D-I-TASSER results for P01019-D2

Input Sequence in FASTA format

>P01019 (202 residues)
SPTAVFGTLASLYLGALDHTADRLQAILGVPWKDKNCTSRLDAHKVLSALQAVQGLLVAQ
GRADSQAQLLLSTVVGVFTAPGLHLKQPFVQGLALYTPVVLPRSLDFTELDVAAEKIDRF
MQAVTGWKTGCSLMGASVDSTLAFNTYVHFQGLVLQGSYDLQDLLAQAELPAILHTELNL
QKLSNDRIRVGEVLNSIFFELE

Predicted Secondary Structure

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Sequence
SPTAVFGTLASLYLGALDHTADRLQAILGVPWKDKNCTSRLDAHKVLSALQAVQGLLVAQGRADSQAQLLLSTVVGVFTAPGLHLKQPFVQGLALYTPVVLPRSLDFTELDVAAEKIDRFMQAVTGWKTGCSLMGASVDSTLAFNTYVHFQGLVLQGSYDLQDLLAQAELPAILHTELNLQKLSNDRIRVGEVLNSIFFELE
Prediction
CCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCSSSSSSSSSSSCCCCCCCHHHHHHHHHHHCHCCSSCCCCCCHHHHHHHHHHHHHHHHCCCCHHHCCCCCCCCSSSSSSCSSSCSSCCCCCCCHHHHHCCCCCCSSSCCSCCCCCCCCCCCHHHHHHHHHHHCCC
Confidence
9166999999999607853599999994999777654321026789999999999998633678986055553332210189882199999999996211211069999799999999999999768601206689987446442022333222678864244300455334421101112223796238899887775069

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200
                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |
Sequence
SPTAVFGTLASLYLGALDHTADRLQAILGVPWKDKNCTSRLDAHKVLSALQAVQGLLVAQGRADSQAQLLLSTVVGVFTAPGLHLKQPFVQGLALYTPVVLPRSLDFTELDVAAEKIDRFMQAVTGWKTGCSLMGASVDSTLAFNTYVHFQGLVLQGSYDLQDLLAQAELPAILHTELNLQKLSNDRIRVGEVLNSIFFELE
Prediction
4241011011102112445025203611514464553444443441252044025214545456743412011101011377061265015204611453304414164275026302510474074305520671345020000000202031555245354124544123222443504414375030141013232528

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                    |                   |                   |                   |                   |                   |                   |                   |                   |                   |
							SS	CCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCSSSSSSSSSSSCCCCCCCHHHHHHHHHHHCHCCSSCCCCCCHHHHHHHHHHHHHHHHCCCCHHHCCCCCCCCSSSSSSCSSSCSSCCCCCCCHHHHHCCCCCCSSSCCSCCCCCCCCCCCHHHHHHHHHHHCCC
							Seq	SPTAVFGTLASLYLGALDHTADRLQAILGVPWKDKNCTSRLDAHKVLSALQAVQGLLVAQGRADSQAQLLLSTVVGVFTAPGLHLKQPFVQGLALYTPVVLPRSLDFTELDVAAEKIDRFMQAVTGWKTGCSLMGASVDSTLAFNTYVHFQGLVLQGSYDLQDLLAQAELPAILHTELNLQKLSNDRIRVGEVLNSIFFELE
1	6ssvA	0.14	0.13	4.57	1.33	DEthreader		CPLGILFTLGILLGGAQGKTGHQIGKAIRLKSTSNPFGAQEEMKSLYKELNDSLGS-EK--TF----EKVVRISTGLFVQRTHEIETSFNESIKNDF-KGELIPVNFLNRTSATLSINRWVDQQSNGLLEKFFMDDIPDTGMILVNVFYFRDFTLKNTLDLVQTLKSMGIVDLFNPAANLSGITHHQLYVDKFMQTNILEAT
2	6ssvA1	0.13	0.12	4.15	2.36	SPARKS-K		CPLGILFTLGILLGSAQGKTGHQIGKAIRLKSTSSSWNPFGAQEEMKSLYKELNDSLGSE-KTFDKEEKVVRISTGLFVQRTHEIETSFNESIKNDFK-GELIPVNFLNRTSATLSINRWVDQQSNGLLEKFMDDIPDDTGMILVNVFYFR----KNTLDLVQTLKSMGIVDLFNPAANLSGITHDQLYVDKFMQTN-----
3	4au2A	0.18	0.17	5.46	0.97	MapAlign		SPVVVASSLGLVSLGGKATTASQAKAVLSA-E-------QLRDEEVHAGLGELLRSLS---------NVTWKLGSRLYGPSSVSFAEDFVRSSKQHY-NCEHSKINFRDKRSALQSINEWAAQTTDGKLPEVTKDVERTDGALLVNAMFFKKGVVEVTHDLQKHLAGLGLTEAIDKKADLSRMSGKKLYLASVFHATAFEWD
4	4au2A	0.18	0.17	5.46	0.59	CEthreader		SPVVVASSLGLVSLGGKATTASQAKAVLSAEQ--------LRDEEVHAGLGELLRSLS---------NVTWKLGSRLYGPSSVSFAEDFVRSSKQHY-NCEHSKINFRDKRSALQSINEWAAQTTDGKLPEVTKDVERTDGALLVNAMFFKPHVVEVTHDLQKHLAGLGLTEAIDKKADLSRMSGKKLYLASVFHATAFEWD
5	2zv6B1	0.21	0.19	5.97	2.01	MUSTER		SPISITSALGMVLLGAKDNTAQQIKKVLHFDQV-------------HHQFQKLLTEFNK-----STDAYELKIANKLFGEKTYLFLQEYLDAIKKFYQTS-VESVDFAAPEESRKKINSWVESQTNEKIKNLIPNIGSNTTLVLVNAIYFKGK-VEESYDLKDTLRTMGMVDIFNGDADLSGMTGRGLVLSGVLHKAFVE--
6	4if8A1	0.19	0.17	5.59	1.59	HHsearch		SPLSISTAFSMLCLGAQDSTLDEIKQGFNFRKMPE--------KDLHEGFHYIIHELTQ-----KTQDLKLSIGNTLFIDQRLQPQRKFLEDAKNFYS-AETILTNFQNLEMAQKQINDFISQKTHGKINNLIENIDPGTVMLLANYIFFRH--MTGTFDLKKTLSYIGVSKIFEEHGDLTKIAPHSLKVGEAVHKAELK--
7	2zv6B1	0.18	0.16	5.17	2.35	FFAS-3D		SPISITSALGMVLLGAKDNTAQQIKKVLHFDQV----------------HHQFQKLLTEFNKSTDAYE--LKIANKLFGEKTYLFLQEYLDAIKKFYQTSVESVDFANAPEESRKKINSWVESQTNEKIKNLIPEIGSNTTLVLVNAIYFKGKVEESYDLKDTL-RTMGMVDIFNGDADLSGMTGSGLVLSGVLHKAFVE--
8	5inwA	0.22	0.19	6.10	1.30	EigenThreader		SPLSIASALGVVTAGANGSTRAELDTALGFK-----------SMKYFARLNGALY-----------KGFELMGKNVVFSKKGLWLYRQFTRTVAHLFK-SNVRSVDFGDSKNAVELMNAYIEKVTSKKFPDVISDVDTDTSLVIVNVIYFKGSWISVSYDLKAYLSAMGMSSMFSYGADLSRITGQKLHVDKITHKSVLHVN
9	5m3yA	0.98	0.95	26.63	1.73	CNFpred		SPTAVFGTLASLYLGALDHTADRLQAILGVPWKDKQCTSRLDAHKVLSALQAVQGLLVAQ-------QLLLSTVVGVFTAPGLHLKQPFVQGLALYTPVVLPRSLDFTELDVAAEKIDRFMQAVTGWKTGSSLMGASVDSTLAFNTYVHFQGKVLQGSYDLQDLLAQAELPAILHTELNLQKLSNDRIRVGEVLNSIFFELE
10	1ovaD	0.16	0.15	5.11	1.33	DEthreader		CPIAIMSALAMVYLGAKDSTRTQINKVVRFDKLFGDSIEAQCSVNVHSSLRDILNQITK-NDV-----YSFSLASRLYAEERYPILPEYLQCVKELY-RGGLEPINFQAADQARELINSWVESQTNGIIRNVLQSVDSQTAMVLVNAIVFKGMKMEEKYNLTSVLMAMGITDVFSSSANLSGISSAELKISQAVHAAHAEIN


(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	0.8594


(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	6ssvA	0.88	2.05	0.137	0.975
2	2ol2A	0.88	1.72	0.211	0.941
3	1ophA	0.87	1.95	0.221	0.941
4	1yxaA	0.87	1.85	0.163	0.941
5	5ncsA	0.87	1.55	0.160	0.926
6	5hgcA	0.86	2.06	0.163	0.941
7	3f1sA	0.86	1.98	0.195	0.941
8	4if8A	0.86	1.76	0.202	0.931
9	3fgqA	0.86	1.77	0.191	0.931
10	1ovaD	0.86	2.23	0.164	0.951



(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:0004867	1.00	serine-type endopeptidase 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:0065007	0.95	biological regulation
GO:0050789	0.94	regulation of biological process
GO:0080090	0.93	regulation of primary metabolic process
GO:0060255	0.93	regulation of macromolecule metabolic process
GO:0050794	0.93	regulation of cellular process
GO:0048519	0.93	negative regulation of biological process
GO:0048523	0.92	negative regulation of cellular process
GO:0031323	0.91	regulation of cellular metabolic process
GO:0044699	0.90	single-organism process
GO:0050896	0.88	response to stimulus
GO:0050790	0.88	regulation of catalytic activity
GO:0032501	0.88	multicellular organismal process
GO:0065008	0.87	regulation of biological quality
GO:0048583	0.87	regulation of response to stimulus
GO:0044763	0.87	single-organism cellular process
GO:0032502	0.85	developmental process
GO:0051239	0.84	regulation of multicellular organismal process
GO:0048522	0.84	positive regulation of cellular process
GO:0044767	0.84	single-organism developmental process
GO:0023051	0.84	regulation of signaling
GO:0010646	0.84	regulation of cell communication
GO:0010468	0.84	regulation of gene expression
GO:0003008	0.84	system process
GO:2000026	0.83	regulation of multicellular organismal development
GO:0051240	0.83	positive regulation of multicellular organismal process
GO:0051130	0.83	positive regulation of cellular component organization
GO:0051049	0.83	regulation of transport
GO:0050880	0.83	regulation of blood vessel size
GO:0048584	0.83	positive regulation of response to stimulus
GO:0045893	0.83	positive regulation of transcription, DNA-templated
GO:0043085	0.83	positive regulation of catalytic activity
GO:0042981	0.83	regulation of apoptotic process
GO:0042127	0.83	regulation of cell proliferation
GO:0030335	0.83	positive regulation of cell migration
GO:0022603	0.83	regulation of anatomical structure morphogenesis
GO:0008217	0.83	regulation of blood pressure
GO:0008152	0.83	metabolic process
GO:0007165	0.83	signal transduction
GO:0003071	0.83	renal system process involved in regulation of systemic arterial blood pressure
GO:1903053	0.82	regulation of extracellular matrix organization
GO:0051046	0.82	regulation of secretion
GO:0043065	0.82	positive regulation of apoptotic process
GO:0040008	0.82	regulation of growth
GO:0008016	0.82	regulation of heart contraction
GO:0007186	0.82	G-protein coupled receptor signaling pathway
GO:0002018	0.82	renin-angiotensin regulation of aldosterone production
GO:0051246	0.74	regulation of protein metabolic process
GO:0032268	0.72	regulation of cellular protein metabolic process
GO:0048585	0.64	negative regulation of response to stimulus
GO:0044707	0.64	single-multicellular organism process
GO:0016043	0.64	cellular component organization
GO:0051094	0.62	positive regulation of developmental process
GO:0044238	0.62	primary metabolic process
GO:0044237	0.62	cellular metabolic process
GO:0043170	0.62	macromolecule metabolic process
GO:0009968	0.62	negative regulation of signal transduction
GO:0008284	0.62	positive regulation of cell proliferation
GO:2000379	0.61	positive regulation of reactive oxygen species metabolic process
GO:1902531	0.61	regulation of intracellular signal transduction
GO:0048146	0.61	positive regulation of fibroblast proliferation
GO:0038166	0.61	angiotensin-activated signaling pathway
GO:0035813	0.61	regulation of renal sodium excretion
GO:0035556	0.61	intracellular signal transduction
GO:0019538	0.61	protein metabolic process
GO:0014873	0.61	response to muscle activity involved in regulation of muscle adaptation
GO:0010959	0.61	regulation of metal ion transport
GO:0010613	0.61	positive regulation of cardiac muscle hypertrophy
GO:0001558	0.61	regulation of cell growth
GO:2001238	0.60	positive regulation of extrinsic apoptotic signaling pathway
GO:1903779	0.60	regulation of cardiac conduction
GO:1903598	0.60	positive regulation of gap junction assembly
GO:1901201	0.60	regulation of extracellular matrix assembly
GO:0090190	0.60	positive regulation of branching involved in ureteric bud morphogenesis
GO:0080134	0.60	regulation of response to stress
GO:0061098	0.60	positive regulation of protein tyrosine kinase activity
GO:0051387	0.60	negative regulation of neurotrophin TRK receptor signaling pathway
GO:0045742	0.60	positive regulation of epidermal growth factor receptor signaling pathway
GO:0014068	0.60	positive regulation of phosphatidylinositol 3-kinase signaling
GO:0010873	0.60	positive regulation of cholesterol esterification
GO:0010595	0.60	positive regulation of endothelial cell migration
GO:0010535	0.60	positive regulation of activation of JAK2 kinase activity
GO:0048856	0.59	anatomical structure development
GO:0032101	0.59	regulation of response to external stimulus
GO:0031347	0.59	regulation of defense response
GO:0050727	0.58	regulation of inflammatory response
GO:0048513	0.58	animal organ development
GO:0010817	0.58	regulation of hormone levels
GO:0001819	0.58	positive regulation of cytokine production
GO:0042445	0.57	hormone metabolic process
GO:0002019	0.57	regulation of renal output by angiotensin
GO:0001822	0.57	kidney development
GO:0010605	0.55	negative regulation of macromolecule metabolic process
GO:0006950	0.54	response to stress
GO:0022414	0.53	reproductive process
GO:0044092	0.51	negative regulation of molecular function
GO:0009628	0.51	response to abiotic stimulus
GO:1903532	0.50	positive regulation of secretion by cell
GO:0045777	0.50	positive regulation of blood pressure
GO:0042756	0.50	drinking behavior
GO:0042310	0.50	vasoconstriction
GO:0006939	0.50	smooth muscle contraction






(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:0005615	1.00	extracellular space






(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	0.060	1gowA	0.436	4.38	0.051	0.639	3.2.1.23	NA
2	0.060	3gmzA	0.439	5.31	0.076	0.728	3.5.3.1	118,120,126
3	0.060	2z1aA	0.441	5.47	0.090	0.743	3.1.3.5	NA
4	0.060	2cerA	0.433	5.07	0.027	0.683	3.2.1.23	NA
5	0.060	3f4vA	0.438	5.39	0.090	0.733	3.2.1.21	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	0.04	3evjI	0.835	2.18	0.151	0.921	0.92	UUU	14,86,92,181,182,184,185
2	0.04	1jrrA	0.780	2.37	0.196	0.911	0.49	III	1,4,5,8,128,129,132,150,151,178,180,183,187,188,189,190,191,192,193,194,195,196,197,198,199
3	0.04	1lk6I	0.801	2.56	0.157	0.946	0.43	III	121,129,133,145,146,147,148,149,150,151,152



(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.