D-I-TASSER P36888-D4

D-I-TASSER results for P36888-D4

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>P36888 (113 residues)
NKALEEGNYFEMSTYSTNRTMIRILFAFVSSVARNDTGYYTCSSSKHPSQSALVTIVEKG
FINATNSSEDYEIDQYEEFCFSVRFKAYPQIRCTWTFSRKSFPCEQKGLDNGY

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| NKALEEGNYFEMSTYSTNRTMIRILFAFVSSVARNDTGYYTCSSSKHPSQSALVTIVEKGFINATNSSEDYEIDQYEEFCFSVRFKAYPQIRCTWTFSRKSFPCEQKGLDNGY
Prediction	CCCCCCCCSSSSSSSSCCHHHHHHHHHHHHHHCCCCCCSSSSSSCCCCCCCSSSSSSCCCCSCCCCCCCSSSSCCCCSSSSSSSSSSCCCSSSSSSSCCCSSCCCCCCCCCCC
Confidence	94213365155335425456766666543332125782599861378983089999615521156775138816995079999975258748999963723204544566899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| NKALEEGNYFEMSTYSTNRTMIRILFAFVSSVARNDTGYYTCSSSKHPSQSALVTIVEKGFINATNSSEDYEIDQYEEFCFSVRFKAYPQIRCTWTFSRKSFPCEQKGLDNGY
Prediction	85535644415344254433203323231331445442312132573443311130345222414545551414654512131415424404031234644141545437758
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCSSSSSSSSCCHHHHHHHHHHHHHHCCCCCCSSSSSSCCCCCCCSSSSSSCCCCSCCCCCCCSSSSCCCCSSSSSSSSSSCCCSSSSSSSCCCSSCCCCCCCCCCC
NKALEEGNYFEMSTYSTNRTMIRILFAFVSSVARNDTGYYTCSSSKHPSQSALVTIVEKGFINATNSSEDYEIDQYEEFCFSVRFKAYPQIRCTWTFSRKSFPCEQKGLDNGY

1rhfA

0.16

0.15

5.02

1.24

FFAS-3D

GAVVQNLDQLYIPVSEQ----HWIGFLSLKSVERSDAGRYWCQVEDGGETEIPVWLTVEGVPFFTVEPKDLAVPPNAPFQLSCEAVGPPEPTIVWWRGTTKIGGPAPSPTQS-

5uv6A

0.12

4.10

1.06

SPARKS-K

LCLAIGRPEPTVTWRHLSGFVSEDEYLEISDIKRDQSGEYECSALNAAPDVRKVKITVNYPPYISKAKN-TGVSVGQKGILSCEASAVPMAEFQWFKEETRLATGLDGMRIEN

3qs7E

1.00

0.97

27.26

1.78

CNFpred

NKALEEGNYFEMSTYSTNRTMIRILFAFVSSVARNDTGYYTCSSSKHPSQSALVTIVEKGFINAT---EDYEIDQYEEFCFSVRFKAYPQIRCTWTFSRKSFPCEQKGLDNGY

3qs7E

0.98

0.96

26.78

1.14

MUSTER

NKALEEGNYFEMSTYSTNRTMIRILFAFVSSVARNDTGYYTCSSSKHPSQSALVTIVEKGFI---NATEDYEIDQYEEFCFSVRFKAYPQIRCTWTFSRKSFPCEQKGLDNGY

1vcaA

0.09

3.37

0.48

CEthreader

LAQIGDSVSLTCSTTGCESNEGTTSTLTMNPVSFGNEHSYLCTATCKLEKGIQVEIYSFPKDPEIHLSGPLEAG--KPITVKCSVADVYPLEIDLLKGDHLMKSQEFLEDADR

6oz2L

0.08

3.13

0.58

EigenThreader

LASPGQSVTISCWCQQQAPKLLIYASLTISGLQADDEGHYFCWAFENIGGGTKLTVLAAPSVTLFPPSSEE--LQANKATLVCLISDFGAVTVAWKADSSPVKAGVETTTPSK

2v44A

0.14

0.13

4.52

1.22

FFAS-3D

GEKIISTQRVVVQKEGV------RSRLTIYNANIEDAGIYRCQATDAKGQTATVVLEIYQKLTFREVVSPQEFKQGEDAEVVCRVSSSPAPAVSWLYHNVTTISDNRFLANN-

2v44A

0.12

4.04

1.05

SPARKS-K

GEKIISTQR--VVVQKEGVR----SRLTIYNANIEDAGIYRCQATDAKEATVVLEIYQKLTFREVVSP--QEFKQGEDAEVVCRVSSSPAPAVSWLYHNVTTISDNRFAMLAN

3qs9E

1.00

0.98

27.50

1.74

CNFpred

NKALEEGNYFEMSTYSTNRTMIRILFAFVSSVARNDTGYYTCSSSKHPSQSALVTIV--GFINATNSSEDYEIDQYEEFCFSVRFKAYPQIRCTWTFSRKSFPCEQKGLDNGY

1qz1A

0.11

0.10

3.49

1.00

DEthreader

------DAVIVCDVVS-------NNYLQIRGIKKTDEGTYRCEGRIINFKDIQVIVNVPPTVQARQSIVNATAN-GQSVTLVCDADGFPEPTMSWTKDGEPIENIFSDDSS--

(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

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4152

(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.	Download Alignment
1	2w59A	0.53	4.07	0.073	0.841	model1_2w59A.pdb.gz
2	1o0vB	0.51	4.20	0.065	0.832	model1_1o0vB.pdb.gz
3	4ll9A	0.51	4.48	0.087	0.894	model1_4ll9A.pdb.gz
4	7k0cA	0.51	4.35	0.056	0.867	model1_7k0cA.pdb.gz
5	1igtB	0.50	4.20	0.037	0.823	model1_1igtB.pdb.gz
6	2atyA	0.49	4.36	0.056	0.823	model1_2atyA.pdb.gz
7	4grgC	0.49	4.41	0.046	0.832	model1_4grgC.pdb.gz
8	7khfH	0.49	4.76	0.077	0.894	model1_7khfH.pdb.gz
9	4cu6A	0.49	4.09	0.028	0.814	model1_4cu6A.pdb.gz
10	7k80G	0.49	4.68	0.048	0.876	model1_7k80G.pdb.gz

(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	0.74	catalytic activity
GO:0016740	0.71	transferase activity
GO:0004872	0.71	receptor activity
GO:0004871	0.71	signal transducer activity
GO:0004888	0.70	transmembrane signaling receptor activity
GO:0004672	0.70	protein kinase activity
GO:0004896	0.69	cytokine receptor activity
GO:0004713	0.69	protein tyrosine kinase activity

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(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:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0071310	1.00	cellular response to organic substance
GO:0048513	1.00	animal organ development
GO:0044767	1.00	single-organism developmental process
GO:0065007	0.80	biological regulation
GO:0050789	0.80	regulation of biological process
GO:0008152	0.79	metabolic process
GO:0071704	0.78	organic substance metabolic process
GO:0050794	0.78	regulation of cellular process
GO:0044238	0.78	primary metabolic process
GO:0044237	0.78	cellular metabolic process
GO:0044260	0.77	cellular macromolecule metabolic process
GO:0080090	0.73	regulation of primary metabolic process
GO:0060255	0.73	regulation of macromolecule metabolic process
GO:0048518	0.73	positive regulation of biological process
GO:0044763	0.73	single-organism cellular process
GO:0031323	0.73	regulation of cellular metabolic process
GO:0048522	0.72	positive regulation of cellular process
GO:0007165	0.72	signal transduction
GO:0044267	0.71	cellular protein metabolic process
GO:0032268	0.71	regulation of cellular protein metabolic process
GO:0031325	0.71	positive regulation of cellular metabolic process
GO:0010604	0.71	positive regulation of macromolecule metabolic process
GO:0065008	0.70	regulation of biological quality
GO:0030154	0.70	cell differentiation
GO:0007166	0.70	cell surface receptor signaling pathway
GO:0006796	0.70	phosphate-containing compound metabolic process
GO:0006464	0.70	cellular protein modification process
GO:0002376	0.70	immune system process
GO:0001934	0.70	positive regulation of protein phosphorylation
GO:0001775	0.70	cell activation
GO:0097028	0.69	dendritic cell differentiation
GO:0071345	0.69	cellular response to cytokine stimulus
GO:0046777	0.69	protein autophosphorylation
GO:0046651	0.69	lymphocyte proliferation
GO:0042127	0.69	regulation of cell proliferation
GO:0035726	0.69	common myeloid progenitor cell proliferation
GO:0030183	0.69	B cell differentiation
GO:0030097	0.69	hemopoiesis
GO:0019221	0.69	cytokine-mediated signaling pathway
GO:0002328	0.69	pro-B cell differentiation
GO:0002318	0.69	myeloid progenitor cell differentiation
GO:0001776	0.69	leukocyte homeostasis

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(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:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	1.00	cell part
GO:0044424	0.78	intracellular part
GO:0016020	0.73	membrane
GO:0044425	0.71	membrane part
GO:0005886	0.71	plasma membrane
GO:0044459	0.70	plasma membrane part
GO:0043226	0.57	organelle
GO:0043229	0.56	intracellular organelle
GO:0043227	0.55	membrane-bounded organelle
GO:0043231	0.54	intracellular membrane-bounded organelle
GO:0005634	0.50	nucleus

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(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:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

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	1cpyA	0.433	4.32	0.010	0.735	3.4.16.5	NA
2	0.060	3hidA	0.431	4.63	0.048	0.796	6.3.4.4	NA
3	0.060	1ua4A	0.438	4.40	0.090	0.752	2.7.1.147	89
4	0.060	1adeA	0.332	4.84	0.023	0.655	6.3.4.4	NA
5	0.060	2vrkA	0.373	5.46	0.065	0.796	3.2.1.55	5

	Click on the radio buttons to visualize predicted active site residues.
(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	Download Complex	Predicted binding site residues
1	0.01	3mlwL	0.448	4.86	0.088	0.832	0.13	III	complex1.pdb.gz	62,63,64,83
2	0.01	1frgH	0.364	4.53	0.068	0.620	0.16	III	complex2.pdb.gz	36,37,38,39,89,92
3	0.01	2h3n0	0.298	3.56	0.041	0.443	0.24	III	complex3.pdb.gz	62,64,65,67,83,85
4	0.01	1o0vA	0.501	4.34	0.073	0.832	0.20	UUU	complex4.pdb.gz	39,41,42,50,51,53,56
5	0.01	1sbs0	0.450	4.81	0.056	0.814	0.30	III	complex5.pdb.gz	54,55,56,57,58,59
6	0.01	1igtB	0.501	4.20	0.037	0.823	0.18	UUU	complex6.pdb.gz	39,56,60,62,63,82,84
7	0.01	1i1aD	0.499	4.36	0.046	0.850	0.24	UUU	complex7.pdb.gz	38,41,56,58,59,89
8	0.01	2h3n4	0.298	3.56	0.041	0.443	0.35	III	complex8.pdb.gz	55,56,57,58,59,60,61,62,63,64,65,66,68
9	0.01	1i1cA	0.494	4.61	0.046	0.858	0.28	UUU	complex9.pdb.gz	39,42,57,58,89
10	0.01	2rgsB	0.501	4.27	0.037	0.841	0.25	UUU	complex10.pdb.gz	37,38,40,55,59,60,63,87

	Click on the radio buttons to visualize predicted binding site and residues.
(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.

[Click result.zip to download all results on this page]

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.