D-I-TASSER P23945-D3

D-I-TASSER results for P23945-D3

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

Input Sequence in FASTA format

>P23945 (66 residues)
TKNFRRDFFILLSKCGCYEMQAQIYRTETSSTVHNTHPRNGHCSSAPRVTNGSTYILVPL
SHLAQN

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| TKNFRRDFFILLSKCGCYEMQAQIYRTETSSTVHNTHPRNGHCSSAPRVTNGSTYILVPLSHLAQN
Prediction	CCCHHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCC
Confidence	930236788988762614788888731222456776654787566777788744553320102479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| TKNFRRDFFILLSKCGCYEMQAQIYRTETSSTVHNTHPRNGHCSSAPRVTNGSTYILVPLSHLAQN
Prediction	865244300001232211444043243543445444435445244444544433333232443478
	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

                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCC
TKNFRRDFFILLSKCGCYEMQAQIYRTETSSTVHNTHPRNGHCSSAPRVTNGSTYILVPLSHLAQN

3fnbA

0.10

0.09

3.41

1.17

DEthreader

HADYLEDEVERVKKV-GYRDLISHLYFSACFSIRAALQFTDNKYASVVLEQ--AQIVYQSQVLYDN

2ziyA

0.06

2.64

1.13

MapAlign

MFIINLAFSDFTFSLVFIGGIFGFMSVWLWSVLWAIGPIFGWGAYTLEGVLCNCSFDYISRDSTTR

6lnwA1

0.08

3.05

0.56

CEthreader

HGVEGFISDIQYFEPNGQIHMHHIVDDRGFVSSIIFFEDGQAAYQEYLNLKGEWQFRERLKEGGQV

6cq0A3

0.03

1.82

0.58

EigenThreader

EKLQVLLNCMTEIYYQFDKQKLYYHATKAMTHFTDECVKKYEAFLNQLLSLTNQCFDIEEEVSKYQ

5z62N

0.08

3.03

0.29

FFAS-3D

-GQAKKSLIPLFVFIGTGATGATLYLLRLALFNPDVCWDRNNPEPWNKLGPNDQYKFYSVNVDYSK

6otjA3

0.11

3.86

0.81

SPARKS-K

EVSDGINAVEALVKTGLAKEARGFVNAKAVLLNGKPAEANNPNHPDDAYRFGKYTILRRGKRNHAL

3i0pA

0.23

0.09

2.85

0.38

CNFpred

IDTIKEFMYQVLLKVGSDEENARMVR----------------------------------------

6xssA

0.03

1.74

1.17

DEthreader

REEEAEEAARKAIEL-KEMDSARRLEGIIELIRRAREAAERAAALATDEVDPRERERLEAE--V--

4rncA

0.02

1.41

1.03

MapAlign

GYDDSANWAGDVAAVGLVICDYLAAHGTGAVAGAVLVGPVLVLHGTDDSVVDVSAGKHAEELIPKS

1jmmA2

0.09

3.45

0.79

MUSTER

ASAVDDAFSKSTSKAKYVQKILQLDDLDITNLEQSNDVASSELYGNFGDKAGWSTTVSNNSQVKWG

(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	0.4963

(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	1a0pA	0.61	2.98	0.152	0.939	model1_1a0pA.pdb.gz
2	4xydA	0.60	2.78	0.082	0.924	model1_4xydA.pdb.gz
3	5t1oB	0.60	3.03	0.031	0.924	model1_5t1oB.pdb.gz
4	6g3dA	0.59	2.79	0.077	0.955	model1_6g3dA.pdb.gz
5	5azbA	0.59	3.31	0.076	0.955	model1_5azbA.pdb.gz
6	1tj7A	0.59	3.30	0.076	1.000	model1_1tj7A.pdb.gz
7	6y5dK2	0.58	3.07	0.048	0.955	model1_6y5dK2.pdb.gz
8	1xfiA	0.58	2.63	0.050	0.833	model1_1xfiA.pdb.gz
9	3o0rB2	0.55	2.63	0.049	0.803	model1_3o0rB2.pdb.gz
10	2uuiA	0.54	3.17	0.117	0.864	model1_2uuiA.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:0004930	1.00	G-protein coupled receptor activity
GO:0016500	0.99	protein-hormone receptor activity
GO:0008528	0.84	G-protein coupled peptide receptor activity
GO:0004963	0.62	follicle-stimulating hormone receptor 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:0065007	0.96	biological regulation
GO:0050789	0.96	regulation of biological process
GO:0050794	0.95	regulation of cellular process
GO:0048518	0.93	positive regulation of biological process
GO:0080090	0.92	regulation of primary metabolic process
GO:0048522	0.92	positive regulation of cellular process
GO:0031323	0.92	regulation of cellular metabolic process
GO:0045937	0.91	positive regulation of phosphate metabolic process
GO:0007165	0.76	signal transduction
GO:0044699	0.74	single-organism process
GO:0007186	0.74	G-protein coupled receptor signaling pathway
GO:0031326	0.73	regulation of cellular biosynthetic process
GO:0019219	0.73	regulation of nucleobase-containing compound metabolic process
GO:0045935	0.72	positive regulation of nucleobase-containing compound metabolic process
GO:0031328	0.72	positive regulation of cellular biosynthetic process
GO:0007190	0.71	activation of adenylate cyclase activity
GO:0007187	0.71	G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger
GO:0007188	0.70	adenylate cyclase-modulating G-protein coupled receptor signaling pathway
GO:0007189	0.69	adenylate cyclase-activating G-protein coupled receptor signaling pathway
GO:0009755	0.67	hormone-mediated signaling pathway
GO:0022414	0.63	reproductive process
GO:0044702	0.62	single organism reproductive process
GO:0022602	0.59	ovulation cycle process
GO:0009966	0.53	regulation of signal transduction
GO:1902531	0.52	regulation of intracellular signal transduction
GO:0009967	0.52	positive regulation of signal transduction
GO:1902533	0.51	positive regulation of intracellular signal transduction
GO:0060255	0.51	regulation of macromolecule metabolic process

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	0.96	cell part
GO:0016021	0.89	integral component of membrane
GO:0005887	0.88	integral component of plasma membrane

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	1yrlC	0.538	3.27	0.094	0.909	1.1.1.86	61
2	0.060	1iwaA	0.535	3.34	0.016	0.909	4.1.1.39	NA
3	0.060	1q2vA	0.519	3.24	0.031	0.879	3.6.4.9	NA
4	0.060	1vdkA	0.551	3.45	0.031	0.970	4.2.1.2	29
5	0.060	2qj3B	0.543	3.32	0.016	0.894	2.3.1.39	NA

	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.