D-I-TASSER P21860-D1

D-I-TASSER results for P21860-D1

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

Input Sequence in FASTA format

>P21860 (96 residues)
MRANDALQVLGLLFSLARGSEVGNGPGGDYAAMGACPASEQGYEEMRAFQGPGHQAPHVH
YARLKTLRSLEATDSAFDNPDYWHSRLFPKANAQRT

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MRANDALQVLGLLFSLARGSEVGNGPGGDYAAMGACPASEQGYEEMRAFQGPGHQAPHVHYARLKTLRSLEATDSAFDNPDYWHSRLFPKANAQRT
Prediction	CCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHCCCCCCCCCC
Confidence	974027999999998630111278888741432368544411899997508999899744223112102355667778952456522666454679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MRANDALQVLGLLFSLARGSEVGNGPGGDYAAMGACPASEQGYEEMRAFQGPGHQAPHVHYARLKTLRSLEATDSAFDNPDYWHSRLFPKANAQRT
Prediction	754442030101113124246236455342443332454452264154256443425324432143045154664425435212532144554668
	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

                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHCCCCCCCCCC
MRANDALQVLGLLFSLARGSEVGNGPGGDYAAMGACPASEQGYEEMRAFQGPGHQAPHVHYARLKTLRSLEATDSAFDNPDYWHSRLFPKANAQRT

6mn8A1

0.04

2.11

0.62

CEthreader

TAFQSKDEAEDEVFKILDLYAQIYIDLLAIPVIKGRKGGDFTATVEAYVPVNGRGIQGATS-HHLGQNFSKMFNISFEDPNGGGKIYAWQNSWGIS

5yysA

0.09

3.53

0.52

EigenThreader

LYAQREEFRKGNWKALAVNHEKSLQMSRIHNRMLRARILKLDGRSPVRIDMAGGWTGGNVVNLAIELGLGTSSILASTVLGAINDFCGGVLQGVKL

6y509

0.12

0.06

2.20

0.35

FFAS-3D

TQIEDAVSLWAKLKLQKASERWQPDTEEEYEDSSGNVVNKKTYEDLKRQ-----------------------------------------------

3lg8A

0.10

0.09

3.51

0.82

SPARKS-K

EYKDKLIKLIKDGAISLGGGELIRLNKRDMIDDSTLWNLEKEVENTKKVTVLKKGEPVDIAGGCIIET--ADGLKSLDNSLEAIFNRNLNVIRARI

5lm1A

0.17

0.04

1.36

0.27

CNFpred

GVFTDVEASLKDIRDLLEEDELL-------------------------------------------------------------------------

4knhA

0.08

0.07

2.92

0.83

DEthreader

QELDFSRLSLVEQHECLASILAVAFQFILWHFLILPSEPF----PSQLRRLSCLDFVCRVWLFVITLINTIHQDSLSASPDSLVVSILRAIQVM-A

4o95A

0.11

4.09

0.87

MapAlign

RAAGDVAGLVGAAFRSARGFRVSARGGVVVDMSRGRGPGAAVARALPVHSAALGGHYVDVNVYELDVVTGKGEVVTCSETENPDLFFFGIITRARI

5njlA3

0.09

0.08

3.23

0.68

MUSTER

ENSADLSAEANSITEKAKTETNGIYKVADVKASYDSAKDKLTLRDKTDTVTSGIGDEKIDLTANPVDSTGTNLDPSTE--GFRVNKIVKLGVAGAK

6cv7A1

0.22

0.14

4.27

0.54

HHsearch

------------------------------------YDDDWQYEDCKLARGGPPANGTILVDNMLIKGTAGGPDSLKDNVDYWKQMLFLNSTG-RV

2r73A

0.06

2.69

0.51

CEthreader

LASSDRSLIEEEGPFRNFIQNITVESGNLNGFFLTRKNGQCIPLYLTAFKTEEARQFKLNYYGTNDVYYESSKFIFYNYHDGKVNVVANLFGRTPN

(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	0.4465

(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	4a5bA	0.48	3.99	0.066	0.844	model1_4a5bA.pdb.gz
2	2hc9A2	0.48	4.28	0.085	0.812	model1_2hc9A2.pdb.gz
3	3agrA	0.47	3.98	0.077	0.833	model1_3agrA.pdb.gz
4	5e8vA	0.47	3.86	0.063	0.771	model1_5e8vA.pdb.gz
5	6kkiA	0.46	4.15	0.082	0.802	model1_6kkiA.pdb.gz
6	3ij3A2	0.46	4.57	0.086	0.812	model1_3ij3A2.pdb.gz
7	3peiA	0.46	4.31	0.063	0.781	model1_3peiA.pdb.gz
8	3h9rA2	0.46	4.03	0.138	0.760	model1_3h9rA2.pdb.gz
9	6sciA	0.46	4.67	0.044	0.854	model1_6sciA.pdb.gz
10	3pfoA	0.45	4.44	0.064	0.771	model1_3pfoA.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:0019838	1.00	growth factor binding
GO:0038132	0.81	neuregulin binding
GO:0003824	0.80	catalytic activity
GO:0004713	0.78	protein tyrosine kinase activity
GO:0004888	0.59	transmembrane signaling 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:0048869	0.81	cellular developmental process
GO:0048856	0.81	anatomical structure development
GO:0044767	0.81	single-organism developmental process
GO:0007169	0.79	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0014037	0.63	Schwann cell differentiation
GO:0050896	0.61	response to stimulus
GO:0051049	0.60	regulation of transport
GO:0048518	0.60	positive regulation of biological process
GO:0009888	0.59	tissue development

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	0.83	cell part
GO:0043235	0.77	receptor complex
GO:0098590	0.76	plasma membrane region
GO:0044421	0.54	extracellular region part
GO:0016323	0.53	basolateral plasma membrane
GO:0005615	0.53	extracellular space
GO:0016021	0.52	integral component of 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	1hylA	0.426	4.28	0.067	0.823	3.4.21.49	NA
2	0.060	1aksB	0.290	4.44	0.044	0.562	3.4.21.4	NA
3	0.060	2qluA	0.454	4.52	0.089	0.802	2.7.11.30	NA
4	0.060	1vncA	0.433	4.74	0.089	0.823	1.11.1.10	NA
5	0.060	1a0jA	0.452	4.09	0.093	0.802	3.4.21.4	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:

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	3socB	0.458	4.17	0.157	0.792	0.14	GVD	complex1.pdb.gz	43,44,46,48
2	0.01	2bdiL	0.448	4.19	0.067	0.823	0.20	PBZ	complex2.pdb.gz	17,35,42,43
3	0.01	3s90B	0.342	4.42	0.027	0.604	0.15	III	complex3.pdb.gz	1,5,8,11,14,15,18
4	0.01	2bdgA	0.448	4.17	0.067	0.823	0.24	PBZ	complex4.pdb.gz	64,77,78,84
5	0.01	2bdiA	0.439	4.42	0.090	0.833	0.29	PBZ	complex5.pdb.gz	63,78,83
6	0.01	2bdhB	0.434	4.47	0.089	0.844	0.13	PBZ	complex6.pdb.gz	13,14,42
7	0.01	2bdiJ	0.445	4.52	0.055	0.833	0.16	PBZ	complex7.pdb.gz	39,44,45,46,57
8	0.01	3aheA	0.452	4.78	0.011	0.802	0.18	THD	complex8.pdb.gz	41,47,48,71,73
9	0.01	3my0P	0.388	4.84	0.090	0.823	0.21	LDN	complex9.pdb.gz	21,32,42
10	0.01	2bdiG	0.444	4.35	0.054	0.844	0.25	PBZ	complex10.pdb.gz	38,40,41

	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.