D-I-TASSER Q07011-D1

D-I-TASSER results for Q07011-D1

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

Input Sequence in FASTA format

>Q07011 (104 residues)
MGNSCYNIVATLLLVLNFERTRSLQDPCSNCPAGTFCDNNRNQICSPCPPNSFSSAGGQR
TCDICRQCKGVFRTRKECSSTSNAECDCTPGFHCLGAGCSMCEQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MGNSCYNIVATLLLVLNFERTRSLQDPCSNCPAGTFCDNNRNQICSPCPPNSFSSAGGQRTCDICRQCKGVFRTRKECSSTSNAECDCTPGFHCLGAGCSMCEQ
Prediction	CCCCCCCSSSSSSSSSCCCCCCCCCCCCCCCCCCCSSCCCCCCCCSCCCCCCSCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCSSSCCCCCSSCCCCCCCCCC
Confidence	99876540357898752367552477666799981337999984232999931389997646056537998089816778876255279981857997322689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MGNSCYNIVATLLLVLNFERTRSLQDPCSNCPAGTFCDNNRNQICSPCPPNSFSSAGGQRTCDICRQCKGVFRTRKECSSTSNAECDCTPGFHCLGAGCSMCEQ
Prediction	86543341110001114144343344325513443214666754144146441475544741442551764443344134445350515533215775155178
	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 DeepPotential. 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

CCCCCCCSSSSSSSSSCCCCCCCCCCCCCCCCCCCSSCCCCCCCCSCCCCCCSCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCSSSCCCCCSSCCCCCCCCCC
MGNSCYNIVATLLLVLNFERTRSLQDPCSNCPAGTFCDNNRNQICSPCPPNSFSSAGGQRTCDICRQCKGVFRTRKECSSTSNAECDCTPGFHCLGAGCSMCEQ

5wi8A1

0.58

0.43

12.42

3.60

SPARKS-K

--------------------------SCDNCQPGTFC-RKYNPVCKSCPPSTFSSIGGQPNCNICRVCAGYFRFKKFCSSTHNAECECIEGFHCLGPQCTRCEK

6bwvD

1.00

0.76

21.27

1.75

MUSTER

-------------------------DPCSNCPAGTFCDNNRNQICSPCPPNSFSSAGGQRTCDICRQCKGVFRTRKECSSTSNAECDCTPGFHCLGAGCSMCEQ

1jmaB

0.29

0.25

7.61

1.45

HHsearch

-------------CKEDEYPV--GSECCPKCSPGYRCGELTGTVCEPCPPGTYIAHNGLSKCLQCQMCDPGLRASRNCSRTENAVCGCSPGHFCIVDHCAACRA

6cprD

1.00

0.77

21.54

2.47

CNFpred

------------------------QDPCSNCPAGTFCDNNRNQICSPCPPNSFSSAGGQRTCDICRQCKGVFRTRKECSSTSNAECDCTPGFHCLGAGCSMCEQ

1d4vA

0.23

0.17

5.41

1.00

DEthreader

--------------------------SPSLCPPGHHISEDGR-DCISCKYQDYSTHWNDLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRC

2aw2B

0.27

0.24

7.37

2.91

SPARKS-K

-------------PSCKEDEYPVGSECCPKCSPGYRVGELTGTVCEPCPPGTYIAHLGLSKCLQCQMCDPGLRASRNCSRTENAVCGCSPGHFCVQDHCAACRA

1jmaB

0.30

0.23

6.99

0.71

MapAlign

-------------------------ECCPKCSPGYRVKELTGTVCEPCPPGTYIAHLNGSKCLQCQMCDPGLRASRNCSRTENAVCGCSPGHFCIQDHCAACRA

3ij2X

0.19

0.16

5.29

0.57

CEthreader

-------------ETCSTGLYTHSGECCKACNLGEGVAQADQTVCEPCLDSTFSDVVSAEPCKPCTECLGLQSMSAPCVEADDAVCRCAYGYYQDEETGHCEAC

5wi8A

0.58

0.43

12.42

1.64

MUSTER

--------------------------SCDNCQPGTFCR-KYNPVCKSCPPSTFSSIGGQPNCNICRVCAGYFRFKKFCSSTHNAECECIEGFHCLGPQCTRCEK

3qd6R

0.22

0.19

6.05

1.42

HHsearch

-------------CREKQYL--INSQCCSLCQPGQKCTEFTETECLPCGESEFLDTNRETHCHQHKYCDPGLRVQQKGTSETDTICTCEEGWHCTSEACESCVL

(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	0.5349

(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 DeepPotential, 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	6bwvD	0.74	0.61	1.000	0.760	model1_6bwvD.pdb.gz
2	5wi8A1	0.70	1.36	0.584	0.740	model1_5wi8A1.pdb.gz
3	3wvtA	0.67	2.12	0.281	0.817	model1_3wvtA.pdb.gz
4	3qd6R	0.65	2.61	0.202	0.808	model1_3qd6R.pdb.gz
5	2aw2B	0.64	2.61	0.258	0.808	model1_2aw2B.pdb.gz
6	5dmjA	0.63	2.64	0.198	0.788	model1_5dmjA.pdb.gz
7	6ng3A	0.63	2.71	0.202	0.817	model1_6ng3A.pdb.gz
8	1d4vA	0.63	2.54	0.200	0.750	model1_1d4vA.pdb.gz
9	3me2R	0.62	2.89	0.178	0.788	model1_3me2R.pdb.gz
10	3ij2X	0.61	2.84	0.205	0.798	model1_3ij2X.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:0004872	0.98	receptor activity
GO:0004888	0.96	transmembrane signaling receptor activity
GO:0005031	0.91	tumor necrosis factor-activated 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:0050794	0.98	regulation of cellular process
GO:0048856	0.88	anatomical structure development
GO:0042981	0.88	regulation of apoptotic process
GO:0050896	0.87	response to stimulus
GO:0044699	0.87	single-organism process
GO:0007165	0.86	signal transduction
GO:0006952	0.85	defense response
GO:0002376	0.85	immune system process
GO:0044767	0.84	single-organism developmental process
GO:0006955	0.83	immune response
GO:0043207	0.81	response to external biotic stimulus
GO:0042127	0.81	regulation of cell proliferation
GO:0010033	0.80	response to organic substance
GO:0032496	0.79	response to lipopolysaccharide
GO:0006954	0.79	inflammatory response
GO:0097190	0.78	apoptotic signaling pathway
GO:0032501	0.68	multicellular organismal process
GO:0007275	0.67	multicellular organism development
GO:0048518	0.66	positive regulation of biological process
GO:0048522	0.64	positive regulation of cellular process
GO:0080090	0.62	regulation of primary metabolic process
GO:0031323	0.61	regulation of cellular metabolic process
GO:0060255	0.58	regulation of macromolecule metabolic process
GO:0051246	0.56	regulation of protein metabolic process
GO:0032268	0.55	regulation of cellular protein metabolic process
GO:0031325	0.55	positive regulation of cellular metabolic process
GO:0010604	0.55	positive regulation of macromolecule metabolic process
GO:0048583	0.54	regulation of response to stimulus
GO:0032270	0.54	positive regulation of cellular protein metabolic process
GO:0048584	0.52	positive regulation of response to stimulus
GO:0031399	0.52	regulation of protein modification process
GO:0019220	0.52	regulation of phosphate metabolic process
GO:0023051	0.51	regulation of signaling
GO:0010646	0.51	regulation of cell communication
GO:0001934	0.51	positive regulation of protein phosphorylation
GO:1902533	0.50	positive regulation of intracellular signal transduction

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:0044425	0.89	membrane part
GO:0044459	0.88	plasma membrane part
GO:0016021	0.86	integral component of membrane
GO:0005887	0.85	integral component of 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	2fenD	0.440	4.25	0.038	0.760	5.5.1.2	NA
2	0.060	3ecdB	0.428	4.47	0.056	0.788	2.1.2.1	NA
3	0.060	3g7qA	0.429	4.43	0.056	0.760	2.6.1.66	NA
4	0.060	1rv3B	0.426	4.37	0.060	0.779	2.1.2.1	NA
5	0.060	2o0rA	0.439	4.65	0.045	0.808	2.6.1.-	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	0.04	2aw21	0.638	2.61	0.258	0.808	0.59	III	complex1.pdb.gz	29,30,32,35,38,44,45,47,57
2	0.04	1jma0	0.622	2.34	0.235	0.798	0.79	III	complex2.pdb.gz	30,32,33,34,35,45,46,47,79,80,81
3	0.01	2f4mA	0.438	4.51	0.042	0.817	0.58	ZN	complex3.pdb.gz	31,34,45,47

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.