D-I-TASSER results for P11831-D1

Input Sequence in FASTA format

>P11831 (70 residues)
MLPTQAGAAAALGRGSALGGSLNRTPTGRPGGGGGTRGANGGRVPGNGAGLGPGRLEREA
AAAAATTPAP

Predicted Secondary Structure

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Sequence
MLPTQAGAAAALGRGSALGGSLNRTPTGRPGGGGGTRGANGGRVPGNGAGLGPGRLEREAAAAAATTPAP
Prediction
CCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCC
Confidence
9863134677623654226643568889989988755677763688887779623567888764168999

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60
                   |                   |                   |
Sequence
MLPTQAGAAAALGRGSALGGSLNRTPTGRPGGGGGTRGANGGRVPGNGAGLGPGRLEREAAAAAATTPAP
Prediction
7344544333334434434442553444444444344336434234534423344145524444454658

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	CCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCC
							Seq	MLPTQAGAAAALGRGSALGGSLNRTPTGRPGGGGGTRGANGGRVPGNGAGLGPGRLEREAAAAAATTPAP
1	5yedA	0.06	0.06	2.54	0.46	CEthreader		TSLSIQGIKYMIVENTEERKIGTNITGKGHVVICPIPIGGTGALITYVNPRAGPRDVLFNVQEYAKKLTD
2	3rx6A	0.05	0.04	2.04	0.58	EigenThreader		TALQ--QAFDTCQNNKA---AWLQR---KNELAAAELRNIIEVRKWQVNQAAGRYIRSHEAVQHISIRDR
3	6f1te	0.41	0.36	10.51	0.37	FFAS-3D		----QAGLRAWTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGLEESYSAVMG-----
4	3bogA	0.32	0.30	9.04	1.37	SPARKS-K		GVGCPGTAGAAGSVGGCDGGHGGNGGNGNPGCAGGVGGAGGASGGGRGGKGGSGTPK----GADGAPGAP
5	4dyeA	0.19	0.07	2.31	0.31	CNFpred		-------------------------------------------GPGLGVSVDEDKLRHYAGVNERDGDLT
6	3rv0A	0.09	0.09	3.27	1.00	DEthreader		--RERVVYDENLENLAFMHLSNERLFLDSGAVSYVRFPSANGMLSKEVNNLADCVEAYIGALVIDRFGT-
7	1escA	0.13	0.11	3.99	0.79	MapAlign		-KRLNDAMKKAAAANTACDGADRGI---GGLLEDSQLELLGTKIPWYAHPNDKGRDIQAKQVADKIE---
8	3boiA	0.30	0.30	9.09	0.85	MUSTER		AHGVNGCPGTAGAAGSVDGGHGGNGGNGNPGCAGGVGGAGGSGGTGVGGRGGKGGSGTPKGADGAPG-AP
9	6gmlV	0.36	0.20	5.96	0.69	HHsearch		------------------------------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-GGGP
10	1wj9A2	0.10	0.10	3.70	0.46	CEthreader		KRLKTPAEKVAWLERRLEEGGFRLLEGERGPWVQILQDTFLEAVLFEGRLEVVDPERALATLRRGVGPGK


(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	0.5646


(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	5na6A	0.56	3.72	0.103	0.971
2	4o9uB	0.55	3.74	0.029	0.986
3	5bp1A2	0.54	3.92	0.125	0.871
4	4tktA2	0.53	3.71	0.141	0.871
5	6kkiA	0.53	3.89	0.047	0.914
6	4m66A	0.53	3.31	0.045	0.886
7	3f2kA	0.53	3.72	0.060	0.900
8	4o9pD	0.52	3.50	0.094	0.900
9	4na1A2	0.51	3.66	0.092	0.871
10	4qyrA	0.51	3.62	0.097	0.829



(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:0043565	1.00	sequence-specific DNA binding
GO:0003700	0.71	transcription factor activity, sequence-specific DNA binding
GO:0046983	0.70	protein dimerization activity
GO:0003723	0.70	RNA binding
GO:0000981	0.70	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000976	0.70	transcription regulatory region sequence-specific DNA binding
GO:0070878	0.69	primary miRNA binding
GO:0042803	0.69	protein homodimerization activity
GO:0010736	0.69	serum response element binding
GO:0008134	0.69	transcription factor binding
GO:0001077	0.69	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0000983	0.69	transcription factor activity, RNA polymerase II core promoter sequence-specific
GO:0000978	0.69	RNA polymerase II core promoter proximal region sequence-specific 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:0051716	1.00	cellular response to stimulus
GO:0048523	1.00	negative regulation of cellular process
GO:0045893	1.00	positive regulation of transcription, DNA-templated
GO:0019725	1.00	cellular homeostasis
GO:0010033	1.00	response to organic substance
GO:0071704	0.78	organic substance metabolic process
GO:0044260	0.77	cellular macromolecule metabolic process
GO:0044238	0.77	primary metabolic process
GO:0032774	0.76	RNA biosynthetic process
GO:0006351	0.75	transcription, DNA-templated
GO:0044767	0.72	single-organism developmental process
GO:0048856	0.71	anatomical structure development
GO:0065009	0.70	regulation of molecular function
GO:0051239	0.70	regulation of multicellular organismal process
GO:0030154	0.70	cell differentiation
GO:0009892	0.70	negative regulation of metabolic process
GO:0009653	0.70	anatomical structure morphogenesis
GO:0006357	0.70	regulation of transcription from RNA polymerase II promoter
GO:1902895	0.69	positive regulation of pri-miRNA transcription from RNA polymerase II promoter
GO:1902894	0.69	negative regulation of pri-miRNA transcription from RNA polymerase II promoter
GO:1900222	0.69	negative regulation of beta-amyloid clearance
GO:0090398	0.69	cellular senescence
GO:0060261	0.69	positive regulation of transcription initiation from RNA polymerase II promoter
GO:0051091	0.69	positive regulation of sequence-specific DNA binding transcription factor activity
GO:0050793	0.69	regulation of developmental process
GO:0048646	0.69	anatomical structure formation involved in morphogenesis
GO:0048468	0.69	cell development
GO:0046716	0.69	muscle cell cellular homeostasis
GO:0045987	0.69	positive regulation of smooth muscle contraction
GO:0045597	0.69	positive regulation of cell differentiation
GO:0042789	0.69	mRNA transcription from RNA polymerase II promoter
GO:0034097	0.69	response to cytokine
GO:0010735	0.69	positive regulation of transcription via serum response element binding
GO:0009725	0.69	response to hormone
GO:0007507	0.69	heart development
GO:0003257	0.69	positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation
GO:0002042	0.69	cell migration involved in sprouting angiogenesis
GO:0001947	0.69	heart looping
GO:0001829	0.69	trophectodermal cell differentiation
GO:0032501	0.64	multicellular organismal process
GO:0044707	0.63	single-multicellular organism process
GO:0048878	0.62	chemical homeostasis
GO:0007611	0.62	learning or memory






(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	0.74	intracellular organelle part
GO:0044428	0.72	nuclear part
GO:0005737	0.69	cytoplasm






(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	2bfyB	0.516	3.62	0.061	0.900	2.7.11.1	31
2	0.060	2vx3A	0.500	3.66	0.061	0.886	2.7.12.1	NA
3	0.060	2ct8A	0.383	4.36	0.029	0.743	6.1.1.10	NA
4	0.060	3bziA	0.516	3.65	0.092	0.929	2.7.11.21	NA
5	0.060	1h2rL	0.502	4.15	0.059	0.929	1.12.2.1	8



(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	0.02	3fjwB	0.515	3.46	0.072	0.843	1.02	MAN	9,12,13,64,65
2	0.01	2q0bB	0.476	3.54	0.030	0.886	0.43	ABG	29,49,50,51



(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.