMLFVL REISIQNQQQ KILVATESWY RQIIEYAPEG IMVLDAQGNI ILANTSIEKL  60
   61 FGYSQTELIG QSIALLGLAE LLQQSLHLLQ EGEDVGPTCP LDQEEFEILG TRYDGSEFPI 120
  121 EVSLTSLPSL SQREMNIFAS VRDISARQEA QQQILRQREH LQSVLDSAPV GVAITVNGIT 180
  181 QFANPHIGEL VD

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	4.88
Match:	1v9yA
Description:	Crystal Structure of the heme PAS sensor domain of Ec DOS (ferric form)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
ion transmembrane transporter activity	1.81312487233411	bayes_pls_golite062009
binding	1.67984576110273	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.60314341650446	bayes_pls_golite062009
two-component response regulator activity	1.41577088905201	bayes_pls_golite062009
cation transmembrane transporter activity	1.40823491489039	bayes_pls_golite062009
metal ion transmembrane transporter activity	1.10325694432704	bayes_pls_golite062009
transcription regulator activity	0.931375605669218	bayes_pls_golite062009
protein binding	0.888256242702267	bayes_pls_golite062009
voltage-gated ion channel activity	0.563198063703829	bayes_pls_golite062009
potassium channel activity	0.563028071397075	bayes_pls_golite062009
voltage-gated channel activity	0.552480950289765	bayes_pls_golite062009
voltage-gated cation channel activity	0.551619757281389	bayes_pls_golite062009
DNA binding	0.533187513797767	bayes_pls_golite062009
voltage-gated potassium channel activity	0.532581714382914	bayes_pls_golite062009
nucleic acid binding	0.510719075994398	bayes_pls_golite062009
ion channel activity	0.483348490364346	bayes_pls_golite062009
two-component sensor activity	0.466388018187262	bayes_pls_golite062009
protein histidine kinase activity	0.452475261443277	bayes_pls_golite062009
cation channel activity	0.445728116294453	bayes_pls_golite062009
phosphotransferase activity, nitrogenous group as acceptor	0.409938237891918	bayes_pls_golite062009
substrate-specific channel activity	0.391671932145714	bayes_pls_golite062009
passive transmembrane transporter activity	0.388177774524707	bayes_pls_golite062009
channel activity	0.388177774524707	bayes_pls_golite062009
gated channel activity	0.383085563903689	bayes_pls_golite062009
signal transducer activity	0.341738261779128	bayes_pls_golite062009
molecular transducer activity	0.341738261779128	bayes_pls_golite062009
catalytic activity	0.335650048048265	bayes_pls_golite062009
transporter activity	0.308330515689802	bayes_pls_golite062009
transcription factor activity	0.15709070306709	bayes_pls_golite062009
transmembrane transporter activity	0.154730712374367	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [435-511]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LKVGDSPQKI YVDLGDRQQM LEELTQFGRS QSRVYKMYNP RGEIRDILAT FLATDYEGQK  60
   61 GILGWLADIT PIKAAEA

[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.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.478	a.39.1	EF-hand
View	Download	0.454	a.77.1	DEATH domain
View	Download	0.576	a.70.1	N-terminal domain of the delta subunit of the F1F0-ATP synthase
View	Download	0.504	a.70.1	N-terminal domain of the delta subunit of the F1F0-ATP synthase
View	Download	0.459	d.54.1	Enolase N-terminal domain-like

Predicted Domain #5

Region A:
Residues: [512-757]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EMKRAKELAE EASRIKADFL ANMSHEIRTP MNAVIGMTHL ALKTDLTPRQ REYLHKIRFS  60
   61 GQHLLGVIND ILDFSKIEAG KLPMESIDFD LDKVLDNVAT LISEKATNKG LELLFDIDRN 120
  121 LPRHFIGDPL RLGQILINYA NNAVKFTEQG DITIVVRLQE YRDQDVVLYL AVKDTGIGIK 180
  181 PEHIANLFNS FQQADSSTTR NFGGTGLGLA ICKRIAELMG GEVGVESEYG QGSTFWAKVC 240
  241 LQKSNV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	44.0
Match:	2c2aA
Description:	Structure of the entire cytoplasmic portion of a sensor histidine kinase protein
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [758-909]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IPHRLVLSKD LEGKRVLVVD DNDHARLVMK DLLEQMKFVV ETVESGPEAL NFLAEADREN  60
   61 HPHSIVFIDW QMPNMDGLEV ARRLKAMGLN HQPSIFIVTA YGREELFVKA KSLGIDDVLV 120
  121 KPISPSVLFD SLARVLGDPT ALAQEMRQSS GI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	27.522879
Match:	1w25A
Description:	Response regulator PleD in complex with c-diGMP
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
two-component response regulator activity	7.02872640261738	bayes_pls_golite062009
signal transducer activity	4.51666042720644	bayes_pls_golite062009
molecular transducer activity	4.51666042720644	bayes_pls_golite062009
transcription regulator activity	3.44888100104099	bayes_pls_golite062009
protein histidine kinase activity	2.35011582062573	bayes_pls_golite062009
two-component sensor activity	2.32303301074957	bayes_pls_golite062009
phosphotransferase activity, nitrogenous group as acceptor	2.28838869071567	bayes_pls_golite062009
binding	1.22427537074115	bayes_pls_golite062009
DNA binding	1.11037597107903	bayes_pls_golite062009
nucleic acid binding	1.05519146337499	bayes_pls_golite062009
protein kinase activity	1.00737355751913	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	0.811771244977462	bayes_pls_golite062009
kinase activity	0.725824770559857	bayes_pls_golite062009
transcription factor activity	0.62886970109503	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.476057209677045	bayes_pls_golite062009

Predicted Domain #7

Region A:
Residues: [910-1261]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GAEDLALEKL RRIRGARILL VEDNEINQEV AAELLRDVGF NVDVAANGLI ALERLNNNAY  60
   61 ALVLMDMQMP EMDGIEATIA IRQNPRYAQL PIVAMTANVM QGDRERCLQA GMNDHLGKPI 120
  121 EPEELWNKLL HWIPVDSPLA PETIEESAIN TSDPEISIPH IPGLNSDDGL RRVLGKKSLY 180
  181 LKMLHKFVAS QSSFLPEITQ ALGEKDYGFA ERLAHTLKGV AGNIGAQELQ QEAAELEKAI 240
  241 KEQWPQPEVE NLLTNLGDRL DNLIAQLTSN LPPEPATVAI TLDQGQLEEI CDHLAQLLGE 300
  301 DDAEAADLLQ NHGDLLRQAF PDHYSAIAAG INNFDFEAAL AALTTARQFS QP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	59.522879
Match:	1ny5A
Description:	Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
protein histidine kinase activity	2.35011582062573	bayes_pls_golite062009
two-component sensor activity	2.32303301074957	bayes_pls_golite062009
phosphotransferase activity, nitrogenous group as acceptor	2.28838869071567	bayes_pls_golite062009
nucleoside-triphosphatase activity	1.95073642969863	bayes_pls_golite062009
pyrophosphatase activity	1.91141407779641	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	1.9017593265179	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	1.90014393273511	bayes_pls_golite062009
anion transmembrane transporter activity	1.84572377553607	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.608578860823	bayes_pls_golite062009
transporter activity	1.55572428045529	bayes_pls_golite062009
anion transmembrane-transporting ATPase activity	1.49339466967388	bayes_pls_golite062009
ATPase activity	1.48474288797022	bayes_pls_golite062009
two-component response regulator activity	1.45919623810582	bayes_pls_golite062009
transmembrane transporter activity	1.38483976298883	bayes_pls_golite062009
ATPase activity, coupled	1.37457738689583	bayes_pls_golite062009
catalytic activity	1.37148167194523	bayes_pls_golite062009
inorganic anion transmembrane transporter activity	1.3654237778347	bayes_pls_golite062009
ion transmembrane transporter activity	1.32358677895008	bayes_pls_golite062009
binding	1.30574971150356	bayes_pls_golite062009
active transmembrane transporter activity	1.24278046928678	bayes_pls_golite062009
phosphate transmembrane transporter activity	1.22440281711103	bayes_pls_golite062009
P-P-bond-hydrolysis-driven transmembrane transporter activity	1.2014318795788	bayes_pls_golite062009
primary active transmembrane transporter activity	1.19670408144267	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	1.17063957238561	bayes_pls_golite062009
ATPase activity, coupled to movement of substances	1.16918853509059	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of substances	1.16885789920943	bayes_pls_golite062009
hydrolase activity	1.09839981963412	bayes_pls_golite062009
phosphate transmembrane-transporting ATPase activity	1.05293225786874	bayes_pls_golite062009
ribonucleotide binding	0.92950870381166	bayes_pls_golite062009
purine ribonucleotide binding	0.9275205656455	bayes_pls_golite062009
purine nucleotide binding	0.91280662021456	bayes_pls_golite062009
nucleotide binding	0.90809801369052	bayes_pls_golite062009
ATP binding	0.59269193555886	bayes_pls_golite062009
cation transmembrane transporter activity	0.575892074401446	bayes_pls_golite062009
adenyl ribonucleotide binding	0.57504013359401	bayes_pls_golite062009
adenyl nucleotide binding	0.54853610492983	bayes_pls_golite062009
inorganic cation transmembrane transporter activity	0.139527952740579	bayes_pls_golite062009
substrate-specific transporter activity	0.0838665746103899	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:

Predicted functions:

Predicted functions: