D-I-TASSER P29460-D1

D-I-TASSER results for P29460-D1

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

Input Sequence in FASTA format

>P29460 (117 residues)
MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITW
TLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDIL

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDIL
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHSCCCCSSSSSSCCCCCCCCCSSSSSCCCCCCCCSSSSSCCCCSSCCCCCSSSSSSSSCCCCCCSSSSCCCCSSSSSSSSSSSCCCCCCCCCCC
Confidence	961689999999999983777863116866999943689999828999828997666089827862330379589999985377774178248807433799999668985201249
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDIL
Prediction	743440112031333332313121403640100103145734444030406247744030336545634453430302045247314110344443143120101347723234436
	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

                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHHHHHSCCCCSSSSSSCCCCCCCCCSSSSSCCCCCCCCSSSSSCCCCSSCCCCCSSSSSSSSCCCCCCSSSSCCCCSSSSSSSSSSSCCCCCCCCCCC
MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDIL

2gy5A

0.11

0.09

3.43

1.17

DEthreader

----A--M--DL-IL--IN-PLYTMKMRQASFLPATTMTVDKGDNVNISFKKLIKEDAVIYKNGSFIH-SVVLEVHLPHAQPQDAGVYSARYIGGNSAFTRLIVRCKCHCCHEDDPG

1f42A1

1.00

0.78

21.78

1.10

SPARKS-K

----------------------IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWS----

1f42A1

1.00

0.78

21.78

1.36

FFAS-3D

----------------------IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWS----

6sffA

0.82

0.66

18.57

1.37

CNFpred

-----------------------WELEKDVYVVEVDWTPDAPGETVNLTCDTPEEDDITWTSDQRHGVIGSGKTLTITVKEFLDAGQYTCHKGGETLSHSHLLLHKKENGIWSTEIL

5whzL

0.16

0.14

4.55

1.00

DEthreader

----F--VL-TQ-SPH-SLTKVD-KD-TASELTQDPAVSVALKQTVTITCRGDRSHYASWYQKPVLLFSGSAASLTITGAQAEDEADYYCSSRSVFGGGTKLTVLDKTHTR------

6sffA1

0.81

0.63

17.85

1.09

SPARKS-K

----------------------MWELEKDVYVVEVDWTPDAPGETVNLTCDTPEEDDITWTSDQRHGVIGSGKTLTITVKEFLDAGQYTCHKGGETLSHSHLLLHKKENGIWS----

6grqA

0.13

4.44

0.55

MapAlign

--VSGNLQKPTIQPSDTLELVVTGIYEHYKPRLSVLSPVVTAGGNMTLHCASFHYDKFILTKEDKKFGSLDTALFIIGPTTPTHTGTFRCYGYWSVPSLQQILISGNLSSEWSASS-

3tf7C2

0.15

0.11

3.74

0.30

CEthreader

----------------------------AAVTQSPRNKVTVTGENVTLSCRQNSHNYMYWYRQDELRLIYYSFFLTLESASPSQTSLYFCASSLYFGEGSKLTVLELEHHHHHH---

1f42A

1.00

0.81

22.74

0.94

MUSTER

----------------------IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDIL

6iaaA2

0.24

0.19

5.85

0.41

HHsearch

--------------------------APPQFVVRPRDQIVAQGRTVTFPCETKGNPAVFWQKEGSQNLVSPTGDLTITNIQRSDAGYYICQALGSILAKAQLEVTDVLTDRPPPIIL

(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	0.6716

(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	2gy5A	0.67	3.25	0.096	0.914	model1_2gy5A.pdb.gz
2	5opiC	0.65	3.15	0.139	0.889	model1_5opiC.pdb.gz
3	3dmkA	0.63	3.17	0.129	0.812	model1_3dmkA.pdb.gz
4	6xqqB	0.62	2.32	0.148	0.752	model1_6xqqB.pdb.gz
5	6wjuL	0.62	2.67	0.244	0.761	model1_6wjuL.pdb.gz
6	7bxvL	0.62	2.29	0.195	0.744	model1_7bxvL.pdb.gz
7	2cdfA	0.62	2.48	0.157	0.752	model1_2cdfA.pdb.gz
8	4jryD	0.62	2.40	0.144	0.752	model1_4jryD.pdb.gz
9	1hxmA	0.62	2.20	0.167	0.735	model1_1hxmA.pdb.gz
10	6lirA	0.62	2.18	0.184	0.727	model1_6lirA.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:0042164	1.00	interleukin-12 alpha subunit binding
GO:0005102	0.84	receptor binding
GO:0070851	0.82	growth factor receptor binding
GO:0005126	0.82	cytokine receptor binding
GO:0008083	0.81	growth factor activity
GO:0005143	0.81	interleukin-12 receptor binding
GO:0045519	0.80	interleukin-23 receptor 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	0.98	biological regulation
GO:0050794	0.97	regulation of cellular process
GO:0048518	0.96	positive regulation of biological process
GO:0032946	0.95	positive regulation of mononuclear cell proliferation
GO:0050671	0.83	positive regulation of lymphocyte proliferation
GO:0050870	0.82	positive regulation of T cell activation
GO:0060255	0.80	regulation of macromolecule metabolic process
GO:0051239	0.80	regulation of multicellular organismal process
GO:0080090	0.79	regulation of primary metabolic process
GO:0051240	0.79	positive regulation of multicellular organismal process
GO:0031325	0.79	positive regulation of cellular metabolic process
GO:0010604	0.79	positive regulation of macromolecule metabolic process
GO:0001817	0.79	regulation of cytokine production
GO:0051246	0.78	regulation of protein metabolic process
GO:0031328	0.78	positive regulation of cellular biosynthetic process
GO:0010557	0.78	positive regulation of macromolecule biosynthetic process
GO:0001819	0.78	positive regulation of cytokine production
GO:0051247	0.77	positive regulation of protein metabolic process
GO:0051135	0.76	positive regulation of NK T cell activation
GO:0045078	0.76	positive regulation of interferon-gamma biosynthetic process
GO:0032816	0.76	positive regulation of natural killer cell activation
GO:0002376	0.74	immune system process
GO:0009987	0.66	cellular process
GO:0044699	0.65	single-organism process
GO:0050896	0.64	response to stimulus
GO:0044763	0.59	single-organism cellular process
GO:0006955	0.53	immune 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:0043514	1.00	interleukin-12 complex
GO:0070743	0.80	interleukin-23 complex
GO:0044464	0.67	cell part

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	0.146	1u2hA	0.542	2.33	0.188	0.667	2.7.11.1	62
2	0.142	2edwA	0.574	2.26	0.135	0.692	2.7.11.1	47,50,84
3	0.132	2gqhA	0.560	2.41	0.129	0.684	2.7.11.1	NA
4	0.120	2edrA	0.558	2.54	0.174	0.692	2.7.11.1	50,85,100
5	0.113	2edtA	0.563	2.53	0.144	0.692	2.7.11.1	85,98

	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	0.26	1jglL	0.593	2.59	0.207	0.744	0.71	EST	complex1.pdb.gz	61,67,70,91,93,94
2	0.16	1yeeL	0.614	2.41	0.218	0.744	0.76	PNB	complex2.pdb.gz	58,91,93,95,97
3	0.16	1ct8A	0.608	2.86	0.244	0.761	0.73	TAA	complex3.pdb.gz	71,92,93,94,96
4	0.11	3sgeL	0.609	2.52	0.218	0.744	0.75	III	complex4.pdb.gz	57,59,66,91,93
5	0.09	1i8mL	0.599	2.58	0.241	0.744	0.79	QNA	complex5.pdb.gz	58,69,92,93,94
6	0.04	1ehlL	0.586	2.62	0.222	0.727	0.75	QNA	complex6.pdb.gz	47,49,103
7	0.03	3cfbL	0.613	2.42	0.195	0.744	0.76	SPB	complex7.pdb.gz	94,96,98
8	0.03	1ikfL	0.613	2.49	0.195	0.744	0.71	III	complex8.pdb.gz	58,93,94
9	0.03	3scmC	0.618	2.45	0.180	0.744	0.72	LGN	complex9.pdb.gz	50,60,91,92
10	0.03	3sdcC	0.620	2.36	0.157	0.744	0.72	3GB	complex10.pdb.gz	59,92,93

	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.