D-I-TASSER results for Q12891-D2

Input Sequence in FASTA format

>Q12891 (221 residues)
VNQNITIFYRDRLGLYPRFDSAGRSVHGGVPQNVSLWAHRKMLQKRVEHYIRTQESAGLA
VIDWEDWRPVWVRNWQDKDVYRRLSRQLVASRHPDWPPDRIVKQAQYEFEFAAQQFMLET
LRYVKAVRPRHLWGFYLFPDCYNHDYVQNWESYTGRCPDVEVARNDQLAWLWAESTALFP
SVYLDETLASSRHGRNFVSFRVQEALRVARTHHANHALPVY

Predicted Secondary Structure

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Sequence
VNQNITIFYRDRLGLYPRFDSAGRSVHGGVPQNVSLWAHRKMLQKRVEHYIRTQESAGLAVIDWEDWRPVWVRNWQDKDVYRRLSRQLVASRHPDWPPDRIVKQAQYEFEFAAQQFMLETLRYVKAVRPRHLWGFYLFPDCYNHDYVQNWESYTGRCPDVEVARNDQLAWLWAESTALFPSVYLDETLASSRHGRNFVSFRVQEALRVARTHHANHALPVY
Prediction
CCCCSSSSSCCCCCCCCSSCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCSSSSSCCCCCCHHHHCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCHHHHHHHCCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Confidence
99818998478898775056999742388688687999999999999986789999822899725876406761675089999999999997899999999999999999999999999999999959997034455886668885668888899899799987222133576424216245134001787679999999999999999622899999989

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220
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Sequence
VNQNITIFYRDRLGLYPRFDSAGRSVHGGVPQNVSLWAHRKMLQKRVEHYIRTQESAGLAVIDWEDWRPVWVRNWQDKDVYRRLSRQLVASRHPDWPPDRIVKQAQYEFEFAAQQFMLETLRYVKAVRPRHLWGFYLFPDCYNHDYVQNWESYTGRCPDVEVARNDQLAWLWAESTALFPSVYLDETLASSRHGRNFVSFRVQEALRVARTHHANHALPVY
Prediction
85540000036410200102776442100001423164015204720461043660400000202513220441264353025202510474247145730442035303520350034004103621450200000001010133554465243604641363045332116402010000103551553740231032002001100434677340104

Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

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                 120                 140                 160                 180                 200                 220                    |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |
							SS	CCCCSSSSSCCCCCCCCSSCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCSSSSSCCCCCCHHHHCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCHHHHHHHCCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
							Seq	VNQNITIFYRDRLGLYPRFDSAGRSVHGGVPQNVSLWAHRKMLQKRVEHYIRTQESAGLAVIDWEDWRPVWVRNWQDKDVYRRLSRQLVASRHPDWPPDRIVKQAQYEFEFAAQQFMLETLRYVKAVRPRHLWGFYLFPDCYNHDYVQNWESYTGRCPDVEVARNDQLAWLWAESTALFPSVYLDETLASSRHGRNFVSFRVQEALRVARTHHANHALPVY
1	2pe4A	0.47	0.46	13.45	1.50	DEthreader		RGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYGFPDCYNYDF-LS-PNYTGQCPSGIRAQNDQLGWLWGQSRALYPSIYMPAVLEGTGKSQMYVQHRVAEAFRVAVAAGD-PNLPVL
2	2pe4A	0.47	0.46	13.45	3.68	SPARKS-K		RGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYGFPDCYNYDF--LSPNYTGQCPSGIRAQNDQLGWLWGQSRALYPSIYMPAVLEGTGKSQMYVQHRVAEAFRVAVAAGD-PNLPVL
3	2pe4A	0.47	0.46	13.45	1.97	MapAlign		RGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYGFPDCYNYDFL--SPNYTGQCPSGIRAQNDQLGWLWGQSRALYPSIYMPAVLEGTGKSQMYVQHRVAEAFRVAVAAGD-PNLPVL
4	2pe4A	0.47	0.46	13.45	1.89	CEthreader		RGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYGFPDCYNYDFLSP--NYTGQCPSGIRAQNDQLGWLWGQSRALYPSIYMPAVLEGTGKSQMYVQHRVAEAFRVAVAAGD-PNLPVL
5	2pe4A	0.47	0.46	13.45	2.87	MUSTER		RGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYGFPDCYNYDFL--SPNYTGQCPSGIRAQNDQLGWLWGQSRALYPSIYMPAVLEGTGKSQMYVQHRVAEAFRVAVAAGD-PNLPVL
6	2pe4A	0.47	0.46	13.45	5.17	HHsearch		RGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYGFPDCYNYDFLS--PNYTGQCPSGIRAQNDQLGWLWGQSRALYPSIYMPAVLEGTGKSQMYVQHRVAEAFRVAVAAGD-PNLPVL
7	2pe4A	0.47	0.46	13.45	2.74	FFAS-3D		RGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYGFPDCYNYDFLS--PNYTGQCPSGIRAQNDQLGWLWGQSRALYPSIYMPAVLEGTGKSQMYVQHRVAEAFRVAVAAG-DPNLPVL
8	2pe4A	0.47	0.46	13.45	1.70	EigenThreader		RGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYGFPDCYNYDF--LSPNYTGQCPSGIRAQNDQLGWLWGQSRALYPSIYMPAVLEGTGKSQMYVQHRVAEAFRVAVAA-GDPNLPVL
9	2pe4A	0.47	0.46	13.45	2.41	CNFpred		RGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYGFPDCYNYDFLS--PNYTGQCPSGIRAQNDQLGWLWGQSRALYPSIYMPAVLEGTGKSQMYVQHRVAEAFRVAVAA-GDPNLPVL
10	1fcvA	0.33	0.32	9.64	1.50	DEthreader		RGEEIAILYD-PGMFPALLKDGNVVARNGVPQLGNLTKHLQVFRDHLINQIPDKSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVRREHPFWDDQRVEQEAKRRFEKYGQLFMEETLKAAKRMRPAANWGYYAYPYCYNLTP-QP---SA-QCEATTMQENDKMSWLFESEDVLLPSVYLRWNL-TSGERVGLVGGRVKEALRIARQMT-TSRKKVL


(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

Rank^a	Estimated TM-score^b
1	0.8672


(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.
1	2pe4A	0.97	0.79	0.468	0.986
2	1fcvA	0.92	1.57	0.347	0.964
3	2atmA	0.90	1.58	0.307	0.959
4	5gslA	0.62	4.45	0.068	0.860
5	1fa2A	0.60	5.11	0.065	0.928
6	1b1yA	0.60	5.12	0.083	0.928
7	4twbA1	0.41	3.45	0.077	0.529
8	2innA	0.39	5.67	0.047	0.629
9	2v7bA	0.31	5.31	0.043	0.489
10	2vk2A	0.31	5.96	0.043	0.543



(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:0003824	1.00	catalytic activity
GO:0015929	0.99	hexosaminidase activity
GO:0004415	0.98	hyalurononglucosaminidase activity
GO:0004872	0.87	receptor activity
GO:0001618	0.85	virus receptor activity
GO:0097367	0.64	carbohydrate derivative binding
GO:0005539	0.61	glycosaminoglycan binding
GO:0033906	0.60	hyaluronoglucuronidase activity
GO:0098772	0.59	molecular function regulator
GO:0030234	0.58	enzyme regulator activity
GO:0005540	0.58	hyaluronic acid binding
GO:0030294	0.57	receptor signaling protein tyrosine kinase inhibitor activity






(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:

Biological Process (BP)


GO term	Cscore^GO	Name
GO:0071704	0.95	organic substance metabolic process
GO:0043170	0.94	macromolecule metabolic process
GO:0009987	0.93	cellular process
GO:0030203	0.92	glycosaminoglycan metabolic process
GO:0009057	0.91	macromolecule catabolic process
GO:0006027	0.90	glycosaminoglycan catabolic process
GO:1903510	0.87	mucopolysaccharide metabolic process
GO:0051704	0.87	multi-organism process
GO:0065007	0.86	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0050794	0.85	regulation of cellular process
GO:0048518	0.84	positive regulation of biological process
GO:0032502	0.84	developmental process
GO:0030212	0.84	hyaluronan metabolic process
GO:0010033	0.84	response to organic substance
GO:0071493	0.83	cellular response to UV-B
GO:0071347	0.83	cellular response to interleukin-1
GO:0048856	0.83	anatomical structure development
GO:0048522	0.83	positive regulation of cellular process
GO:0030214	0.83	hyaluronan catabolic process
GO:0009615	0.83	response to virus
GO:0006950	0.83	response to stress
GO:0051216	0.82	cartilage development
GO:0048523	0.82	negative regulation of cellular process
GO:0051240	0.81	positive regulation of multicellular organismal process
GO:0051128	0.81	regulation of cellular component organization
GO:0009719	0.81	response to endogenous stimulus
GO:0071495	0.80	cellular response to endogenous stimulus
GO:0071363	0.80	cellular response to growth factor stimulus
GO:0030334	0.80	regulation of cell migration
GO:0030308	0.80	negative regulation of cell growth
GO:0000302	0.80	response to reactive oxygen species
GO:0044699	0.74	single-organism process
GO:0044763	0.68	single-organism cellular process
GO:0016043	0.63	cellular component organization
GO:0080090	0.59	regulation of primary metabolic process
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:0032501	0.59	multicellular organismal process
GO:0031323	0.59	regulation of cellular metabolic process
GO:0080134	0.58	regulation of response to stress
GO:0044344	0.58	cellular response to fibroblast growth factor stimulus
GO:0006810	0.58	transport
GO:0065008	0.57	regulation of biological quality
GO:0061025	0.57	membrane fusion
GO:0048584	0.57	positive regulation of response to stimulus
GO:0044765	0.57	single-organism transport
GO:0032268	0.57	regulation of cellular protein metabolic process
GO:0050878	0.56	regulation of body fluid levels
GO:0048585	0.56	negative regulation of response to stimulus
GO:0044707	0.56	single-multicellular organism process
GO:0043408	0.56	regulation of MAPK cascade
GO:0043086	0.56	negative regulation of catalytic activity
GO:0032755	0.56	positive regulation of interleukin-6 production
GO:0032269	0.56	negative regulation of cellular protein metabolic process
GO:0032101	0.56	regulation of response to external stimulus
GO:0031349	0.56	positive regulation of defense response
GO:0002376	0.56	immune system process
GO:2000778	0.55	positive regulation of interleukin-6 secretion
GO:2000484	0.55	positive regulation of interleukin-8 secretion
GO:0071560	0.55	cellular response to transforming growth factor beta stimulus
GO:0070295	0.55	renal water absorption
GO:0061099	0.55	negative regulation of protein tyrosine kinase activity
GO:0051898	0.55	negative regulation of protein kinase B signaling
GO:0050729	0.55	positive regulation of inflammatory response
GO:0046718	0.55	viral entry into host cell
GO:0043407	0.55	negative regulation of MAP kinase activity
GO:0042117	0.55	monocyte activation
GO:0035810	0.55	positive regulation of urine volume
GO:0019087	0.55	transformation of host cell by virus
GO:0019064	0.55	fusion of virus membrane with host plasma membrane
GO:0010764	0.55	negative regulation of fibroblast migration






(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:

Cellular Component (CC)


GO term	Cscore^GO	Name
GO:0044464	0.99	cell part
GO:0044424	0.97	intracellular part
GO:0044444	0.96	cytoplasmic part
GO:0043231	0.96	intracellular membrane-bounded organelle
GO:0031410	0.95	cytoplasmic vesicle
GO:0005764	0.90	lysosome
GO:0016020	0.75	membrane
GO:0044425	0.70	membrane part
GO:0031988	0.69	membrane-bounded vesicle
GO:0044459	0.68	plasma membrane part
GO:0016023	0.65	cytoplasmic, membrane-bounded vesicle
GO:0031224	0.64	intrinsic component of membrane
GO:0031226	0.62	intrinsic component of plasma membrane
GO:0005829	0.62	cytosol
GO:0098590	0.61	plasma membrane region
GO:0045121	0.61	membrane raft
GO:0048471	0.60	perinuclear region of cytoplasm
GO:0046658	0.60	anchored component of plasma membrane
GO:0030139	0.60	endocytic vesicle
GO:0016324	0.60	apical plasma membrane
GO:0005902	0.60	microvillus






(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:

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	0.131	2atmA	0.903	1.58	0.305	0.964	3.2.1.35	NA
2	0.060	1v03A	0.579	4.72	0.073	0.842	3.2.1.21	NA
3	0.060	3f4vA	0.568	4.70	0.074	0.828	3.2.1.21	NA
4	0.060	1b90A	0.593	5.00	0.057	0.914	3.2.1.2	NA
5	0.060	1oc5A	0.573	3.97	0.116	0.778	3.2.1.91	NA



(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	Predicted binding site residues
1	0.22	2pe4A	0.968	0.79	0.468	0.986	0.21	UUU	16,66,67,69
2	0.02	2xffA	0.603	5.13	0.088	0.928	0.16	QPS	16,18,29,31
3	0.01	1itcA	0.597	4.94	0.083	0.896	0.20	GLC	15,16,27
4	0.01	1qjwA	0.579	3.93	0.092	0.783	0.11	UUU	11,29,66
5	0.01	1b9zA	0.597	4.83	0.068	0.891	0.21	MAL	13,25,26,29,38
6	0.01	1q6eA	0.602	5.21	0.065	0.932	0.15	UUU	16,28,30
7	0.01	1j10A	0.594	4.92	0.057	0.905	0.23	UUU	47,48,50,62
8	0.01	1j0zC	0.593	4.93	0.057	0.905	0.13	GLC	15,29,65,114
9	0.01	1v3hA	0.604	5.08	0.060	0.923	0.11	GLC	14,18,134,135,138
10	0.01	1j0yA	0.599	4.87	0.063	0.896	0.16	BGC	14,29,112



(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.

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.