D-I-TASSER results for P43246-D2

Input Sequence in FASTA format

>P43246 (160 residues)
NNDMSASIGVVGVKMSAVDGQRQVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPK
ECVLPGGETAGDMGKLRQIIQRGGILITERKKADFSTKDIYQDLNRLLKGKKGEQMNSAV
LPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFS

Predicted Secondary Structure

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Sequence
NNDMSASIGVVGVKMSAVDGQRQVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKECVLPGGETAGDMGKLRQIIQRGGILITERKKADFSTKDIYQDLNRLLKGKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFS
Prediction
CCCCCCCSSSSSSSSSSCCCCSSSSSSSSSCCCCSSSSSSSSCCHHHHHHHHHHHHCCCSSSSSSCCCCCHHHHHHHHHHHHCCCSSSSCCHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHCCCSSSSSCCCC
Confidence
9520234079999998449952899999978888799999715633556778775218818999479888689999999972595355246332772219999998604644443330004422517999999999999998156544375269971699

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

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Sequence
NNDMSASIGVVGVKMSAVDGQRQVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKECVLPGGETAGDMGKLRQIIQRGGILITERKKADFSTKDIYQDLNRLLKGKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFS
Prediction
8643441000000213367642100000001343302012043364104020001114042010237644541430240065451333324554044541352034114466356433520453626101200100031052143643354132452528

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                    |                   |                   |                   |                   |                   |                   |                   |
							SS	CCCCCCCSSSSSSSSSSCCCCSSSSSSSSSCCCCSSSSSSSSCCHHHHHHHHHHHHCCCSSSSSSCCCCCHHHHHHHHHHHHCCCSSSSCCHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHCCCSSSSSCCCC
							Seq	NNDMSASIGVVGVKMSAVDGQRQVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKECVLPGGETAGDMGKLRQIIQRGGILITERKKADFSTKDIYQDLNRLLKGKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFS
1	2o8cB1	0.17	0.17	5.54	1.33	DEthreader		PSENY-SKYLLSLKEKEEDSTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLS-CSLQEGLIPGFWDASKTLRTLLEEYFREKLSVMLPQVLKGMGSELALSALGGCVFYLKKCLIDQELSMANFEEYIPL
2	5x9wA3	0.13	0.11	3.90	1.91	SPARKS-K		LLEDKETNRIVAVSPD----KKYIGLAWASLQSGEFKTKLTTADK----LNDELARLQAAEILLPDSKNAPQLQ--------TASGVTRLNAWQFAADAGEKLLTEYFGCQDLRGFG---LDSKEHAVSIGAAGALLNYIRLTQNLMPQHLDGLSLE---
3	2o8cB	0.19	0.17	5.66	1.29	MapAlign		------SKYLLSLKEKEDSSHRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKG---NLSKETKTILSLSCSLQEGLIPGFWDASKTLRTLLEYFKLSDGIVMLPQVLKGMKSELALSALGGCVFYLKKCLIDELLSMANFEEYIP-
4	3thwB	0.14	0.13	4.48	1.05	CEthreader		IMTDTSTSYLLCISENKEKGNIFIGIVGVQPATGEVVFDSFQDSASRSELETRMSSLQPVELLLPSALSEQTEALIHRATSVDRIRVERMDNIYFEYSHAFQAVTEFYAKGIVN----------LEKPVICSLAAIIKYLKEFNEKMLSKPENFKQLSSK
5	2o8fA	0.95	0.93	26.12	1.51	MUSTER		DILFGNNIGVVGVKMSAVDQ-RQVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKECVLPGGETAGDMGKLRQIIQRGGILITERKKADFSTKDIYQDLNR--KGKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFS
6	3thwB1	0.15	0.14	4.64	2.79	HHsearch		IMTDTSTSYLLCISENKEKGNIFIGIVGVQPATGEVVFDSFQDSASRSELETRMSSLQPVELLLPSALSEQTEALIHRAVQDDRIRVERMDNIYFEYSHAFQAVTEFYAKGI---------V-NLEKPVICSLAAIIKYLKEFNLEKLSKPENFKQLS--
7	5x9wA3	0.13	0.11	3.88	1.61	FFAS-3D		--EDKETNRIVAVSP----DKKYIGLAWASLQSGEFKTKLTTADK----LNDELARLQAAEILLPDSKNAPQL--------QTASGVTRLNAWQFAADAGEKLLTEYFGCQDLRGFG---LDSKEHAVSIGAAGALLNYIRLTQNLMPQHLDGLS-----
8	2o8fA	0.77	0.71	19.98	1.32	EigenThreader		DILFGNNIGVVGVKMS-AVDQRQVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKECVLPGGETAGDMGKLRQIIQRGGILITERKK--ADFSTKDIYQDLNRKGKKGEQMNSAVLPEMENQVAVSSLSAVIKFL----ELLSDDSN-------F
9	2o8bA	1.00	0.95	26.60	1.19	CNFpred		NN-----IGVVGVKMSAVDGQRQVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKECVLPGGETAGDMGKLRQIIQRGGILITERKKADFSTKDIYQDLNR---GKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFS
10	2o8cB	0.17	0.17	5.54	1.33	DEthreader		PSENY-SKYLLSLKEKEEDSTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLS-CSLQEGLIPGFWDASKTLRTLLEEYFREKLSVMLPQVLKGMGSELALSALGGCVFYLKKCLIDQELSMANFEEYIPL


(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	0.874


(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	2o8cB	0.85	2.33	0.164	0.994
2	3thwB	0.79	2.43	0.133	0.938
3	1e3mA	0.77	2.09	0.122	0.869
4	2o8fA2	0.76	2.68	0.804	0.912
5	1nneA	0.67	1.82	0.117	0.750
6	1iy8A	0.40	4.34	0.073	0.644
7	1nktA1	0.38	4.94	0.054	0.644
8	1zl0A1	0.37	4.96	0.058	0.637
9	1qi6A1	0.35	4.75	0.104	0.569
10	3ljxA	0.34	5.01	0.048	0.588



(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:0032137	1.00	guanine/thymine mispair binding
GO:0003684	0.93	damaged DNA binding
GO:0032138	0.92	single base insertion or deletion binding
GO:0000406	0.92	double-strand/single-strand DNA junction binding
GO:0000404	0.92	heteroduplex DNA loop binding
GO:0000403	0.92	Y-form DNA binding
GO:0000400	0.92	four-way junction DNA 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:0043570	1.00	maintenance of DNA repeat elements
GO:0006298	1.00	mismatch repair
GO:0065007	0.95	biological regulation
GO:0050794	0.94	regulation of cellular process
GO:1903046	0.93	meiotic cell cycle process
GO:0051052	0.93	regulation of DNA metabolic process
GO:0045786	0.93	negative regulation of cell cycle
GO:0031324	0.93	negative regulation of cellular metabolic process
GO:0010605	0.93	negative regulation of macromolecule metabolic process
GO:0045128	0.92	negative regulation of reciprocal meiotic recombination
GO:0006311	0.92	meiotic gene conversion
GO:0006301	0.92	postreplication repair
GO:0000710	0.92	meiotic mismatch repair
GO:0007131	0.91	reciprocal meiotic recombination
GO:0044699	0.60	single-organism process
GO:1903047	0.58	mitotic cell cycle process
GO:0007346	0.58	regulation of mitotic cell cycle
GO:0007165	0.58	signal transduction
GO:0000075	0.58	cell cycle checkpoint
GO:0044773	0.57	mitotic DNA damage checkpoint
GO:0042771	0.57	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:0009411	0.57	response to UV
GO:0006302	0.57	double-strand break repair
GO:0031573	0.56	intra-S DNA damage checkpoint
GO:0010224	0.56	response to UV-B
GO:0010165	0.56	response to X-ray
GO:0044763	0.54	single-organism cellular process
GO:0044710	0.52	single-organism metabolic process






(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:0032301	1.00	MutSalpha complex
GO:0032302	0.96	MutSbeta complex
GO:0043229	0.95	intracellular organelle
GO:0043232	0.93	intracellular non-membrane-bounded organelle
GO:0000228	0.92	nuclear chromosome






(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	1hjrC	0.639	2.52	0.127	0.769	3.1.22.4	16,77,89
2	0.060	2a1sC	0.560	4.24	0.058	0.819	3.1.13.4	NA
3	0.060	1q18A	0.542	3.46	0.057	0.750	2.7.1.2	94
4	0.060	1u6zB	0.539	3.71	0.056	0.744	3.6.1.11	87,142
5	0.060	3ifrA	0.543	4.32	0.058	0.825	2.7.1.17	28



(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	0.03	1e3mB	0.793	1.97	0.113	0.881	0.70	QNA	12,14,27,38
2	0.03	1oh8B	0.791	2.00	0.113	0.881	0.57	QNA	12,14,27
3	0.02	1kcf0	0.638	3.55	0.080	0.831	0.50	III	47,48,51,74,75,77,78,79,81,82



(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.