YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|8163249, gi\|1...
Organism:	Chlamydia muridarum Nigg
Length:	223 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|8163249, gi|1....

Description	E-value	Query Range	Subject Range
gi\|29840113, gi\|... - gi\|29840113\|ref\|NP_829219.1\| DNA binding protein/PTS system, IIA component [Chlamydophila caviae GPI...	180.0	[0..1]	[223..1]
gi\|62148038, gi\|... - gi\|62184971\|ref\|YP_219756.1\| PTS system, IIA component [Chlamydophila abortus S26/3], gi\|62148038\|em...	176.0	[0..1]	[223..1]
gi\|89898464, gi\|... - gi\|89898464\|ref\|YP_515574.1\| phosphotransferase system mannitol/fructose-specific Pts IIA [Chlamydop...	174.0	[0..1]	[223..1]
gi\|7468533 - pir\|\|F72124 pts iia protein + hth dna-binding domain - Chlamydophila pneumoniae (strain CWL029) gi\|15617985, gi\|... - gi\|4376317\|gb\|AAD18214.1\| PTS IIA Protein + HTH DNA-Binding Domain [Chlamydophila pneumoniae CWL029]...	173.0	[0..1]	[223..1]
gi\|15835597, gi\|... - gi\|8978435\|dbj\|BAA98272.1\| Pts IIA protein with HTH DNA-Binding domain [Chlamydophila pneumoniae J13... gi\|33241397, gi\|... - gi\|33241397\|ref\|NP_876338.1\| phosphotransferase system enzyme II [Chlamydophila pneumoniae TW-183], ... gi\|8163486, gi\|1... - gi\|8163486\|gb\|AAF73698.1\| PTS system, IIA component [Chlamydophila pneumoniae AR39], gi\|16752983\|ref... gi\|25403716 - pir\|\|F86498 Pts IIA protein with HTH DNA-Binding domain [imported] - Chlamydophila pneumoniae (strai...	173.0	[0..1]	[223..1]
gi\|39982605, gi\|... - gi\|39995841\|ref\|NP_951792.1\| PTS system fructose subfamily IIA subunit [Geobacter sulfurreducens PCA...	173.0	[0..1]	[222..1]
gi\|231273947, gi... - gi\|237802713\|ref\|YP_002887907.1\| PTS-family membrane transport protein IIA component [Chlamydia trac... gi\|255311092 - gi\|255311092\|ref\|ZP_05353662.1\| PTS-family membrane transport protein IIA component [Chlamydia trach... gi\|255503191 - gi\|255503191\|ref\|ZP_05381581.1\| PTS-family membrane transport protein IIA component [Chlamydia trach... gi\|255506869 - gi\|255506869\|ref\|ZP_05382508.1\| PTS-family membrane transport protein IIA component [Chlamydia trach... gi\|3328704, gi\|1... - gi\|3328704\|gb\|AAC67883.1\| PTS IIA Protein + HTH DNA-Binding Domain [Chlamydia trachomatis D/UW-3/CX]... gi\|255317393 - gi\|255317393\|ref\|ZP_05358639.1\| PTS-family membrane transport protein IIA component [Chlamydia trach... gi\|231272935, gi... - pir\|\|G71533 probable pts iia protein + hth dna-binding domain - Chlamydia trachomatis (serotype D, s... gi\|76167542, gi\|... - gi\|76789012\|ref\|YP_328098.1\| nitrogen regulatory IIA protein [Chlamydia trachomatis A/HAR-13], gi\|76... gi\|255348651 - gi\|255348651\|ref\|ZP_05380658.1\| PTS-family membrane transport protein IIA component [Chlamydia trach...	164.0	[0..1]	[223..1]
gi\|78223801, gi\|... - gi\|78223801\|ref\|YP_385548.1\| putative PTS IIA-like nitrogen-regulatory protein PtsN [Geobacter metal...	162.0	[0..1]	[222..1]
gi\|88918244, gi\|... - gi\|88934979\|ref\|ZP_01140617.1\| Excisionase/Xis, DNA-binding [Geobacter uraniumreducens Rf4], gi\|8891...	162.0	[0..1]	[222..1]
gi\|46399541, gi\|... - gi\|46445900\|ref\|YP_007265.1\| putative nitrogen regulatory IIA protein (enzyme IIA-ntr) (phosphotrans...	161.0	[0..2]	[222..4]

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Predicted Domain #1

Region A:
Residues: [1-68]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDLRLDELAV LLDVAEDSIR QWVSFEGIPS YKINDELRFN REEVEDWLIH NHGVIVAEKD  60
   61 KRESKDLS

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	2.04
Match:	1j9iA
Description:	Terminase gpNU1 subunit domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	3.15084451351262	bayes_pls_golite062009
DNA binding	1.89121395172205	bayes_pls_golite062009
nucleic acid binding	1.85709490142946	bayes_pls_golite062009
transcription factor activity	1.63947569382682	bayes_pls_golite062009
binding	1.25832675558318	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [69-223]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LRYSLYRAIY RGGVLKNVLV DSKEEALQHT AKYIANKFEL DSGVLFEMLM HRESLMSTGI  60
   61 GEGIALPHAK DFLINIGYDI VVPVFLSQSI EYGALDGKPV DTMFFLFANQ DRHHLNLVNK 120
  121 IVHLGMSLEA RLFLKEHPDQ PQLLAFIKNW EARIH

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	32.69897
Match:	1a3aA
Description:	Phosphotransferase IIa-mannitol
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
protein-N(PI)-phosphohistidine-sugar phosphotransferase activity	4.89047341597444	bayes_pls_golite062009
carbohydrate transmembrane transporter activity	3.92377913213665	bayes_pls_golite062009
transporter activity	2.16741930408232	bayes_pls_golite062009
transmembrane transporter activity	2.05879816720019	bayes_pls_golite062009
active transmembrane transporter activity	1.87457143976439	bayes_pls_golite062009
substrate-specific transporter activity	1.82451780056478	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.7251575499811	bayes_pls_golite062009
transcription regulator activity	0.789390286938302	bayes_pls_golite062009
catalytic activity	0.547925219495929	bayes_pls_golite062009
binding	0.396676636991646	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	0.19707628828681	bayes_pls_golite062009
ion transmembrane transporter activity	0.12881601139602	bayes_pls_golite062009
anion transmembrane transporter activity	0.10209580008722	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: