D-I-TASSER P09651-D3

D-I-TASSER results for P09651-D3

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

Input Sequence in FASTA format

>P09651 (173 residues)
GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGGGGPG
YSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGGGFGGGSGSNFGGGGSYNDFGNYN
NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGGGFGGGSGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	98778788887989988878888888888889888988888888888888888888998887887888888988788888888887778878888888788887777888877777766777777777778887888887878888665678888887888787777777769
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGGGFGGGSGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF
Prediction	86344463442144552341442544323333543342145464442344644446444143334543144353214734444342333333534445344444442454443541243455444334354452346431322333422343644343345544544455455
	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 DeepPotential. 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                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGGGFGGGSGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF

7jjvA

0.32

0.23

6.79

1.97

SPARKS-K

--------------------------------MQCDGLDGADGTSNGQAGASGL-AGGPNCNGGKGGKGAPGVGTAGGAGGVGGAG---------------GTGNTNGGAGGSG--GNSDVAAGGAGA-AGGAAGGAGTGGTGGNGGAGKPGGAPGAGGAGTPAGSAGSPGQT

6ar6A

0.09

0.08

3.12

1.05

MapAlign

KYFAPANTLDENLEGEAIDFTGKLIIDENIY------YFDDNYRGAVEWKELDGEMHYFSPETGKAFKGLNQIGDYKYYFNSDGVMQKGFVSINDNKHYFDDSGVMKVGYTEIDGKHFYFAENGEMQIGVFNTEDGFKYFAHHNEDLGN-----EEGEEISYSGILNFNNKIY

1vt4I4

0.47

0.45

12.96

1.29

MUSTER

GGGGGGGGGGGGGGG--GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-----GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG---

6edoA

0.48

0.43

12.43

1.40

HHsearch

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-GGGGGGGGGGGGGGGGGGGGGG----G--GG------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-------

6ar6A

0.10

3.81

0.57

CEthreader

APANTLDENLEGEAIDFTGKLIIDENIYYFDDNYAVEWKELDGEMHYFSPETGKAFKGLNQIGDYKYYFNSDGVMQKGFVSINDNKHYFDDSGVMKVGYTEIDGKHFYFAENGEMQIGVFNTEDGFKYFAHHNEDLGNEEGEEISYSGILNFNNKIYYFDDSFTAVVGWKDLE

2yikA

0.08

3.18

0.48

EigenThreader

KGVVQGEDGPKGYYGSSKWQDDYCWAAAWLYLATQNEHYLDEAFKYYDYYAPPGWIHWKPIQDLLDKWSGGSARYNTAAQLIALVYDKHHGDTPSKYANWARSQMDYLLGKNPLNRCYVVGYSSNSVKYPHHHKYVLALVGGPDASDQHVDRTNDYIYNEVADSSMQIDPSMP

6edoA

0.45

13.00

0.82

FFAS-3D

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG---

1vt4I3

0.46

0.45

12.99

1.63

SPARKS-K

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG----GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

3v0aB

0.03

1.67

0.83

DEthreader

AIPF--PYGYYRETNYLASVITSLYFKPSDLVIPYRLRSELENIPEEIINLSLMRSNLQAQSFYSFLNVYREIFRNYSDITATQVTWFGALYFICMAKRSVLQETLIKIITDGLTNS-SGWFMISVDR------------LNKPTTQEVLSNYFE-L---YIRDLVQKLDEVK

5xtsA

0.07

2.84

0.84

MapAlign

KRCVDAVSPSAVQTAACQKFRWVSESQIMSVAFKLCLGLYACDSKSEFQKWECKNDTLLGIKGEDLFFNYGNRQEKNIMLYKGSGLWSRWKIYGTTDNLCSRGYEAMYTANGATCAFPFKFENKWYADCTSAGRSDGWLWCGTTTDYDTDKLFGYCPLKFEGSESLWN-----

(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	0.465

(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 DeepPotential, 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	7jq9A	0.39	4.64	0.029	0.613	model1_7jq9A.pdb.gz
2	7qtta	0.38	4.81	0.023	0.607	model1_7qtta.pdb.gz
3	5xjcA	0.34	6.00	0.035	0.670	model1_5xjcA.pdb.gz
4	6h3iA	0.33	5.74	0.047	0.619	model1_6h3iA.pdb.gz
5	7oriA	0.33	6.54	0.035	0.705	model1_7oriA.pdb.gz
6	6l42A	0.33	6.21	0.023	0.636	model1_6l42A.pdb.gz
7	8pkpA	0.32	4.32	0.024	0.497	model1_8pkpA.pdb.gz
8	7q97A	0.31	3.94	0.012	0.462	model1_7q97A.pdb.gz
9	3lxuX1	0.31	4.58	0.030	0.491	model1_3lxuX1.pdb.gz
10	7ptxA	0.31	5.12	0.029	0.532	model1_7ptxA.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:1901363	0.93	heterocyclic compound binding
GO:0097159	0.93	organic cyclic compound binding
GO:0003676	0.90	nucleic acid binding
GO:0003677	0.83	DNA binding
GO:0003697	0.82	single-stranded DNA binding
GO:0003723	0.78	RNA binding
GO:0044822	0.72	poly(A) RNA binding
GO:0003727	0.64	single-stranded RNA binding

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:0051170	1.00	nuclear import
GO:0051168	1.00	nuclear export
GO:0016070	1.00	RNA metabolic process
GO:0065007	0.83	biological regulation
GO:0006396	0.83	RNA processing
GO:0050789	0.82	regulation of biological process
GO:0006397	0.81	mRNA processing
GO:0060255	0.80	regulation of macromolecule metabolic process
GO:0009893	0.79	positive regulation of metabolic process
GO:0008380	0.79	RNA splicing
GO:0065008	0.78	regulation of biological quality
GO:0010604	0.78	positive regulation of macromolecule metabolic process
GO:0000398	0.78	mRNA splicing, via spliceosome
GO:0050794	0.63	regulation of cellular process
GO:0080090	0.59	regulation of primary metabolic process
GO:0031323	0.59	regulation of cellular metabolic process
GO:2000112	0.58	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.58	regulation of nitrogen compound metabolic process
GO:0048519	0.58	negative regulation of biological process
GO:0071702	0.57	organic substance transport
GO:0051173	0.57	positive regulation of nitrogen compound metabolic process
GO:0048523	0.57	negative regulation of cellular process
GO:0031325	0.57	positive regulation of cellular metabolic process
GO:0019219	0.57	regulation of nucleobase-containing compound metabolic process
GO:0007165	0.57	signal transduction
GO:0045935	0.56	positive regulation of nucleobase-containing compound metabolic process
GO:0031328	0.56	positive regulation of cellular biosynthetic process
GO:0031327	0.56	negative regulation of cellular biosynthetic process
GO:0010605	0.56	negative regulation of macromolecule metabolic process
GO:0010557	0.56	positive regulation of macromolecule biosynthetic process
GO:0010467	0.56	gene expression
GO:0007166	0.56	cell surface receptor signaling pathway
GO:0006405	0.56	RNA export from nucleus
GO:0032212	0.55	positive regulation of telomere maintenance via telomerase
GO:0032211	0.55	negative regulation of telomere maintenance via telomerase
GO:0008543	0.55	fibroblast growth factor receptor signaling pathway

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:0044424	1.00	intracellular part
GO:0044446	0.86	intracellular organelle part
GO:0044428	0.84	nuclear part
GO:0005654	0.77	nucleoplasm
GO:0032991	0.73	macromolecular complex
GO:0030529	0.69	intracellular ribonucleoprotein complex
GO:0043226	0.54	organelle
GO:0043229	0.53	intracellular organelle
GO:0043227	0.50	membrane-bounded organelle

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	1ej6A	0.246	5.30	0.053	0.428	2.7.7.50	NA
2	0.060	3hmjA	0.240	5.65	0.024	0.445	2.3.1.86	NA
3	0.060	3dsxA	0.190	5.12	0.014	0.324	2.5.1.60	NA
4	0.060	3l9oA	0.226	5.13	0.015	0.393	3.6.4.13	NA
5	0.060	3b9jC	0.184	3.88	0.012	0.260	1.17.3.2 1.17.1.4	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	3lplA	0.212	6.23	0.059	0.433	0.15	TDP	complex1.pdb.gz	45,46,47
2	0.01	3lq2A	0.242	5.90	0.060	0.491	0.17	TDP	complex2.pdb.gz	6,8,47,48,49
3	0.01	2qtcB	0.243	5.86	0.033	0.474	0.11	TDK	complex3.pdb.gz	5,7,8,9,49

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.