D-I-TASSER O95751-D2

D-I-TASSER results for O95751-D2

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

Input Sequence in FASTA format

>O95751 (98 residues)
CPVPFPETFNGESSRLPEFIVQTASYMLVNENRFCNDAMKVAFLISLLTGEAEEWVVPYI
EMDSPILGDYRAFLDEMKQCFGWDDDEDDDDEEEEDDY

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| CPVPFPETFNGESSRLPEFIVQTASYMLVNENRFCNDAMKVAFLISLLTGEAEEWVVPYIEMDSPILGDYRAFLDEMKQCFGWDDDEDDDDEEEEDDY
Prediction	CCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHC
Confidence	99999999899989999999999999997532179889999999997489099999999981896004899999999999699965889999988629
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| CPVPFPETFNGESSRLPEFIVQTASYMLVNENRFCNDAMKVAFLISLLTGEAEEWVVPYIEMDSPILGDYRAFLDEMKQCFGWDDDEDDDDEEEEDDY
Prediction	67364266263547405500410331132345315444310100021043403500331156545326316401520472054457755045515768
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHC
CPVPFPETFNGESSRLPEFIVQTASYMLVNENRFCNDAMKVAFLISLLTGEAEEWVVPYIEMDSPILGDYRAFLDEMKQCFGWDDDEDDDDEEEEDDY

6tapA

0.14

0.12

4.20

1.17

DEthreader

KGFACTHSFGGTRDVVEEFIGNIETYKDVEG--ISDE-NALKGISLLFYGMASTWWQGVR---K-EATTWKEAIALIREHFS--P-TKPAYQIYMEFQ

6tapA

0.15

0.14

4.79

1.84

HHsearch

NFSACTHSFGGTHDVVEEFIGNIETYKDVEG---ISDENALKGISLLFYGMASTWWQGVR----KEATTWKEAIALIREHFSPTKPAYQIYMEFFQNK

6r24A

0.19

0.15

4.94

1.00

DEthreader

-----------DSHKLKNFISEIMLNMSMI-S-WPNDASRIVYCRRHLLNPAAQWANDFVQEQGILEITFDTFIQGLYQHFY--K--PPDI-NK-FNT

4x3hA

0.13

0.10

3.53

0.94

SPARKS-K

LGSPEFPGLDTQFEDPREFLSHLEEYLRQVGG---SEEYWLSQIQNHMNGPAKKWWEFKQGSVK----NWVEFKKEFLQYSEG---------------

1e6yA

0.05

2.36

0.89

MapAlign

DDIDNNDVYIVVKDIATESTLYGIETYEKALEDHFGGSQRATVLAAAAAATGWYLSMYLHKEAWGRLGFDLQDAGIAQAAHPFNFAEPRREFGRGA--

6taqB

0.16

0.15

5.06

0.69

CEthreader

SFSNCTVRFSGQHDAVDEFINAVETYKEVEG---ISDKDALKGLPLLFKSIAVVWWKGVRR----DAKTWSDALQLLRDHFSPTKPSYQIYMEIFETK

6taqB

0.16

0.15

5.06

0.95

MUSTER

SFSNCTVRFSGDHDAVDEFINAVETYKEVEG---ISDKDALKGLPLLFKSIAVVWWKGVR----RDAKTWSDALQLLRDHFSPTKPSYQIYMEIFETK

6gseA

0.12

0.10

3.63

1.80

HHsearch

-----SPGLDTQFEDPREFLSHLEEYLRQVG---GSEEYWLSQIQNHMNGPAKKWWEFKQ----GSVKNWVEFKKEFLQYSEGTLSREAIQRELDLPQ

6tapA

0.16

0.14

4.77

0.98

FFAS-3D

--SACTHSFGGDHDVVEEFIGNIETYKDVEG---ISDENALKGISLLFYGMASTWWQGVRKEAT----TWKEAIALIREHFSPTKPAYQIYMEFFQNK

6rwgA

0.05

0.04

1.97

0.88

EigenThreader

TSILDIRQGPK---EP--FRDYVDRFYKTLRAKNA---ATETLLVQNANPDCKTILKALG--PGATLE---EMMTACQGVGGPGHRVLAEAMSQVTNP

(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	0.7486

(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	6tapA	0.65	2.45	0.132	0.827	model1_6tapA.pdb.gz
2	6taqB	0.64	2.74	0.143	0.837	model1_6taqB.pdb.gz
3	6r24A	0.64	2.63	0.188	0.775	model1_6r24A.pdb.gz
4	1d1dA	0.57	2.33	0.040	0.745	model1_1d1dA.pdb.gz
5	4x3hA	0.57	2.31	0.153	0.704	model1_4x3hA.pdb.gz
6	6sieA	0.57	2.66	0.104	0.765	model1_6sieA.pdb.gz
7	5t77A	0.57	3.84	0.022	0.929	model1_5t77A.pdb.gz
8	3zuxA	0.57	3.49	0.044	0.898	model1_3zuxA.pdb.gz
9	5m1hA	0.57	3.65	0.044	0.908	model1_5m1hA.pdb.gz
10	6wtwA	0.57	3.73	0.065	0.918	model1_6wtwA.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:1901363	0.36	heterocyclic compound binding
GO:0097159	0.36	organic cyclic compound binding
GO:0003676	0.30	nucleic acid 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:0065007	1.00	biological regulation
GO:0050794	0.80	regulation of cellular process
GO:0048523	0.76	negative regulation of cellular process
GO:0009987	0.61	cellular process
GO:0044699	0.56	single-organism 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:0043231	1.00	intracellular membrane-bounded organelle
GO:0005634	0.89	nucleus
GO:0044446	0.63	intracellular organelle part
GO:0044428	0.61	nuclear part
GO:0043232	0.60	intracellular non-membrane-bounded organelle
GO:0005730	0.58	nucleolus

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	0.060	3lm0A	0.517	4.10	0.074	0.847	2.7.11.1	64
2	0.060	2ppqA	0.517	4.07	0.089	0.847	2.7.1.39	NA
3	0.060	1e6jP	0.546	2.72	0.056	0.735	2.7.7.49	51
4	0.060	3hngA	0.357	5.61	0.011	0.837	2.7.10.1	NA
5	0.060	3ewhA	0.528	4.04	0.104	0.888	2.7.10.1	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	0.08	2ewpE	0.473	4.41	0.054	0.878	0.21	TXF	complex1.pdb.gz	12,15,16,19,20,22,43,78
2	0.07	2ewpD	0.475	4.29	0.053	0.867	0.20	TXF	complex2.pdb.gz	23,77,80,81
3	0.07	2gppA	0.532	4.36	0.042	0.939	0.13	1BA	complex3.pdb.gz	12,16,19
4	0.06	2ewpB	0.473	4.36	0.053	0.888	0.22	TXF	complex4.pdb.gz	52,53,55,73,74,77
5	0.01	2gpv4	0.420	4.03	0.024	0.745	0.16	III	complex5.pdb.gz	12,17,20,21,41,44,45
6	0.01	2gpoA	0.422	4.05	0.061	0.735	0.20	III	complex6.pdb.gz	51,52,56,70
7	0.01	3zuxA	0.567	3.49	0.044	0.898	0.31	PTY	complex7.pdb.gz	19,43,47
8	0.01	3fs1A	0.531	4.27	0.074	0.918	0.16	MYR	complex8.pdb.gz	12,49,50
9	0.01	1m7w0	0.530	4.11	0.085	0.878	0.19	III	complex9.pdb.gz	19,20,24,40,44,45,46,48
10	0.01	1s9qB	0.422	4.02	0.060	0.735	0.20	OHT	complex10.pdb.gz	77,80,81

	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.