D-I-TASSER results for Q9BQA5-D5

Input Sequence in FASTA format

>Q9BQA5 (54 residues)
SEPRYKCHVCDKCFTRGNNLTVHLRKKHQFKWPSGHPRFRYKEHEDGYMRLQLV

Predicted Secondary Structure

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Sequence
SEPRYKCHVCDKCFTRGNNLTVHLRKKHQFKWPSGHPRFRYKEHEDGYMRLQLV
Prediction
CCCCSSSSCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCSSSSSCCCCSSSSSSC
Confidence
998636762787003334377999985387789998744776469962777629

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

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Sequence
SEPRYKCHVCDKCFTRGNNLTVHLRKKHQFKWPSGHPRFRYKEHEDGYMRLQLV
Prediction
864413022155326414403420354272642542530413547413131457

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                    |                   |
							SS	CCCCSSSSCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCSSSSSCCCCSSSSSSC
							Seq	SEPRYKCHVCDKCFTRGNNLTVHLRKKHQFKWPSGHPRFRYKEHEDGYMRLQLV
1	5d06A2	0.02	0.02	1.39	1.17	DEthreader		GHWAV------YVVMFALVVGIMYGCCRLRAMQMSDNVGSTVFVQSLAMTSIQM
2	6e93A2	0.21	0.20	6.48	3.24	SPARKS-K		-LKEFVCQYCNKAFTLNETLKIHERIHKRYHCQFCFQRFLYLSTKRNHEQRHIR
3	1vt4I3	0.06	0.06	2.44	0.61	MapAlign		GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG---
4	1tf6D1	0.20	0.20	6.50	0.36	CEthreader		VYKRYICSFCGAAYNKNWKLQAHLCKHKPFPCKECEKGFTSLHHLTRHSLTHTG
5	4gznC	0.20	0.20	6.50	2.91	MUSTER		SERPFFCNFCGKTYRDASGLSRHRRAHRPRSCPECGKCFRDQSEVNRHLKVHQN
6	1x6fA	0.17	0.17	5.48	1.02	HHsearch		QNSTYQCKHCDSKLQSTAELTSHLNIHNE-EFQKRAKRQERRKQLLSKQKYADG
7	1x6eA	0.25	0.24	7.48	0.94	FFAS-3D		GEKPYGCVECGKAFSRSSILVQHQRGEKPYKCLECGKAFSQNSGLINHQRIHT-
8	2rsiA	0.11	0.11	4.00	0.60	EigenThreader		TGEKFACDYCSFTCLSKGHLKVHIERVIKQHCRFCKKKYSDVKNLIKHIRDAHD
9	5yelA	0.24	0.24	7.50	2.77	CNFpred		IEQGKKCRYCDAVFHERYALIQHQKSHKRFKCDQCDYASRQERHMIMHKRTHTG
10	3e9pA	0.02	0.02	1.39	1.00	DEthreader		---DWASRLLLWPSFTDEQWITIESQMRDLILTYGKYVILTQTEIKDIILG---


(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	0.2109


(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	2wbtA	0.48	2.59	0.159	0.722
2	6e93A	0.48	2.12	0.186	0.593
3	6ar1A	0.48	2.98	0.081	0.648
4	1llmC	0.48	1.43	0.162	0.556
5	2kmkA	0.47	2.11	0.163	0.593
6	6ki6A	0.47	2.99	0.176	0.759
7	2i13A	0.47	2.15	0.279	0.593
8	6j0dA	0.47	3.03	0.136	0.722
9	2lt7A	0.47	2.22	0.243	0.611
10	2rsiA	0.47	3.04	0.286	0.685



(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:1901363	0.95	heterocyclic compound binding
GO:0097159	0.95	organic cyclic compound binding
GO:0003676	0.93	nucleic acid binding
GO:0003677	0.92	DNA binding
GO:0044212	0.91	transcription regulatory region DNA binding
GO:0003700	0.91	transcription factor activity, sequence-specific DNA binding
GO:0042393	0.80	histone binding
GO:0019899	0.80	enzyme binding
GO:0003713	0.80	transcription coactivator activity
GO:1990837	0.52	sequence-specific double-stranded DNA binding
GO:0000981	0.52	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000987	0.51	core promoter proximal region sequence-specific DNA binding
GO:0000982	0.51	transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific 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:0048869	1.00	cellular developmental process
GO:0045893	1.00	positive regulation of transcription, DNA-templated
GO:0044767	1.00	single-organism developmental process
GO:0033554	1.00	cellular response to stress
GO:0071704	0.93	organic substance metabolic process
GO:0044237	0.93	cellular metabolic process
GO:0044260	0.92	cellular macromolecule metabolic process
GO:0044238	0.92	primary metabolic process
GO:0006807	0.92	nitrogen compound metabolic process
GO:0090304	0.91	nucleic acid metabolic process
GO:0045892	0.89	negative regulation of transcription, DNA-templated
GO:0045445	0.89	myoblast differentiation
GO:0045184	0.89	establishment of protein localization
GO:0006281	0.89	DNA repair
GO:0001701	0.89	in utero embryonic development
GO:0000083	0.89	regulation of transcription involved in G1/S transition of mitotic cell cycle
GO:0000082	0.89	G1/S transition of mitotic cell cycle
GO:0000077	0.89	DNA damage checkpoint
GO:0006357	0.57	regulation of transcription from RNA polymerase II promoter
GO:0016070	0.56	RNA metabolic process
GO:1901576	0.54	organic substance biosynthetic process
GO:0044249	0.54	cellular biosynthetic process
GO:0034654	0.53	nucleobase-containing compound biosynthetic process
GO:0009059	0.53	macromolecule biosynthetic process
GO:0034645	0.52	cellular macromolecule biosynthetic process
GO:0032774	0.52	RNA biosynthetic process
GO:0006351	0.51	transcription, DNA-templated






(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:0005634	1.00	nucleus
GO:0044446	0.92	intracellular organelle part
GO:0044428	0.90	nuclear part
GO:0015030	0.89	Cajal body
GO:0005730	0.89	nucleolus
GO:0005654	0.89	nucleoplasm






(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	2oi2A	0.428	2.88	0.081	0.611	2.7.1.36	NA
2	0.060	1u8wD	0.439	3.16	0.023	0.759	2.7.4.6	NA
3	0.060	3fcvA	0.420	3.35	0.023	0.759	2.7.4.6	NA
4	0.060	3c7bE	0.427	2.75	0.081	0.630	1.8.99.3	NA
5	0.060	1r64A	0.444	3.24	0.020	0.833	3.4.21.61	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	0.10	1f2iG	0.440	1.28	0.286	0.518	0.68	QNA	3,14,16,19,22,23
2	0.04	1f2iG	0.440	1.28	0.286	0.518	0.69	ZN	5,13,19,23
3	0.03	1f2i0	0.440	1.28	0.286	0.518	0.51	III	4,5,8,9,15,16,20,21,24
4	0.02	1llmD	0.471	2.66	0.115	0.630	0.61	QNA	12,15,16,19,23



(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.