D-I-TASSER O00192-D3

D-I-TASSER results for O00192-D3

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

Input Sequence in FASTA format

>O00192 (61 residues)
STVDRRERRPRGASSAGEASEKEPLKLDPSRKAPPPGPSRPAVRLVDAVGDAKPQPVDSW
V

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| STVDRRERRPRGASSAGEASEKEPLKLDPSRKAPPPGPSRPAVRLVDAVGDAKPQPVDSWV
Prediction	CCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSHSHHCCCCCCCCCCCCC
Confidence	9511120256777899985534557789787789999997423301111578998777779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| STVDRRERRPRGASSAGEASEKEPLKLDPSRKAPPPGPSRPAVRLVDAVGDAKPQPVDSWV
Prediction	8545555654545565454565542556664644465664321411432473445436638
	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

                   |                   |                   |

SS
Seq

CCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSHSHHCCCCCCCCCCCCC
STVDRRERRPRGASSAGEASEKEPLKLDPSRKAPPPGPSRPAVRLVDAVGDAKPQPVDSWV

5hi8A

0.05

2.33

0.44

CEthreader

IEYVCPELIIVHNPACDIIFKWTGIYFEGESEPDCQWNGQPLDSKARLYADEYHTWDVGYW

2bsgA

0.03

1.89

0.65

EigenThreader

RANVSWLNQIVSLLNRVSTIETSVSGGNNSAGIKGQVVALNTLVNGTNPNGSTVEERGLTN

6ybdx

0.16

0.13

4.36

0.29

FFAS-3D

QPFSKGDRLGKVADWTGATYQDKRYTNKYSQYAYFHEEDESSFQLVDTAR-----------

3gawA4

0.13

0.11

4.00

1.21

SPARKS-K

SCKSPDVINGSPISQKIIYKENERFQYKCNMGYEYSERG----DAVCTESGWRPLPSCE--

1e2uA

0.06

0.02

0.72

0.29

CNFpred

--------------------------------------------LLTTNCLVPLKKENTYL

3dyjA

0.04

0.03

1.79

1.00

DEthreader

KDAVWQLKNSAK-VVTNTSLLKVAVEATSCQVITLSRRAIADRACKEAAFHPEVA-D----

6ar6A

0.02

1.44

0.89

MapAlign

YFNPINGGAASIGETIIDDKNYYFNQSGVLQTGVFSTEDGFKYFAPANTLDENLEGEAIDF

2k4fA

0.18

0.16

5.33

0.80

MUSTER

CSKNRKAKAKPVTRGTGAGSRPRGQNKEPPVPNPDYEPIRKGQR--DLYSGLNQRAV----

4adgA

0.32

0.30

8.90

0.44

HHsearch

YIMNQQSRNCHGPDWASPVCQRHSPD--CSRL-VGATPERPRLRLVDA-DDTAPGPGEVWV

2re3B

0.07

2.77

0.44

CEthreader

ILKREEDRFYLVTPVEKVGIRVDDAPFVAVDVEVAGQGRKQVLTFTTHVGDSAVAGEGNPI

(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	0.5373

(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	2iirA1	0.46	3.36	0.070	0.918	model1_2iirA1.pdb.gz
2	1wdpA	0.45	3.34	0.034	0.853	model1_1wdpA.pdb.gz
3	6ioyA1	0.45	3.75	0.036	0.918	model1_6ioyA1.pdb.gz
4	5id6A	0.45	3.44	0.034	0.853	model1_5id6A.pdb.gz
5	4ijnA1	0.45	3.53	0.123	0.918	model1_4ijnA1.pdb.gz
6	1venA	0.44	3.43	0.055	0.803	model1_1venA.pdb.gz
7	4h0pA	0.44	3.74	0.018	0.934	model1_4h0pA.pdb.gz
8	5u30A	0.43	3.33	0.070	0.787	model1_5u30A.pdb.gz
9	4uaqA	0.43	3.52	0.050	0.820	model1_4uaqA.pdb.gz
10	3p4iA	0.42	3.71	0.053	0.918	model1_3p4iA.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	0.56	heterocyclic compound binding
GO:0097159	0.56	organic cyclic compound binding
GO:0043169	0.55	cation binding
GO:0032555	0.53	purine ribonucleotide binding
GO:0032550	0.53	purine ribonucleoside binding
GO:0035639	0.52	purine ribonucleoside triphosphate 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:0007155	1.00	cell adhesion
GO:0044699	0.71	single-organism process
GO:0044767	0.60	single-organism developmental process
GO:0048856	0.59	anatomical structure development
GO:0044707	0.58	single-multicellular organism process
GO:0007275	0.57	multicellular organism development

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	1.00	cell part
GO:0044424	0.74	intracellular part
GO:0016020	0.58	membrane
GO:0005622	0.57	intracellular
GO:0043226	0.56	organelle
GO:0043229	0.54	intracellular organelle
GO:0043227	0.54	membrane-bounded organelle
GO:0043231	0.53	intracellular membrane-bounded organelle
GO:0005886	0.53	plasma membrane

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	3a9bA	0.390	4.00	0.071	0.836	3.2.1.91	NA
2	0.060	3f63A	0.414	3.42	0.036	0.803	2.5.1.18	NA
3	0.060	1fa2A	0.427	3.38	0.035	0.820	3.2.1.2	NA
4	0.060	1fq1A	0.403	3.91	0.075	0.803	3.1.3.16	NA
5	0.060	1wdpA	0.448	3.34	0.034	0.853	3.2.1.2	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	0.09	2xgbA	0.456	3.52	0.052	0.869	0.15	EPG	complex1.pdb.gz	3,12,14,17,19
2	0.01	1j0zC	0.346	3.90	0.034	0.803	0.13	GLC	complex2.pdb.gz	3,13,15,18,24
3	0.01	1j12D	0.308	4.30	0.019	0.721	0.15	EBG	complex3.pdb.gz	4,13,15,19,21
4	0.01	1fa2A	0.427	3.38	0.035	0.820	0.13	DOM	complex4.pdb.gz	1,2,4,13,16
5	0.01	3g7jB	0.416	3.54	0.018	0.803	0.14	GTX	complex5.pdb.gz	36,43,47,48,49
6	0.01	3g7jA	0.413	3.47	0.036	0.803	0.11	GTX	complex6.pdb.gz	1,2,10,53
7	0.01	1j12B	0.396	4.12	0.052	0.853	0.15	EBG	complex7.pdb.gz	4,12,14,17,19,21
8	0.01	1b1yA	0.418	3.62	0.052	0.853	0.18	UUU	complex8.pdb.gz	4,12,19,21,52
9	0.01	1bfnA	0.428	3.46	0.088	0.836	0.11	GLC	complex9.pdb.gz	17,48,49,50
10	0.01	1b9zA	0.380	3.81	0.051	0.853	0.11	MAL	complex10.pdb.gz	4,9,17

	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.