D-I-TASSER P00558-D2

D-I-TASSER results for P00558-D2

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>P00558 (230 residues)
FLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKV
LNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGI
PAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGC
ITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| FLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI
Prediction	CHHHHHHHHHHHHHHCCCCCSSSSSCCCCHHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCSSSCCCCHHHHHHHCCCCCSSSSCCCCCCCCCCSCCCCCHHHHHHHHHHHHHCCSSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCSSSSSCCHHHHHHHHHCCCCCCCSSSCCHHHHHHHHCCCCCCHHHHHHCC
Confidence	80899999999998189997799981873336999999999985342452038999999980998765534456689999999999982998990560434432158998158705447999971100488999999999985997999579875436426699999999999986149929991848999999949876782685664899999839998388987519
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| FLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI
Prediction	62144005103501742520000000123144214004200530230000100010001014426234421456216304500530573614020020130054047616344134575046522020113501530250056041000021001012450350032004100502754120000111001003415254321111111200031154450201300577
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHHCCCCCSSSSSCCCCHHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCSSSCCCCHHHHHHHCCCCCSSSSCCCCCCCCCCSCCCCCHHHHHHHHHHHHHCCSSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCSSSSSCCHHHHHHHHHCCCCCCCSSSCCHHHHHHHHCCCCCCHHHHHHCC
FLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI

1fw8A

0.67

19.08

1.50

DEthreader

FLLEKELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEF

1v6sA2

0.43

0.42

12.37

3.15

SPARKS-K

FLMEKEVRALSRLLKDPERPYAVVLGGAKVSDKIGVIESLLPRIDRLLIGGAMAFTFLKAL-GGEVGRSLVEEDRLDLAKDLLGRAEALGVRVYLPEDVVAAERIEAGVET-RVFPARAIPVPYMGLDIGPKTREAFARALEGARTVFWNGPMGVFEVPPFDEGTLAVGQAIAA--LEGAFTVVGGGDSVAAVNRLGLKERFGHVSTGGGASLEFLEKGTLPGLEVLEG-

1fw8A

0.67

0.66

18.70

1.24

MapAlign

-LLEKELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTK-TVTDEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFL---

1fw8A

0.67

19.08

0.84

CEthreader

FLLEKELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEK

1fw8A

0.67

19.08

2.39

MUSTER

FLLEKELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEK

1kf0A

0.97

27.06

2.48

HHsearch

FLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVN-NMEIGTSLFDEEGAKIVKNLMSKAEKNGVKITLPVDFVTADKFDEHAKTGQATVASGIPAGWMGLDCGPESSKKYSEAVARAKQIVWNGPVGVFEWEAFAQGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNV

1kf0A2

0.97

0.90

25.23

2.93

FFAS-3D

-----------------ERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKNLMSKAEKNGVKITLPVDFVTADKFDEHAKTGQATVASGIPAGWMGLDCGPESSKKYSEAVARAKQIVWNGPVGVFEWEAFAQGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNV

1kf0A

0.90

25.42

1.25

EigenThreader

LPKFLMKKELNYFAKAPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKNLMSKAEKNGVKITLPVDFVTADKFDEHAKTGQATVASGIPAGWMGLDCGPESSKKYSEAVARAKQIVWNGPVGVFEWEAFAQGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNV

2wzdA

1.00

27.88

2.44

CNFpred

FLMKKELNYFAKALESPERPFLAILGGAKVADAIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI

1kf0A

0.97

0.96

26.94

1.50

DEthreader

FLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKNLMSKAEKNGVKITLPVDFVTADKFDEHAKTGQATVASGIPAGWMGLDCGPESSKKYSEAVARAKQIVWNGPVGVFEWEAFAQGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDA-LSN

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.893

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1fw8A	0.99	0.64	0.670	1.000	model1_1fw8A.pdb.gz
2	1kf0A	0.98	0.79	0.974	1.000	model1_1kf0A.pdb.gz
3	1phpA	0.95	1.06	0.496	0.983	model1_1phpA.pdb.gz
4	16pkA	0.93	1.57	0.452	0.991	model1_16pkA.pdb.gz
5	1v6sA	0.93	1.30	0.427	0.978	model1_1v6sA.pdb.gz
6	1ltkC	0.93	1.19	0.596	0.970	model1_1ltkC.pdb.gz
7	1vpeA	0.93	1.66	0.476	0.996	model1_1vpeA.pdb.gz
8	4dg5A	0.92	1.38	0.462	0.970	model1_4dg5A.pdb.gz
9	4ng4A	0.92	1.46	0.429	0.974	model1_4ng4A.pdb.gz
10	4ehjA	0.92	1.40	0.439	0.970	model1_4ehjA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003824	0.97	catalytic activity
GO:0016740	0.96	transferase activity
GO:0016301	0.95	kinase activity
GO:0004618	0.94	phosphoglycerate kinase activity
GO:1901363	0.80	heterocyclic compound binding
GO:0097159	0.80	organic cyclic compound binding
GO:0000166	0.75	nucleotide binding
GO:0032555	0.74	purine ribonucleotide binding
GO:0032550	0.74	purine ribonucleoside binding
GO:0032559	0.73	adenyl ribonucleotide binding
GO:0035639	0.70	purine ribonucleoside triphosphate binding
GO:0005524	0.69	ATP binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009987	0.92	cellular process
GO:0008152	0.92	metabolic process
GO:0044237	0.89	cellular metabolic process
GO:0016310	0.84	phosphorylation
GO:0044699	0.72	single-organism process
GO:0071704	0.71	organic substance metabolic process
GO:0044238	0.68	primary metabolic process
GO:0044710	0.65	single-organism metabolic process
GO:0044281	0.64	small molecule metabolic process
GO:0006807	0.64	nitrogen compound metabolic process
GO:0044763	0.63	single-organism cellular process
GO:0034641	0.63	cellular nitrogen compound metabolic process
GO:0006139	0.61	nucleobase-containing compound metabolic process
GO:1901564	0.58	organonitrogen compound metabolic process
GO:0044723	0.57	single-organism carbohydrate metabolic process
GO:1901575	0.56	organic substance catabolic process
GO:0006082	0.56	organic acid metabolic process
GO:0044712	0.55	single-organism catabolic process
GO:0019752	0.55	carboxylic acid metabolic process
GO:0009150	0.55	purine ribonucleotide metabolic process
GO:0009116	0.55	nucleoside metabolic process
GO:0006091	0.55	generation of precursor metabolites and energy
GO:0006096	0.54	glycolytic process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	0.99	cell part
GO:0044424	0.95	intracellular part
GO:0044444	0.75	cytoplasmic part
GO:0043226	0.67	organelle
GO:0043227	0.60	membrane-bounded organelle
GO:0043229	0.57	intracellular organelle

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.413	1fw8A	0.988	0.64	0.670	1.000	2.7.2.3	33,186,188,190,207,209,213,215,217,222
2	0.378	1zmrA	0.914	1.27	0.377	0.957	2.7.2.3	29,187,210
3	0.366	1v6sA	0.934	1.30	0.427	0.978	2.7.2.3	29,187,210
4	0.129	1vpeA	0.931	1.66	0.476	0.996	2.7.2.3	187,210
5	0.083	2bruC	0.473	3.78	0.159	0.622	1.6.1.2	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.95	1kf0A	0.985	0.79	0.974	1.000	2.00	ACP	complex1.pdb.gz	27,28,33,51,52,55,126,154,155,157,188
2	0.88	2wzcA	0.932	1.67	0.983	0.996	1.21	UUU	complex2.pdb.gz	27,28,29,33,51,52,70,126,127,150,152,154,155,157,186,187,188,189
3	0.27	13pkD	0.919	1.83	0.452	0.991	0.85	PO4	complex3.pdb.gz	186,187,209
4	0.06	2cunA	0.868	1.98	0.301	0.952	0.96	MPD	complex4.pdb.gz	187,189,205,206,207

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.