D-I-TASSER Q6P3W7-D1

D-I-TASSER results for Q6P3W7-D1

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

Input Sequence in FASTA format

>Q6P3W7 (123 residues)
MESMLNKLKSTVTKVTADVTSAVMGNPVTREFDVGRHIASGGNGLAWKIFNGTKKSTKQE
VAVFVFDKKLIDKYQKFEKDQIIDSLKRGVQQLTRLRHPRLLTVQHPLEESRDCLAFCTE
PVF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MESMLNKLKSTVTKVTADVTSAVMGNPVTREFDVGRHIASGGNGLAWKIFNGTKKSTKQEVAVFVFDKKLIDKYQKFEKDQIIDSLKRGVQQLTRLRHPRLLTVQHPLEESRDCLAFCTEPVF
Prediction	CHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCSSCCSSCCCCCCCSSSSSSSSSCCCCCSSSSSSSSSHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCSSSSSSSSSCCCCSSSSSSSSCC
Confidence	666999999999876320124578987565517701332368863279996488799987999999722212226213789999999999999855899863899977338987999998449
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MESMLNKLKSTVTKVTADVTSAVMGNPVTREFDVGRHIASGGNGLAWKIFNGTKKSTKQEVAVFVFDKKLIDKYQKFEKDQIIDSLKRGVQQLTRLRHPRLLTVQHPLEESRDCLAFCTEPVF
Prediction	755025404431442344347424455236505035422623432202024034374634000000225315636454254115303510530442513300412320433652000001337
	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                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCSSCCSSCCCCCCCSSSSSSSSSCCCCCSSSSSSSSSHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCSSSSSSSSSCCCCSSSSSSSSCC
MESMLNKLKSTVTKVTADVTSAVMGNPVTREFDVGRHIASGGNGLAWKIFNGTKKSTKQEVAVFVFDKKLIDKYQKFEKDQIIDSLKRGVQQLTRLRHPRLLTVQHPLEESRDCLAFCTEPVF

4qnyA

0.12

0.10

3.44

1.17

DEthreader

--------------TKSLAELAEVCRLD-DRYLLERIIGAG---SYGVVIRARDTKSNRLVAMKRVNK-EIF--E---EVILAKRILREIKLLAHFNDDNIIGLRNILTPNFDHFYIVMDIME

6ygnA2

0.14

0.12

4.16

1.62

SPARKS-K

DKTRAMNYDEEVDEVSMTKASHSSTKELYEKYMIAEDLGRGEF---GIVHRCVETSSKKTYMAKFVKV----------KGTDQVLVKKEISILNIARHRNILHLHESFES-MEELVMIFEF--

4yhjA

0.12

0.11

3.76

0.39

MapAlign

-TLKRHIEFLDAVAEFLQWKWLERQPVTKNTFRHYRVLGKG---GFGEVCACQVRATGKMYACKKLQKKRIKKR------KGEAMALNEKRILEKVQSRFVVSLAYAYET-KDALCLVLTIM-

1cdkA

0.16

0.15

4.87

0.23

CEthreader

QESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGS---FGRVMLVKHKETGNHFAMKILDKQKVVKL------KQIEHTLNEKRILQAVNFPFLVKLEYSFK-DNSNLYMVMEYVP

1cdkA

0.16

0.15

4.87

1.15

MUSTER

QESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGT---GSFGRVMLVKHKETGNHFAMKILDKQKVVKLK------QIEHTLNEKRILQAVNFPFLVKLEYSFKD-NSNLYMVMEYVP

3i7bA

0.24

0.17

5.32

0.65

HHsearch

--------------------------IFSDRYKGQRVLGKGS---FGEVILCKDKITGQECAVKVISKRQVK------QKTDKESLLREVQLLKQLDHPNIMKLYEFFE-DKGYFYLVGEVYT

5o0yA1

0.14

0.11

3.60

1.63

FFAS-3D

-------------------------PTLNDRYLLLHLLGRGGFS---EVYKAFDLTEQRYVAVKIHQLN--KNWRDEKKENYHKHACREYRIHKELDHPRIVKLYDYFSLDTDSFCTVLEYC-

4tnbA2

0.13

0.12

4.20

0.62

EigenThreader

FSACAQSVHEYLRDRFLQWKWLERQPVTKNTFRQYRVLGGG----FGEVCACQVRATGKMYACKRLEKKRIKKR---KG---ESMALNEKQILEKVNSQFVVNLAYAYET-KDALCLVLTIVY

3utoA

0.16

0.11

3.50

1.47

CNFpred

------------------------------HYDIHEELGTGA---FGVVHRVTERATGNNFAAKFVMTP---------HESDKETVRKEIQTMSVLRHPTLVNLHDAFEDD-NEMVMIYEFMS

4qnyA1

0.12

0.10

3.44

1.17

DEthreader

--------------TKSLAELAEVCRLD-DRYLLERIIGAG---SYGVVIRARDTKSNRLVAMKRVNK-EIF--E---EVILAKRILREIKLLAHFNDDNIIGLRNILTPNFDHFYIVMDIME

(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	0.7719

(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	1ql6A	0.70	1.82	0.135	0.780	model1_1ql6A.pdb.gz
2	4qnyA	0.70	1.82	0.122	0.797	model1_4qnyA.pdb.gz
3	2y7jA	0.70	2.14	0.129	0.789	model1_2y7jA.pdb.gz
4	5hnvA	0.69	2.23	0.170	0.805	model1_5hnvA.pdb.gz
5	2owbA	0.68	2.22	0.188	0.780	model1_2owbA.pdb.gz
6	5o0yA	0.67	1.78	0.140	0.756	model1_5o0yA.pdb.gz
7	3pg1A	0.67	2.93	0.162	0.854	model1_3pg1A.pdb.gz
8	3c0gB	0.66	1.87	0.165	0.740	model1_3c0gB.pdb.gz
9	5ig1A	0.66	1.32	0.187	0.707	model1_5ig1A.pdb.gz
10	3ll6A	0.66	2.25	0.128	0.764	model1_3ll6A.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:0005102	0.63	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:0009987	0.89	cellular process
GO:0071704	0.85	organic substance metabolic process
GO:0044237	0.85	cellular metabolic process
GO:0044260	0.83	cellular macromolecule metabolic process
GO:0065007	0.80	biological regulation
GO:0050789	0.80	regulation of biological process
GO:0050794	0.79	regulation of cellular process
GO:0044699	0.71	single-organism process
GO:0006810	0.69	transport
GO:0044763	0.66	single-organism cellular process
GO:0016192	0.65	vesicle-mediated transport
GO:0044710	0.63	single-organism metabolic process
GO:0048518	0.62	positive regulation of biological process
GO:0019222	0.62	regulation of metabolic process
GO:0060255	0.61	regulation of macromolecule metabolic process
GO:0048522	0.61	positive regulation of cellular process
GO:0031323	0.61	regulation of cellular metabolic process
GO:0048519	0.60	negative regulation of biological process
GO:0031325	0.60	positive regulation of cellular metabolic process
GO:0010604	0.60	positive regulation of macromolecule metabolic process
GO:0009966	0.60	regulation of signal transduction
GO:0051130	0.59	positive regulation of cellular component organization
GO:0048523	0.59	negative regulation of cellular process
GO:0046907	0.59	intracellular transport
GO:0031623	0.59	receptor internalization
GO:2000370	0.58	positive regulation of clathrin-mediated endocytosis
GO:2000286	0.58	receptor internalization involved in canonical Wnt signaling pathway
GO:0090090	0.58	negative regulation of canonical Wnt signaling pathway
GO:0008333	0.58	endosome to lysosome transport
GO:0002092	0.58	positive regulation of receptor internalization

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	0.99	intracellular part
GO:0044444	0.85	cytoplasmic part
GO:0043226	0.78	organelle
GO:0043229	0.77	intracellular organelle
GO:0005737	0.75	cytoplasm
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0016020	0.69	membrane
GO:0005829	0.66	cytosol
GO:0005634	0.58	nucleus
GO:0044422	0.55	organelle part
GO:0044446	0.50	intracellular organelle 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	1zrzA	0.638	1.51	0.253	0.707	2.7.11.13	54
2	0.060	2zoqA	0.634	2.30	0.141	0.756	2.7.11.24	119
3	0.060	3dlsA	0.642	2.65	0.143	0.780	2.7.11.1	NA
4	0.060	3db8A	0.676	2.14	0.168	0.772	2.7.11.21	83,85
5	0.060	1z57A	0.640	2.25	0.118	0.748	2.7.12.1	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	0.27	2yabA	0.648	2.07	0.223	0.732	0.77	AMP	complex1.pdb.gz	38,39,40,47,49,62,103,119,120,121,122
2	0.26	2yaaA	0.648	2.08	0.221	0.732	0.62	ATP	complex2.pdb.gz	38,41,42,48,50,61,63,120,122
3	0.24	2ckeA	0.649	2.57	0.206	0.748	0.61	IQU	complex3.pdb.gz	38,39,40,49,61,120,122
4	0.24	2owbA	0.682	2.22	0.188	0.780	0.64	626	complex4.pdb.gz	36,37,38,40,41,48,49,62,64,120
5	0.23	2yakA	0.650	2.26	0.198	0.740	0.66	OSV	complex5.pdb.gz	38,39,40,41,63,89,102,117,119,120,122

	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.