D-I-TASSER P51790-D3

D-I-TASSER results for P51790-D3

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

Input Sequence in FASTA format

>P51790 (92 residues)
AVLTQDNMTVDDIENMINETSYNGFPVIMSKESQRLVGFALRRDLTIAIESARKKQEGIV
GSSRVCFAQHTPSLPAESPRPLKLRSILDMSP

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| AVLTQDNMTVDDIENMINETSYNGFPVIMSKESQRLVGFALRRDLTIAIESARKKQEGIVGSSRVCFAQHTPSLPAESPRPLKLRSILDMSP
Prediction	CSSCCCCCSHHHHHHHHHHCCCCCSSSSSCCCCCSSSSSSSHHHHHHHHHHHHHCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCHHHCCCCC
Confidence	91346897099999999978965455886399996999986799999999986136899999658961788889889987334155236899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| AVLTQDNMTVDDIENMINETSYNGFPVIMSKESQRLVGFALRRDLTIAIESARKKQEGIVGSSRVCFAQHTPSLPAESPRPLKLRSILDMSP
Prediction	73344672316304510672614110003267343000103343033005504455771467230302643454477544414045234638
	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

                   |                   |                   |                   |

SS
Seq

CSSCCCCCSHHHHHHHHHHCCCCCSSSSSCCCCCSSSSSSSHHHHHHHHHHHHHCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCHHHCCCCC
AVLTQDNMTVDDIENMINETSYNGFPVIMSKESQRLVGFALRRDLTIAIESARKKQEGIVGSSRVCFAQHTPSLPAESPRPLKLRSILDMSP

2ja3C

0.60

0.59

16.83

1.17

DEthreader

TVLTQDSMTVEDVETIISETTYSGFPVVVSRESQRLVGFVLRRDLIISIENARKKQDGVVSTSIIYFT-EH-SPPLPTPPTLKLRNILDLPF

2ja3C

0.63

18.02

1.35

SPARKS-K

TVLTQDSMTVEDVETIISETTYSGFPVVVSRESQRLVGFVLRRDLIISIENARKKQDGVVSTSIIYFTEHSPPLPPYTPPTLKLRNILDLSP

2ja3C

0.63

0.62

17.72

1.16

MapAlign

TVLTQDSMTVEDVETIISETTYSGFPVVVSRESQRLVGFVLRRDLIISIENARKKQDGVVSTSIIYFTEHSPPLPPYTPPTLKLRNILDLS-

2ja3C

0.63

18.02

1.44

MUSTER

TVLTQDSMTVEDVETIISETTYSGFPVVVSRESQRLVGFVLRRDLIISIENARKKQDGVVSTSIIYFTEHSPPLPPYTPPTLKLRNILDLSP

2ja3C

0.44

0.43

12.72

1.20

EigenThreader

TVLTQDSMTVEDVETIISET-TYSGFPVVVSSQRLVGFVL-RRDLIISIENARKKQDGVVSTSIIYFTEHSPPLPPYTPPTLKLRNILSPFT

2j9lA

0.63

18.02

1.17

CNFpred

TVLTQDSMTVEDVETIISETTYSGFPVVVSRESQRLVGFVLRRDLIISIENARKKQDGVVSTSIIYFTEHSPPLPPYTPPTLKLRNILDLSP

2d4zB

0.16

0.13

4.35

1.00

DEthreader

VTSIASTSTYGDLLHVLRQTKLKFFPFVDTPDTNTLLGSIDRTEVEGLLQRRISAYRWEEKNVVV----------------NFETCRIDQSP

2qh1B1

0.16

0.15

5.04

1.06

SPARKS-K

KTVNW-NTTVFDAVKIMNENHLYGLVVKD--DNGNDVGLLSERSIIKRFIPRNKKPDEVPIRLVM---RKPIHLCPKCGVGVLEPVYNEKGE

6cozA

0.18

0.17

5.64

1.06

MUSTER

VKFVSASYTYGELRTLLQTTTVKTLPLVDSKDSMILLGSVERSELQALLQRHLCPERRMSPEEIEAWEQEQLSQPVCFDSCC-----IDQSP

7jm6A2

0.18

0.14

4.61

1.00

DEthreader

TCLRRI-ERVGTVVDILSDSNHNGFPVVESNPTVGLRGLILRSQLIVLLKHKV-R-VSDERECMIDLS----------------EFMNPSPY

(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	0.7539

(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	2ja3C	0.97	0.69	0.630	1.000	model1_2ja3C.pdb.gz
2	2d4zB	0.67	1.92	0.137	0.793	model1_2d4zB.pdb.gz
3	7jm6A	0.65	2.28	0.203	0.761	model1_7jm6A.pdb.gz
4	6cozA	0.64	2.09	0.176	0.804	model1_6cozA.pdb.gz
5	2pfiB	0.64	2.34	0.181	0.783	model1_2pfiB.pdb.gz
6	7cq5C	0.63	2.07	0.243	0.717	model1_7cq5C.pdb.gz
7	3lv9A	0.60	1.68	0.190	0.685	model1_3lv9A.pdb.gz
8	5tqqA	0.59	1.79	0.203	0.696	model1_5tqqA.pdb.gz
9	2v9jE1	0.59	3.09	0.130	0.826	model1_2v9jE1.pdb.gz
10	3kh5A	0.58	2.48	0.125	0.783	model1_3kh5A.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:0015075	0.94	ion transmembrane transporter activity
GO:0022838	0.93	substrate-specific channel activity
GO:0005216	0.92	ion channel activity
GO:0005254	0.91	chloride channel activity
GO:0022836	0.86	gated channel activity
GO:0005244	0.85	voltage-gated ion channel activity
GO:0008308	0.83	voltage-gated anion channel activity
GO:0005247	0.82	voltage-gated chloride channel activity
GO:0043167	0.57	ion binding
GO:0031404	0.54	chloride ion 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:0006810	0.95	transport
GO:0006811	0.94	ion transport
GO:0015698	0.90	inorganic anion transport
GO:0006821	0.89	chloride transport
GO:0055085	0.80	transmembrane transport
GO:0034220	0.79	ion transmembrane transport
GO:0098660	0.71	inorganic ion transmembrane transport
GO:1902476	0.70	chloride transmembrane transport
GO:0065007	0.63	biological regulation
GO:0065008	0.53	regulation of biological quality

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	0.95	intracellular part
GO:0044444	0.93	cytoplasmic part
GO:0043226	0.90	organelle
GO:0043231	0.89	intracellular membrane-bounded organelle
GO:0005768	0.88	endosome
GO:0044425	0.73	membrane part
GO:0016020	0.71	membrane
GO:0031224	0.64	intrinsic component of membrane
GO:0016021	0.63	integral component of membrane
GO:0044422	0.60	organelle part
GO:0031090	0.56	organelle membrane
GO:0044459	0.51	plasma membrane 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	0.060	1nx9A	0.474	4.25	0.074	0.880	3.1.1.43	22
2	0.060	3n0lA	0.466	4.08	0.056	0.815	2.1.2.1	NA
3	0.060	3l8cB	0.485	3.61	0.072	0.793	6.1.1.13	48
4	0.060	1ry2A	0.503	4.03	0.056	0.826	6.2.1.1	NA
5	0.060	2cu2A	0.513	3.28	0.065	0.772	2.7.7.13	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	0.20	2ja3C	0.970	0.69	0.630	1.000	0.60	ADP	complex1.pdb.gz	22,23,24,25,26
2	0.02	1yav0	0.542	2.74	0.155	0.750	0.43	III	complex2.pdb.gz	15,17,18,19,21,46,47,50,51,53,54
3	0.01	2rifC	0.533	2.29	0.061	0.717	0.61	AMP	complex3.pdb.gz	24,39,41,43,44,89,90,92

	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.