D-I-TASSER P62906-D1

D-I-TASSER results for P62906-D1

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

Input Sequence in FASTA format

>P62906 (124 residues)
MSSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPS
TIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKP
QRLY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQRLY
Prediction	CCCCHCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCHHHHHHCCCSSSSSSCCCSSSSSSSSCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSSCCCCCCSSCC
Confidence	9741122789999887615546767874853576666433224555411221235540322899846715899997427899999999999999999997223644411799974899855179
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQRLY
Prediction	7644234630263045212533454432344153746165244545542543441651443030424433101031143714573025003200420253065436203102020334454647
	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 AttentionPotential. 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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCHCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCHHHHHHCCCSSSSSSCCCSSSSSSSSCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSSCCCCCCSSCC
MSSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQRLY

1dwuA

0.28

0.27

8.13

1.33

DEthreader

----MDRENILKAVKEARSLA--KPRNFTQSLDLIINLKELDLSRENRLKEQVVLPNGRKPVLINTRDKPLFHVLVGNEKMSDEELAENIEAILNTVSRKY-EKGYHVKSAYTKLTMGPPAQIK

3j39z2

0.73

20.81

2.60

SPARKS-K

MASKVSRDTLYEGVNGLLEASAKKKRGFLETVELQIGLKNYDPQKDKRFSGTVKLKHIPRPIKFQMKKVLCLSVAVGHVGMKSDELAQNVNLSINFLVSLLKKNWQNVRSLHVKSSMGPPQRLY

1dwuA1

0.30

0.28

8.57

1.21

MapAlign

----MDRENILKAVKEARSLA--KPRNFTQSLDLIINLKELDLRPENRLKEQVVLPNGRGTVLINTRDKPLFHVLVGNEKMSDEELAENIEAILNTVSRKYEKGLYHVKSAYTKLTMGPPAQIE

1dwuA

0.29

0.27

8.35

0.98

CEthreader

----MDRENILKAVKEARSLA--KPRNFTQSLDLIINLKELDLSRENRLKEQVVLPNGRGKVLINTRDKPLFHVLVGNEKMSDEELAENIEAILNTVSRKYEKGLYHVKSAYTKLTMGPPAQIE

3j39z2

0.73

20.81

2.58

MUSTER

MASKVSRDTLYEGVNGLLEASAKKKRGFLETVELQIGLKNYDPQKDKRFSGTVKLKHIPRPIKFQMKKVLCLSVAVGHVGMKSDELAQNVNLSINFLVSLLKKNWQNVRSLHVKSSMGPPQRLY

3zf7J1

0.59

0.57

16.44

2.49

HHsearch

-MSKIPPALLSEAIQNVLKD--RKERKFKESIDLQVNLKNYDPQKDKRFSGSVRLPHVCRPLEVKFKKVLCLGTCVGHVDMTEDQVRQNVVMAINFLVSLLKKNWQNLKSAYIKSTMGKSQRIY

3j39z2

0.73

20.81

1.81

FFAS-3D

MASKVSRDTLYEGVNGLLEASAKKKRGFLETVELQIGLKNYDPQKDKRFSGTVKLKHIPRPIKFQMKKVLCLSVAVGHVGMKSDELAQNVNLSINFLVSLLKKNWQNVRSLHVKSSMGPPQRLY

5it7qq

0.63

17.98

1.13

EigenThreader

-MSKITSSHVREHVKELLKYSETKKRNFLETVELQVGLKNYDPQRDKRFSGTLKLPVCPRPIKFQLKKVLCLAVAVGNVEMDEDTLVNQILMSVNFLVSLLKKNWQNVGSLVIKSTMGPAYRLY

2oumA

0.30

0.27

8.08

1.42

CNFpred

--------TIDEAAHLVKELA---TAKFDETVEVHAKLG-IDPRRDQNVRGTVSLPHGG-RIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPAKGTFLRSVYVTTTMGPSVRIN

1dwuA1

0.28

0.27

8.13

1.33

DEthreader

----MDRENILKAVKEARSLA--KPRNFTQSLDLIINLKELDLSRENRLKEQVVLPNGRGKVLINTRDKPLFHVLVGNEKMSDEELAENIEAILNTVSRKY-EKGYHVKSAYTKLTMGPPAQIK

(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	0.8676

(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 AttentionPotential, 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	1dwuA	0.90	1.10	0.288	0.952	model1_1dwuA.pdb.gz
2	2zkr5	0.85	1.39	0.252	0.927	model1_2zkr5.pdb.gz
3	3qoyA	0.84	1.93	0.244	0.935	model1_3qoyA.pdb.gz
4	3j39z	0.83	1.72	0.642	0.911	model1_3j39z.pdb.gz
5	2wroC	0.82	1.86	0.283	0.911	model1_2wroC.pdb.gz
6	3e1dZ	0.82	1.83	0.239	0.944	model1_3e1dZ.pdb.gz
7	3jywA1	0.81	1.80	0.581	0.944	model1_3jywA1.pdb.gz
8	3iz5A	0.80	1.95	0.183	0.911	model1_3iz5A.pdb.gz
9	3bboD	0.79	2.27	0.208	0.911	model1_3bboD.pdb.gz
10	3zf7J1	0.77	2.19	0.548	0.927	model1_3zf7J1.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:0003723	1.00	RNA binding
GO:0005524	0.95	ATP binding
GO:0003735	0.53	structural constituent of ribosome

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	1.00	cellular process
GO:0006412	0.99	translation
GO:0000470	0.99	maturation of LSU-rRNA
GO:0044763	0.97	single-organism cellular process
GO:1902578	0.96	single-organism localization
GO:0065007	0.96	biological regulation
GO:0035437	0.95	maintenance of protein localization in endoplasmic reticulum

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:0015934	1.00	large ribosomal subunit
GO:0005840	1.00	ribosome
GO:0022625	0.99	cytosolic large ribosomal subunit
GO:0005788	0.95	endoplasmic reticulum lumen

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	0.066	1unnC	0.507	2.94	0.055	0.677	2.7.7.7	NA
2	0.060	1g87B	0.545	3.81	0.073	0.839	3.2.1.4	NA
3	0.060	3ju5C	0.549	3.85	0.025	0.863	2.7.3.3	NA
4	0.060	1bg0A	0.528	4.12	0.080	0.871	2.7.3.3	NA
5	0.060	1qk1A	0.569	4.08	0.043	0.911	2.7.3.2	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	0.18	1rl9A	0.559	4.11	0.085	0.903	0.16	IOM	complex1.pdb.gz	75,119,120
2	0.18	3l2fP	0.567	4.08	0.051	0.919	0.19	ADP	complex2.pdb.gz	73,75,76,78,114,117,118
3	0.08	3j0qB	0.644	3.50	0.581	0.935	0.27	RQA	complex3.pdb.gz	5,6,8,11,12,13,14,19
4	0.01	1bg0A	0.528	4.12	0.080	0.871	0.29	ADP	complex4.pdb.gz	34,73,77,112
5	0.01	1qh40	0.572	4.03	0.043	0.911	0.11	III	complex5.pdb.gz	83,84,85,87
6	0.01	2bvcA	0.523	3.68	0.051	0.798	0.18	P3S	complex6.pdb.gz	77,114,119
7	0.01	2qc8H	0.550	3.96	0.066	0.855	0.15	ADP	complex7.pdb.gz	59,77,78,115
8	0.01	2whiA	0.557	3.97	0.050	0.855	0.13	1AZ	complex8.pdb.gz	21,25,27,117
9	0.01	1bg0A	0.528	4.12	0.080	0.871	0.13	DAR	complex9.pdb.gz	24,25,79
10	0.01	2ojwA	0.541	3.65	0.060	0.815	0.14	PO4	complex10.pdb.gz	21,23,118

	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.