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Sequence analysis results for job: test

ID: b442cb7a-446d-11e2-b2c3-00163e110593


Secondary Structure Map

Feature predictions are colour coded onto the sequence according to the sequence feature key shown below.

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Key Helix Sheet Disordered Dompred Boundary DomSSEA Boundary
Annotations M L E A D
TM Helix Map

Feature predictions are colour coded onto the sequence according to the sequence feature key shown below.

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Key Transmembrane Helix Pore lining Helix Extracellular Region Cytoplasmic Region Disordered Dompred Boundary DomSSEA Boundary
Annotations M M L E E A D


Sequence Resubmission
StartStop


Select Methods
PSIPRED v3.3 (Predict Secondary Structure) DISOPRED2 (Disorder Prediction)
pGenTHREADER (Profile Based Fold Recognition) MEMSAT3 & MEMSAT-SVM (Membrane Helix Topology Prediction)
 
BioSerf v2.0 (Automated Homology Modelling) DomPred (Protein Domain Prediction)
FFPred v2.0 (Eukaryotic Function Prediction) GenTHREADER (Rapid Fold Recognition)
MEMPACK (SVM Prediction of TM Topology and Helix Packing) pDomTHREADER (Fold Domain Recognition)
Resubmit

The sequence segment you've selected is too short to process. The sequence must be greater than 30 residues

The sequence segment you've selected is too long to process (>1,500 residues). Please return to the PSIPRED main page and try using DomPred to find shorter domains

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GenTHREADER Summary
Build Model
0 50 100 150 200 262
  1. 1m0kA0
    1 222
  2. 1uazA0
    1 238
  3. 3nl6A0
    1 450
  4. 3ei3A0
    481 283
  5. 2tpsA0
    1 296
  6. 3e96A0
    1 505
0 50 100 150 200 262
Build Model

Disopred Graph

PSI-BLAST Domain Profile

Putative Domain boundaries found by PSI-BLAST:

Putative domain boundaries located in PSI-BLAST alignment profile:

Number of predicted domains by DPS: 2

Domain Bounary locations predicted DPS: 93

Number of PSIBLAST hits = 679

DomSSEA Results

Score

Match

No. Doms

Boundaries

SCOP code
0.8167939 1rkeA 2 136 a.24.9.1, a.24.9.1
0.8162476 1t01A 2 136 a.24.9.1, a.24.9.1
0.7924866 1sj8A 2 147 a.215.1.1, a.216.1.1
0.7845304 1nu9F 2 117 a.8.6.1, a.8.6.1
0.7830882 1nu7H 2 117 a.8.6.1, a.8.6.1
0.75288683 1fpoB 2 147 a.2.3.1, a.23.1.1
0.7504762 1hfaA 2 147 a.7.8.2, a.118.9.3
0.74896264 1h99A 2 147 a.142.1.1, a.142.1.1
0.74285716 1hf8A 2 147 a.7.8.2, a.118.9.3
Strict Gene Ontology Predictions
GO term Name Type Prob Reliable SVM
GO:0006810 transport biological_process 0.672 Y
GO:0006811 ion transport biological_process 0.669 Y
GO:0007165 signal transduction biological_process 0.584 Y

Strict prediction terms represent terms predicted where SVM training requires that the positive training set uses only assigned GO terms with the IDA evidence code. SVM is regarded as reliable when the selectivity, sensitivity and MCC are all above a critical threshold.

Full Gene Ontology Predictions
GO term Name Type Prob Reliable SVM
GO:0006810 transport biological_process 0.886 Y
GO:0006629 lipid metabolic process biological_process 0.825 Y
GO:0055114 oxidation-reduction process biological_process 0.817 Y
GO:0015075 ion transmembrane transporter activity molecular_function 0.807 Y
GO:0006811 ion transport biological_process 0.806 Y
GO:0005215 transporter activity molecular_function 0.795 Y
GO:0006814 sodium ion transport biological_process 0.723 Y
GO:0005102 receptor binding molecular_function 0.722 Y
GO:0007166 cell surface receptor signaling pathway biological_process 0.715 Y
GO:0016491 oxidoreductase activity molecular_function 0.604 Y
GO:0006066 alcohol metabolic process biological_process 0.584 Y
GO:0007267 cell-cell signaling biological_process 0.568 Y
GO:0008610 lipid biosynthetic process biological_process 0.563 Y
GO:0015081 sodium ion transmembrane transporter activity molecular_function 0.560 Y
GO:0042592 homeostatic process biological_process 0.557 Y
GO:0035725 sodium ion transmembrane transport biological_process 0.556 Y
GO:0015267 channel activity molecular_function 0.553 Y
GO:0006631 fatty acid metabolic process biological_process 0.550 Y
GO:0051716 cellular response to stimulus biological_process 0.872 N
GO:0007165 signal transduction biological_process 0.848 N
GO:0032502 developmental process biological_process 0.732 N
GO:0006950 response to stress biological_process 0.662 N
GO:0046872 metal ion binding molecular_function 0.648 N
GO:0007275 multicellular organismal development biological_process 0.647 N
GO:0045184 establishment of protein localization biological_process 0.618 N
GO:0010033 response to organic substance biological_process 0.570 N
GO:0030154 cell differentiation biological_process 0.565 N
GO:0019725 cellular homeostasis biological_process 0.551 N
GO:0048513 organ development biological_process 0.544 N
GO:0019899 enzyme binding molecular_function 0.510 N

Lax prediction terms represent terms predicted where SVM training includes assigned GO terms across all evidence code types. SVM is regarded as reliable when the selectivity, sensitivity and MCC are all above a critical threshold.

Sequence Feature Map

Position dependent feature predictions are mapped onto the sequence schematic shown below. The line height of the Phosphorylation and Glycosylation features reflects the confidence of the residue prediction.

Amino Acid Map

Feature predictions are colour coded onto the sequence according to the sequence feature key shown below.

1 M L E L L P T A V E G V S Q A Q I T G R P E W I W L A L G T A L M G L G T L Y F L V K G M G V S D P 50
51 D A K K F Y A I T T L V P A I A F T M Y L S M L L G Y G L T M V P F G G E Q N P I Y W A R Y A D W L 100
101 F T T P L L L L D L A L L V D A D Q G T I L A L V G A D G I M I G T G L V G A L T K V Y S Y R F V W 150
151 W A I S T A A M L Y I L Y V L F F G F T S K A E S M R P E V A S T F K V L R N V T V V L W S A Y P V 200
201 V W L I G S E G A G I V P L N I E T L L F M V L D V S A K V G F G L I L L R S R A I F G E A E A P E 250
251 P S A G D G A A A T S D 300


Key Helix Sheet Disordered Phosphorylated N/O Glycosylated Phosphorylated + Glycosylated
- M L E Q N S
Disordered K E R Q N T
Predicted Transmembrane Topology
Amino Acid Composition (percentages)
A C D E F G H I K L M N P Q R S T V W Y
  11.45     0.00     3.82     4.20     4.96     9.92     0.00     5.73     2.67     14.89     3.82     1.15     4.58     1.53     2.67     5.34     7.25     8.78     3.05     4.20  
Significance Key
low   high
p < 0.01 p < 0.02 p < 0.05 p < 0.1 p >= 0.1 p < 0.1 p < 0.05 p < 0.02 p < 0.01
Significance p value is calculated using the Z score of the percent amino acid composition
Global Features

Global features are calculated directly from sequence. Localisation values are predicted by the Psort algorithm and reflect the relative likelihood of the protein occupying different cellular localisations. The bias column is highlighted according to the significance of the feature value calculated from Z score of the feature.

Feature Name Value Bias
aliphatic index 117.29    
charge -6.94    
hydrophobicity 0.72    
isoelectric point 4.32    
molar extinction coefficient 59600.00    
molecular weight 28256.00    
percent negative residues 8.02    
percent positive residues 5.34    
lysosome 0.09    
plasma membrane 0.81    

GenTHREADER Scores (alignments displayed against the first of the input sequences)

Conf. Net Score p-value PairE SolvE Aln Score Aln Len Str Len Seq Len View Alignment SCOP Codes CATH Codes Structure CATH Entry
CERT 130.262 4e-12 -556.1 11.8 703.1 222 222 262 Search SCOP for 1m0kA Search CATH for 1m0k pdbImage CATH Summary
CERT 118.846 5e-11 -482.3 15.1 655.7 236 236 262 Search SCOP for 1uazA Search CATH for 1uaz pdbImage CATH Summary
MEDIUM 42.240 0.003 -350.1 -7.7 66.0 182 518 262 Search SCOP for 3nl6A Search CATH for 3nl6 pdbImage CATH Summary
MEDIUM 41.090 0.004 -444.1 -7.5 31.0 203 983 262 Search SCOP for 3ei3A Search CATH for 3ei3 pdbImage CATH Summary
LOW 36.596 0.010 -389.1 -4.8 31.0 173 226 262 Search SCOP for 2tpsA Search CATH for 2tps pdbImage CATH Summary
LOW 35.240 0.014 -230.3 -10.6 42.0 148 296 262 Search SCOP for 3e96A Search CATH for 3e96 pdbImage CATH Summary

MEMSAT-SVM Schematic

MEMSAT-SVM Cartoon

MEMSAT Cartoon

MEMSAT-SVM Prediction

Summary of MEMSAT-SVM Topology Analysis

Signal peptide Not detected.
Signal score 0
Topology 23-43,58-75,94-110,122-140,146-166,188-209,215-235
Re-entrant helices Not detected.
Pore-lining helices 94-110,215-235
Helix count 7
N-terminal out
Score 19.0597
Pore stoichiometry 1

MEMSAT-SVM Prediction

Summary of MEMSAT-SVM Topology Analysis

Signal peptide Not detected.
Signal score 0
Topology 23-43,58-75,94-110,122-140,146-166,188-209,215-235
Re-entrant helices Not detected.
Pore-lining helices 94-110,215-235
Helix count 7
N-terminal out
Score 19.0597
Pore stoichiometry 1

MEMSAT3 Prediction

Summary of MEMSAT3 Topology Analysis

Number

Type

Direction

Score

1helix+31.529
1helix-47.715
2helices+85.379
2helices-74.797
3helices+93.432
3helices-128.647
4helices+147.282
4helices-140.778
5helices+126.979
5helices-194.628
6helices+180.829
6helices-174.325
7helices-228.175

MEMSAT3 Prediction

Segment

Range

Score

1(out) 22-45 30.40
253-77 25.20
393-111 10.49
4116-140 20.46
5146-168 18.89
6186-210 34.29
7216-240 33.45

MEMSAT3 Prediction

Summary of MEMSAT3 Topology Analysis

Number

Type

Direction

Score

1helix+31.529
1helix-47.715
2helices+85.379
2helices-74.797
3helices+93.432
3helices-128.647
4helices+147.282
4helices-140.778
5helices+126.979
5helices-194.628
6helices+180.829
6helices-174.325
7helices-228.175

MEMSAT3 Prediction

Segment

Range

Score

1(out) 22-45 30.40
253-77 25.20
393-111 10.49
4116-140 20.46
5146-168 18.89
6186-210 34.29
7216-240 33.45

MEMPACK Cartoon

DomTHREADER Scores

Conf. Net Score p-value PairE SolvE Aln Score Aln Len Str Len Seq Len Domain Start Domain End Domain Code View Alignment Structure CATH Entry
CERT 11.876 1e-08 -576.8 9.2 819.5 222 222 262 18 244 1c8rA00 pdbImage CATH Summary
CERT 11.873 1e-08 -556.1 12.0 820.0 222 222 262 18 244 1m0kA00 pdbImage CATH Summary
LOW 2.163 0.001 -230.2 8.6 83.0 163 212 262 1 178 1pw4A02 pdbImage CATH Summary
LOW 2.116 0.001 -0.0 -0.6 88.8 14 178 262 249 262 1hqvA00 pdbImage CATH Summary

pGenTHREADER Scores (alignments displayed against the first of the input sequences)

Conf. Net Score p-value PairE SolvE Aln Score Aln Len Str Len Seq Len View Alignment SCOP Codes CATH Codes Structure CATH Entry
CERT 164.380 1e-15 -556.1 12.0 912.5 222 222 262 Search SCOP for 1m0kA Search CATH for 1m0k pdbImage CATH Summary
CERT 138.187 6e-13 -527.2 12.9 737.4 237 238 262 Search SCOP for 2ei4A Search CATH for 2ei4 pdbImage CATH Summary
MEDIUM 46.411 0.001 -458.9 -2.0 95.0 242 358 262 Search SCOP for 3rauA Search CATH for 3rau pdbImage CATH Summary
MEDIUM 45.740 0.001 -422.6 -12.7 87.0 228 287 262 Search SCOP for 4djnA Search CATH for 4djn pdbImage CATH Summary