YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|41584042, gi\|...
Organism:	Lactobacillus johnsonii NCC 533
Length:	661 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|41584042, gi|....

Description	E-value	Query Range	Subject Range
gi\|116630280, gi... - gi\|23002973\|ref\|ZP_00046644.1\| hypothetical protein Lgas_03000980 [Lactobacillus gasseri ATCC 33323]... gi\|226819377 - gi\|226819377\|ref\|ZP_03808496.1\| fusion of IIA, IIB and IIC component of mannitol/fructose-specific p... gi\|23002973 - gi\|23002973\|ref\|ZP_00046644.1\| COG1299: Phosphotransferase system, fructose-specific IIC component [...	483.0	[0..1]	[661..1]
gi\|18144243, gi\|... - gi\|18309566\|ref\|NP_561500.1\| PTS system [Clostridium perfringens str. 13], gi\|18144243\|dbj\|BAB80290....	470.0	[0..1]	[657..1]
gi\|110674944, gi... - gi\|110800297\|ref\|YP_695018.1\| PTS system, fructose-specific, IIABC component [Clostridium perfringen...	464.0	[0..1]	[657..1]
gi\|227902793, gi... - gi\|227902793\|ref\|ZP_04020598.1\| PTS system, fructose-specific enzyme II [Lactobacillus acidophilus A... gi\|58338030, gi\|... - gi\|58338030\|ref\|YP_194615.1\| PTS system, fructose-specific enzyme II [Lactobacillus acidophilus NCFM...	463.0	[0..1]	[661..1]
gi\|62516288, gi\|... - gi\|62516288\|ref\|ZP_00387645.1\| COG1299: Phosphotransferase system, fructose-specific IIC component [...	459.0	[0..1]	[657..1]
gi\|103423772, gi... - gi\|104774691\|ref\|YP_619671.1\| PTS system, fructose-specific enzyme IIABC component [Lactobacillus de...	457.0	[0..1]	[657..1]
gi\|110681997, gi... - gi\|110801496\|ref\|YP_697878.1\| fructose specific permease [Clostridium perfringens SM101], gi\|1106819...	457.0	[0..1]	[657..1]
gi\|22776518, gi\|... - gi\|23098293\|ref\|NP_691759.1\| PTS system fructose-specific enzyme II BC component [Oceanobacillus ihe...	443.0	[0..1]	[657..1]
gi\|51975240, gi\|... - gi\|52141771\|ref\|YP_085058.1\| PTS fructose-specific enzyme IIBC component [Bacillus cereus E33L], gi\|...	440.0	[0..1]	[656..1]
gi\|152976110, gi... - gi\|89202202\|ref\|ZP_01180931.1\| Phosphotransferase system PTS, fructose-specific IIB subunit:PTS syst...	439.0	[0..1]	[655..1]

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Predicted Domain #1

Region A:
Residues: [1-163]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKIEDLLSPD LMIMDLKATT QEEAIKEMAD LEVKQGVVNN EEEFIKSIWA REKESTTGIG  60
   61 EGIAMPHARN KYINRAAVLF AKSPKGIDYK ALDGQPVHLF FMITAPAGAD NTHLQALAKL 120
  121 SSLLINPDVV NALKAATTPE EVIDIFKKAE AEKDAQDKAD AEK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	30.30103
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
anion transmembrane transporter activity	4.24001113213235	bayes_pls_golite062009
inorganic anion transmembrane transporter activity	3.94111218055933	bayes_pls_golite062009
carbohydrate transmembrane transporter activity	3.92377913213665	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	3.64568675122187	bayes_pls_golite062009
ion transmembrane transporter activity	2.5059397756077	bayes_pls_golite062009
transporter activity	2.16741930408232	bayes_pls_golite062009
bicarbonate transmembrane transporter activity	2.067679569708	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
chloride transmembrane transporter activity	1.57532948941308	bayes_pls_golite062009
anion exchanger activity	1.57532948941308	bayes_pls_golite062009
anion:anion antiporter activity	1.07225541736305	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
cation transmembrane transporter activity	0.191423093908067	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [164-292]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RKAEAAKEAS KPASEQKPLI VGVTACINGI AHTYMAQEAL IKAGKKLGVD VRIETNGSEG  60
   61 VKDKLTPEEI KRAKGVIIAS DKKVDMPRFN GKELVMKPVV DGINHPKELI EDILENKAPI 120
  121 YHADSSASS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	23.0
Match:	2r48A
Description:	No description for 2r48A was found.

Predicted functions:

Term	Confidence	Notes
protein-N(PI)-phosphohistidine-sugar phosphotransferase activity	5.08041453921791	bayes_pls_golite062009
carbohydrate transmembrane transporter activity	4.49138214292642	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	3.13779788020777	bayes_pls_golite062009
fructose transmembrane transporter activity	2.02791322402201	bayes_pls_golite062009
sugar transmembrane transporter activity	1.77053981674308	bayes_pls_golite062009
transporter activity	1.6837050020547	bayes_pls_golite062009
transmembrane transporter activity	1.5685227361887	bayes_pls_golite062009
monosaccharide transmembrane transporter activity	1.38987536600292	bayes_pls_golite062009
substrate-specific transporter activity	1.32293422112884	bayes_pls_golite062009
active transmembrane transporter activity	1.12964417923438	bayes_pls_golite062009
hexose transmembrane transporter activity	0.80355002679172	bayes_pls_golite062009
catalytic activity	0.676259875978821	bayes_pls_golite062009
binding	0.472595683811139	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	0.37663629577414	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.0296784994545702	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [293-485]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SDNDAKEKQG LWASIYKNLM SGISHMLPFV IGGGILMAIS FIVENYMAGG AKNPAFIFLN  60
   61 SAGNLAFAFM VPVLAAYIAE SIGDLPALMP GFVGGYMAAI VNGTNGLQVN AQAHAVSPAG 120
  121 FLGGIAAGFI AGYMMIGLKK LFAKLPKSVE GMKPMLLYPI LGLLFIALIM FYIINPIFSS 180
  181 VNFAITHFLN SMG

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #4

Region A:
Residues: [486-661]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TGNLVILTMI LAGMMAIDMG GPFNKAAYVF ASGAFANDPH SATAAVMMAA VMVGGMVPPF  60
   61 ATAIGTTFFK NRYTKEERRA GVSNWILGFS FITEGAIPFA AADPGRVIPS CVIGSAVGGL 120
  121 LVGLWHIQVP APHGGLWVSP LSNHILLYFV ATIVGSIVAG LIMSFWKKPI SEDPDE

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

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: