YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|29840113, gi\|...
Organism:	Chlamydophila caviae GPIC
Length:	226 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|29840113, gi|....

Description	E-value	Query Range	Subject Range
gi\|62148038, gi\|... - gi\|62184971\|ref\|YP_219756.1\| PTS system, IIA component [Chlamydophila abortus S26/3], gi\|62148038\|em...	174.0	[0..1]	[226..1]
gi\|89898464, gi\|... - gi\|89898464\|ref\|YP_515574.1\| phosphotransferase system mannitol/fructose-specific Pts IIA [Chlamydop...	171.0	[0..1]	[226..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...	167.0	[0..1]	[226..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]...	167.0	[0..1]	[226..1]
gi\|39982605, gi\|... - gi\|39995841\|ref\|NP_951792.1\| PTS system fructose subfamily IIA subunit [Geobacter sulfurreducens PCA...	166.0	[0..1]	[225..1]
gi\|62182179, gi\|... - gi\|62182179\|ref\|YP_218596.1\| PTS family, mannitol-specific enzyme IIABC components [Salmonella enter...	163.0	[0..4]	[223..419]
gi\|197938947, gi... - gi\|198244431\|ref\|YP_002217646.1\| pts system mannitol-specific eiicba component [Salmonella enterica ... gi\|16504929, gi\|... - gi\|25287848\|pir\|\|AI0976 mannitol-specific enzyme II of phosphotransferase system [imported] - Salmon... gi\|197364504, gi... - gi\|197364504\|ref\|YP_002144141.1\| mannitol-specific enzyme II of phosphotransferase system [Salmonell... gi\|213650628 - gi\|213650628\|ref\|ZP_03380681.1\| pts system mannitol-specific eiicba component [Salmonella enterica s... gi\|213610022 - gi\|213610022\|ref\|ZP_03369848.1\| pts system mannitol-specific eiicba component [Salmonella enterica s... gi\|16762624 - gi\|16762624\|ref\|NP_458241.1\| mannitol-specific enzyme II of phosphotransferase system [Salmonella en... gi\|194449488, gi... - gi\|194449488\|ref\|YP_002047714.1\| pts system mannitol-specific eiicba component [Salmonella enterica ... gi\|194400974, gi... - gi\|194442311\|ref\|YP_002042933.1\| pts system mannitol-specific eiicba component [Salmonella enterica ... gi\|16766970, gi\|... - gi\|16766970\|ref\|NP_462585.1\| mannitol-specific enzyme IIABC component [Salmonella typhimurium LT2], ... gi\|197211207, gi... - gi\|197247504\|ref\|YP_002148616.1\| pts system mannitol-specific eiicba component [Salmonella enterica ... gi\|29139750, gi\|... - gi\|29144113\|ref\|NP_807455.1\| mannitol-specific enzyme II of phosphotransferase system [Salmonella en... gi\|194456379, gi... - gi\|194470015\|ref\|ZP_03075999.1\| pts system mannitol-specific eiicba component [Salmonella enterica s... gi\|56415577, gi\|... - gi\|56415577\|ref\|YP_152652.1\| mannitol-specific enzyme II of phosphotransferase system [Salmonella en... gi\|205338747, gi... - gi\|205338747\|gb\|EDZ25511.1\| pts system mannitol-specific eiicba component [Salmonella enterica subsp... lcl\|NC_016856.1_... - [gene=mtlA] [protein=mannitol-specific enzyme IIABC component] [protein_id=YP_005239923.1] [location... gi\|168232528, gi... - gi\|205333241\|gb\|EDZ20005.1\| pts system mannitol-specific eiicba component [Salmonella enterica subsp... gi\|168818485, gi... - gi\|205344403\|gb\|EDZ31167.1\| pts system mannitol-specific eiicba component [Salmonella enterica subsp... gi\|205350428, gi... - gi\|205350428\|gb\|EDZ37059.1\| pts system mannitol-specific eiicba component [Salmonella enterica subsp... gi\|161616759, gi... - gi\|161616759\|ref\|YP_001590724.1\| hypothetical protein SPAB_04578 [Salmonella enterica subsp. enteric... gi\|205330644, gi... - gi\|205330644\|gb\|EDZ17408.1\| pts system mannitol-specific eiicba component [Salmonella enterica subsp... gi\|205325653, gi... - gi\|205325653\|gb\|EDZ13492.1\| pts system mannitol-specific eiicba component [Salmonella enterica subsp... gi\|224470012, gi... - gi\|224585484\|ref\|YP_002639283.1\| mannitol-specific enzyme II of phosphotransferase system [Salmonell... gi\|214001133 - gi\|214001133\|ref\|ZP_03411868.1\| pts system mannitol-specific eiicba component [Salmonella enterica s...	161.0	[0..4]	[223..419]
EG10615 - mannitol-specific PTS enzyme: IIA, IIB and IIC components / Mannitol-specific Enzyme IIABC of PTS tr... gi\|170083106, gi... - gi\|170083106\|ref\|YP_001732426.1\| fused mannitol-specific PTS enzymes: IIA components; IIB components... gi\|218362929, gi... - gi\|218556161\|ref\|YP_002389074.1\| fused mannitol-specific PTS enzymes: IIA components ; IIB component... gi\|209921068, gi... - gi\|209921068\|ref\|YP_002295152.1\| PTS system mannitol-specific IIABC components [Escherichia coli SE1... gi\|218354052, gi... - gi\|218697320\|ref\|YP_002404987.1\| fused mannitol-specific PTS enzymes: IIA components ; IIB component... gi\|188493211, gi... - gi\|75514334\|ref\|ZP_00736642.1\| COG2213: Phosphotransferase system, mannitol-specific IIBC component ... gi\|89110413, gi\|... - gi\|89110413\|ref\|AP_004193.1\| fused mannitol-specific PTS enzyme IIABC components [Escherichia coli s... gi\|238902689, gi... - gi\|238902689\|ref\|YP_002928485.1\| fused mannitol-specific PTS enzymes: IIA components/IIB components/... gi\|242379120, gi... - gi\|251786847\|ref\|YP_003001151.1\| hypothetical protein B21_03405 [Escherichia coli BL21], gi\|24237912... EG10615 - mannitol-specific PTS enzyme: IIA, IIB and IIC components / Mannitol-specific Enzyme IIABC of PTS tr... gi\|83588549, gi\|... - gi\|83588549\|ref\|ZP_00927173.1\| COG2213: Phosphotransferase system, mannitol-specific IIBC component ... gi\|253979583, gi... - gi\|254290276\|ref\|YP_003056024.1\| fused mannitol-specific PTS enzymes: IIA components/IIB components/... PTM3C_ECOLI, PTM... - (P00550) PTS system, mannitol-specific IIABC component (EIIABC-Mtl) (Mannitol-permease IIABC compone... gi\|157068758, gi... - gi\|75197506\|ref\|ZP_00707576.1\| COG2213: Phosphotransferase system, mannitol-specific IIBC component ... gi\|254038798, gi... - gi\|254038798\|ref\|ZP_04872850.1\| PTS system [Escherichia sp. 1_1_43], gi\|226838763\|gb\|EEH70790.1\| PTS... gi\|75237539, gi\|... - gi\|75237539\|ref\|ZP_00721572.1\| COG2213: Phosphotransferase system, mannitol-specific IIBC component ... gi\|254163526, gi... - gi\|254163526\|ref\|YP_003046634.1\| fused mannitol-specific PTS enzymes: IIA components/IIB components/...	160.0	[0..4]	[218..419]
gi\|117625875, gi... - gi\|117625875\|ref\|YP_859198.1\| fused mannitol-specific PTS enzymes: IIA components/IIB components/IIC... gi\|237703365, gi... - gi\|237703365\|ref\|ZP_04533846.1\| mannitol-specific PTS system enzyme IIABC component [Escherichia sp.... gi\|91074684, gi\|... - gi\|91213110\|ref\|YP_543096.1\| mannitol-specific PTS system enzyme IIABC components [Escherichia coli ... gi\|218560670, gi... - gi\|218560670\|ref\|YP_002393583.1\| fused mannitol-specific PTS enzymes: IIA components ; IIB component...	160.0	[0..4]	[218..419]
gi\|227839344, gi... - gi\|227883764\|ref\|ZP_04001569.1\| protein-N(pi)-phosphohistidine--sugar phosphotransferase [Escherichi... gi\|110345432, gi... - gi\|110643840\|ref\|YP_671570.1\| PTS system, mannitol-specific IIABC component [Escherichia coli 536], ... gi\|215266950, gi... - gi\|215488878\|ref\|YP_002331309.1\| fused mannitol-specific PTS enzymes: IIA components /IIB components... gi\|218691882, gi... - gi\|218691882\|ref\|YP_002400094.1\| fused mannitol-specific PTS enzymes: IIA components ; IIB component... gi\|26250238, gi\|... - gi\|26250238\|ref\|NP_756278.1\| PTS system, mannitol-specific IIABC component [Escherichia coli CFT073]... gi\|191170342, gi... - gi\|75242618\|ref\|ZP_00726362.1\| COG2213: Phosphotransferase system, mannitol-specific IIBC component ...	160.0	[0..4]	[218..419]

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Predicted Domain #1

Region A:
Residues: [1-66]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDLKLDELAS LLDVSENTVR RWLDEGAIPS YSMNNEHRFN REEIEDWILH NQALIGLEQD  60
   61 EKQDSE

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	2.07
Match:	1j9iA
Description:	Terminase gpNU1 subunit domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	1.3695638465841	bayes_pls_golite062009
binding	1.25832675558318	bayes_pls_golite062009
DNA binding	0.248046419970394	bayes_pls_golite062009
transcription factor activity	0.142555021912665	bayes_pls_golite062009
nucleic acid binding	0.118048144195768	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [67-226]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FRDLSLKYSL YKAIYRGGII RDVTVNNKAE ALQYASSYIA EKFNLDASVL FEMLSHRESL  60
   61 MSTGIGEGIA LPHAKDFLIN AYYDVVVPMF LSTSIDFGAL DGKPVSVLFF LFASQDKSHL 120
  121 NLINKIVHLG MSLEARSFLT SYPEKEQLLA YIKNWESQIH

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	31.0
Match:	1a6jA
Description:	Nitrogen regulatory bacterial protein IIa-ntr
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
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: