D-I-TASSER results for Q5W5X9-D3

Input Sequence in FASTA format

>Q5W5X9 (66 residues)
RHEHHDVAEQYFQESMAHLKDSEGMGRTKFLSIQDEFCHFLQMTGQKERATSILRESLEA
KVEAFG

Predicted Secondary Structure

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Sequence
RHEHHDVAEQYFQESMAHLKDSEGMGRTKFLSIQDEFCHFLQMTGQKERATSILRESLEAKVEAFG
Prediction
CCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Confidence
922778999999999999997049886215667999999999966289999999999998886259

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60
                   |                   |                   |
Sequence
RHEHHDVAEQYFQESMAHLKDSEGMGRTKFLSIQDEFCHFLQMTGQKERATSILRESLEAKVEAFG
Prediction
866345204421450153146464474342232334104103434655402411453054435638

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                    |                   |                   |
							SS	CCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
							Seq	RHEHHDVAEQYFQESMAHLKDSEGMGRTKFLSIQDEFCHFLQMTGQKERATSILRESLEAKVEAFG
1	2qfcA	0.08	0.08	3.02	1.50	DEthreader		-NGYLKKGIDLFEQILKQLEALHD-NEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINS
2	4y6cA3	0.16	0.15	5.03	1.38	SPARKS-K		----VQEAVELLEQVVAIQAKTLRSEHPSRLASQHELARAYQANGQRQEAQELLEQVRAIQAKTQR
3	4y6cA3	0.16	0.15	5.03	1.65	MUSTER		----VQEAVELLEQVVAIQAKTLRSEHPSRLASQHELARAYQANGQRQEAQELLEQVRAIQAKTQR
4	4y6cA3	0.16	0.15	5.03	1.40	FFAS-3D		----VQEAVELLEQVVAIQAKTLRSEHPSRLASQHELARAYQANGQRQEAQELLEQVRAIQAKTQR
5	3sf4A2	0.11	0.11	3.83	1.50	DEthreader		EEDALQAAVDFYEENLSLVTALGD--RAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGD
6	3ceqB3	0.15	0.14	4.61	1.27	SPARKS-K		----YKEAEPLCKRALEIREKVLGKFHPDVAKQLSNLALLCQNQGKAEEVEYYYRRALEIYATRL-
7	2ifuA	0.09	0.09	3.44	0.76	MapAlign		-AAQKISEAHEHIAKAEKYLKTWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRS
8	3n71A	0.08	0.08	3.05	0.44	CEthreader		YLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHG
9	3ceqB3	0.15	0.14	4.61	1.62	MUSTER		----YKEAEPLCKRALEIREKVLGKFHPDVAKQLSNLALLCQNQGKAEEVEYYYRRALEIYATRL-
10	5o09C	0.14	0.14	4.68	0.69	HHsearch		QLRKFERAEGYYCEALETFQRLDGEQSARVASVYNNLGVLYYSHMDVDRAQVMHERALAIRQNLHE


(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	0.8171


(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	3ceqB	0.89	1.59	0.121	0.985
2	5o09C	0.88	1.76	0.136	0.985
3	1ya0B	0.86	1.92	0.106	0.985
4	2qfcA	0.86	1.76	0.077	0.955
5	3zheB1	0.77	1.79	0.081	0.939
6	4ui9J	0.74	1.74	0.154	0.894
7	3cvnA2	0.74	1.54	0.069	0.833
8	3rkvA1	0.74	2.18	0.113	0.909
9	3pe3A1	0.73	1.91	0.086	0.818
10	3hymH2	0.73	1.95	0.125	0.879



(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	0.58	catalytic activity
GO:0008289	0.57	lipid binding
GO:0035091	0.54	phosphatidylinositol binding
GO:0097159	0.53	organic cyclic compound binding
GO:1901981	0.52	phosphatidylinositol phosphate binding
GO:0033218	0.52	amide binding
GO:0030246	0.52	carbohydrate binding
GO:0016758	0.52	transferase activity, transferring hexosyl groups
GO:0010485	0.52	H4 histone acetyltransferase activity
GO:0008194	0.52	UDP-glycosyltransferase activity
GO:1901363	0.50	heterocyclic compound binding






(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:0044699	0.86	single-organism process
GO:0009987	0.84	cellular process
GO:0044763	0.73	single-organism cellular process
GO:0032502	0.72	developmental process
GO:0044767	0.71	single-organism developmental process
GO:0071840	0.70	cellular component organization or biogenesis
GO:0051179	0.69	localization
GO:0016043	0.68	cellular component organization
GO:0050794	0.66	regulation of cellular process
GO:0008152	0.65	metabolic process
GO:0071704	0.62	organic substance metabolic process
GO:0044238	0.62	primary metabolic process
GO:0048856	0.61	anatomical structure development
GO:0006996	0.60	organelle organization
GO:0006810	0.60	transport
GO:0051641	0.59	cellular localization
GO:0044237	0.59	cellular metabolic process
GO:0044710	0.58	single-organism metabolic process
GO:0044260	0.58	cellular macromolecule metabolic process
GO:0080090	0.57	regulation of primary metabolic process
GO:0048513	0.57	animal organ development
GO:0043933	0.57	macromolecular complex subunit organization
GO:0019220	0.57	regulation of phosphate metabolic process
GO:0044281	0.56	small molecule metabolic process
GO:0006807	0.56	nitrogen compound metabolic process
GO:2000026	0.55	regulation of multicellular organismal development
GO:0050896	0.55	response to stimulus
GO:0048585	0.55	negative regulation of response to stimulus
GO:0048523	0.55	negative regulation of cellular process
GO:0031399	0.55	regulation of protein modification process
GO:0009966	0.55	regulation of signal transduction
GO:0006139	0.55	nucleobase-containing compound metabolic process
GO:0022607	0.54	cellular component assembly
GO:0051716	0.53	cellular response to stimulus
GO:0016310	0.53	phosphorylation
GO:0007165	0.53	signal transduction
GO:0006464	0.53	cellular protein modification process
GO:1900542	0.52	regulation of purine nucleotide metabolic process
GO:0051640	0.52	organelle localization
GO:0050790	0.52	regulation of catalytic activity
GO:0045595	0.52	regulation of cell differentiation
GO:0042327	0.52	positive regulation of phosphorylation
GO:0031401	0.52	positive regulation of protein modification process
GO:0006461	0.52	protein complex assembly
GO:0001932	0.52	regulation of protein phosphorylation
GO:1901575	0.51	organic substance catabolic process
GO:1901564	0.51	organonitrogen compound metabolic process
GO:0065008	0.51	regulation of biological quality
GO:0044723	0.51	single-organism carbohydrate metabolic process
GO:0044712	0.51	single-organism catabolic process
GO:0019752	0.51	carboxylic acid metabolic process
GO:2000379	0.50	positive regulation of reactive oxygen species metabolic process
GO:1903829	0.50	positive regulation of cellular protein localization
GO:1903578	0.50	regulation of ATP metabolic process
GO:1903426	0.50	regulation of reactive oxygen species biosynthetic process
GO:1903321	0.50	negative regulation of protein modification by small protein conjugation or removal
GO:1901071	0.50	glucosamine-containing compound metabolic process
GO:1900180	0.50	regulation of protein localization to nucleus
GO:1900076	0.50	regulation of cellular response to insulin stimulus
GO:1900037	0.50	regulation of cellular response to hypoxia
GO:0090317	0.50	negative regulation of intracellular protein transport
GO:0090313	0.50	regulation of protein targeting to membrane
GO:0071396	0.50	cellular response to lipid
GO:0071331	0.50	cellular response to hexose stimulus
GO:0071229	0.50	cellular response to acid chemical
GO:0071219	0.50	cellular response to molecule of bacterial origin
GO:0070206	0.50	protein trimerization
GO:0061085	0.50	regulation of histone H3-K27 methylation
GO:0051569	0.50	regulation of histone H3-K4 methylation
GO:0051291	0.50	protein heterooligomerization
GO:0051260	0.50	protein homooligomerization
GO:0051196	0.50	regulation of coenzyme metabolic process
GO:0051129	0.50	negative regulation of cellular component organization
GO:0048311	0.50	mitochondrion distribution
GO:0048017	0.50	inositol lipid-mediated signaling
GO:0046578	0.50	regulation of Ras protein signal transduction
GO:0045893	0.50	positive regulation of transcription, DNA-templated
GO:0044093	0.50	positive regulation of molecular function
GO:0043967	0.50	histone H4 acetylation
GO:0043470	0.50	regulation of carbohydrate catabolic process
GO:0043467	0.50	regulation of generation of precursor metabolites and energy
GO:0042326	0.50	negative regulation of phosphorylation
GO:0033135	0.50	regulation of peptidyl-serine phosphorylation
GO:0032526	0.50	response to retinoic acid
GO:0032496	0.50	response to lipopolysaccharide
GO:0031667	0.50	response to nutrient levels
GO:0031396	0.50	regulation of protein ubiquitination
GO:0031062	0.50	positive regulation of histone methylation
GO:0030852	0.50	regulation of granulocyte differentiation
GO:0030162	0.50	regulation of proteolysis
GO:0018023	0.50	peptidyl-lysine trimethylation
GO:0016601	0.50	Rac protein signal transduction
GO:0012501	0.50	programmed cell death
GO:0010941	0.50	regulation of cell death
GO:0010799	0.50	regulation of peptidyl-threonine phosphorylation
GO:0009749	0.50	response to glucose
GO:0009636	0.50	response to toxic substance
GO:0008361	0.50	regulation of cell size
GO:0008286	0.50	insulin receptor signaling pathway
GO:0007623	0.50	circadian rhythm
GO:0007420	0.50	brain development
GO:0006486	0.50	protein glycosylation
GO:0006357	0.50	regulation of transcription from RNA polymerase II promoter
GO:0006111	0.50	regulation of gluconeogenesis
GO:0006096	0.50	glycolytic process
GO:0002763	0.50	positive regulation of myeloid leukocyte differentiation
GO:0001678	0.50	cellular glucose homeostasis






(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	0.98	intracellular part
GO:0043226	0.85	organelle
GO:0005737	0.83	cytoplasm
GO:0044444	0.81	cytoplasmic part
GO:0044422	0.79	organelle part
GO:0043229	0.78	intracellular organelle
GO:0044446	0.77	intracellular organelle part
GO:0016020	0.73	membrane
GO:0043227	0.70	membrane-bounded organelle
GO:0032991	0.68	macromolecular complex
GO:0043234	0.67	protein complex
GO:0043231	0.66	intracellular membrane-bounded organelle
GO:0005829	0.62	cytosol
GO:0044430	0.54	cytoskeletal part






(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	0.067	3eabA	0.649	2.12	0.049	0.924	3.6.4.3	NA
2	0.067	1fyjA	0.565	2.40	0.056	0.727	6.1.1.15 6.1.1.17	NA
3	0.066	1r1bA	0.511	2.78	0.077	0.742	6.1.1.15 6.1.1.17	NA
4	0.060	1tqgA	0.801	1.89	0.030	1.000	2.7.13.3	NA
5	0.060	1r03A	0.668	2.06	0.061	0.924	1.16.3.1	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	0.09	3lw10	0.768	2.06	0.182	1.000	0.23	III	37,44,48,49,52,56
2	0.04	2j9q1	0.783	1.23	0.103	0.849	0.34	III	35,36,39,42,43,45,47,50,51,54,55
3	0.03	3m500	0.774	1.85	0.077	0.985	0.15	III	33,36,46,49,52,56
4	0.01	2xs1A	0.770	1.75	0.015	0.985	0.20	III	24,36,40,43
5	0.01	2j9q0	0.595	3.42	0.076	0.970	0.15	III	52,58,59,62,63



(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.