D-I-TASSER Q04912-D4

D-I-TASSER results for Q04912-D4

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

Input Sequence in FASTA format

>Q04912 (66 residues)
LHPSGLVPEGTHQVTVGQSPCRPLPKDSSKLRPVPRKDFVEEFECELEPLGTQAVGPTNV
SLTVTN

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| LHPSGLVPEGTHQVTVGQSPCRPLPKDSSKLRPVPRKDFVEEFECELEPLGTQAVGPTNVSLTVTN
Prediction	CCCCCCCCCCCSSSSSCCCCCSCCCCCCCCCCCCCHHHHHHHHSSSSSCCCCCCCCCCSSSSSSCC
Confidence	987788899853898658875114687665687753544544056762078767785317999539
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| LHPSGLVPEGTHQVTVGQSPCRPLPKDSSKLRPVPRKDFVEEFECELEPLGTQAVGPTNVSLTVTN
Prediction	744753447443414234440433466375345444551154141314446654434341413258
	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

CCCCCCCCCCCSSSSSCCCCCSCCCCCCCCCCCCCHHHHHHHHSSSSSCCCCCCCCCCSSSSSSCC
LHPSGLVPEGTHQVTVGQSPCRPLPKDSSKLRPVPRKDFVEEFECELEPLGTQAVGPTNVSLTVTN

1n32I

0.10

0.09

3.33

0.51

CEthreader

-------EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFRFDAYITVRGGGKSGQIDA-IKLGIAR

6smcA3

0.08

3.05

0.52

EigenThreader

ILKNFKNKTFLNIKSSSSRAVTCGMASLSAEKVTLDQRDYEKYSCQEDVTCPTAEETLPIELALEA

5ihbA2

0.21

0.18

5.79

0.33

FFAS-3D

--PGTLEPGHSKNLT-----CSVSWACEQGTPPPRPQDHGTNLTCQVKFAGAGVTTERTIQLNVT-

6dldA2

0.12

4.26

0.79

SPARKS-K

PVTVNEGGNVNLLCLAVGRPPTVTWRQLRDGFTSEGEILAGEYECVTHNGVNSAPDSRRVLVTVN-

5l56A

0.21

0.12

3.86

0.71

CNFpred

-----------VAVSIGGRPCSFSWR------------NSREIRCLTPPG----PGSAPIVININR

3fcyA

0.11

0.09

3.32

0.83

DEthreader

--FA-ECY--DLYFTGVGARIHAKYSGDWNKLYVFT--VV--AMDVRQDVGGVGNMRHLDQLIVMP

2ka0A

0.04

0.03

1.68

0.63

MapAlign

---------MRVELLFESGKCVIDLNIGDVGYWPPASAVNVIGKIVEGLEDLKKIKDGEKVAVRFA

5l56A2

0.23

0.18

5.71

0.64

MUSTER

LRFEDVRL----GVHVGKVLCSPVESEYIS---------AEQIVCEIGDASTLRAHDALVEVCVRD

2uzyB

0.17

0.12

3.98

1.15

HHsearch

FRRNNKFDLKKTRVLLGNESCTLTLSESTMNT----------LKCTVG-------F--NMSIIISN

4dzgA

0.14

4.68

0.48

CEthreader

IHYTLVAAGQTMTVIGGNANFNVFAPGAQIGRNDGDGQWQGALLIQVYQMRASAREQVPHSLAVSI

(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	0.6463

(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	6kbhA2	0.53	3.27	0.071	0.833	model1_6kbhA2.pdb.gz
2	4zkdA2	0.53	3.32	0.066	0.924	model1_4zkdA2.pdb.gz
3	4c20A2	0.53	3.21	0.063	0.894	model1_4c20A2.pdb.gz
4	1fuiA2	0.52	3.22	0.016	0.879	model1_1fuiA2.pdb.gz
5	3a9rA	0.52	3.27	0.047	0.894	model1_3a9rA.pdb.gz
6	5ganm	0.44	3.26	0.089	0.758	model1_5ganm.pdb.gz
7	3uv0A	0.36	3.83	0.058	0.697	model1_3uv0A.pdb.gz
8	3uboA	0.35	4.09	0.062	0.773	model1_3uboA.pdb.gz
9	1j2gA2	0.34	4.14	0.034	0.727	model1_1j2gA2.pdb.gz
10	3ri6A	0.34	4.40	0.033	0.788	model1_3ri6A.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:0019899	1.00	enzyme binding
GO:0004872	0.65	receptor activity
GO:0004871	0.64	signal transducer activity
GO:0003824	0.64	catalytic activity
GO:0004888	0.62	transmembrane signaling receptor activity
GO:0004672	0.61	protein kinase activity
GO:0004714	0.60	transmembrane receptor protein tyrosine kinase activity
GO:0005011	0.59	macrophage colony-stimulating factor receptor activity

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:0051897	1.00	positive regulation of protein kinase B signaling
GO:0043406	1.00	positive regulation of MAP kinase activity
GO:0009615	1.00	response to virus
GO:0044699	0.69	single-organism process
GO:0044763	0.65	single-organism cellular process
GO:0007165	0.65	signal transduction
GO:0007166	0.61	cell surface receptor signaling pathway
GO:0007167	0.60	enzyme linked receptor protein signaling pathway
GO:0006950	0.60	response to stress
GO:0006928	0.60	movement of cell or subcellular component
GO:0048012	0.59	hepatocyte growth factor receptor signaling pathway
GO:0008284	0.59	positive regulation of cell proliferation
GO:0007338	0.59	single fertilization
GO:0006952	0.59	defense response

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:0009986	1.00	cell surface
GO:0005886	1.00	plasma membrane
GO:0044424	0.70	intracellular part
GO:0044425	0.63	membrane part
GO:0031224	0.62	intrinsic component of membrane
GO:0044459	0.61	plasma membrane part
GO:0016021	0.61	integral component of membrane
GO:0005887	0.60	integral component of plasma membrane
GO:0044444	0.55	cytoplasmic part
GO:0043226	0.54	organelle
GO:0043229	0.53	intracellular organelle
GO:0043227	0.52	membrane-bounded organelle
GO:0043231	0.51	intracellular membrane-bounded 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	0.060	1d2eA	0.476	3.44	0.067	0.864	3.6.5.3	NA
2	0.060	1sezA	0.501	2.84	0.093	0.773	1.3.3.4	NA
3	0.060	1kzlA	0.480	3.26	0.132	0.803	2.5.1.9	NA
4	0.060	2kaiB	0.386	3.13	0.035	0.651	3.4.21.35 3.4.21.8	NA
5	0.060	1eloA	0.463	3.48	0.073	0.833	3.6.5.3	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	0.01	2y16Z	0.480	3.42	0.017	0.879	0.12	KIR	complex1.pdb.gz	15,22,23,24
2	0.01	1ob5A	0.452	3.56	0.052	0.879	0.11	ENX	complex2.pdb.gz	7,9,10
3	0.01	1tttB	0.494	3.37	0.000	0.879	0.28	PHE	complex3.pdb.gz	16,46,47,48
4	0.01	1tttA	0.492	3.41	0.017	0.879	0.19	PHE	complex4.pdb.gz	18,47,48
5	0.01	1lo6A	0.385	4.13	0.083	0.818	0.27	BEN	complex5.pdb.gz	18,19,60
6	0.01	1tttC	0.495	3.39	0.017	0.879	0.28	PHE	complex6.pdb.gz	16,59,60
7	0.01	2c77A	0.464	3.58	0.068	0.894	0.14	III	complex7.pdb.gz	12,14,16,18,21,23,44,45,47
8	0.01	1b23P	0.480	3.47	0.017	0.879	0.11	GNP	complex8.pdb.gz	17,18,52,53

	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.