D-I-TASSER Q05469-D4

D-I-TASSER results for Q05469-D4

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

Input Sequence in FASTA format

>Q05469 (36 residues)
SYDLREGQDSEELSSLIKSNGQRSLELWPRPQQAPR

Predicted Secondary Structure

Sequence	20 \| SYDLREGQDSEELSSLIKSNGQRSLELWPRPQQAPR
Prediction	CCCCCCCCCHHHHHHHHCCCCCCSSSSCCCCCCCCC
Confidence	954324756799999751479840241237888999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 \| SYDLREGQDSEELSSLIKSNGQRSLELWPRPQQAPR
Prediction	846356465474145224672444251335557468
	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

                   |

SS
Seq

CCCCCCCCCHHHHHHHHCCCCCCSSSSCCCCCCCCC
SYDLREGQDSEELSSLIKSNGQRSLELWPRPQQAPR

6adqK

0.06

2.50

0.43

CEthreader

VNAQAGQVSLRNVHLRAVEPGTTVELLFVAANDSSN

4bzjA1

0.11

4.00

0.63

EigenThreader

SRTATSHTVSGDSSLELWSLLAKPIASSKFNDLNKI

2cf2C2

0.24

0.19

6.06

0.22

FFAS-3D

--DKRESYTKEDLLASGRGEL-----FGAKGPQLPA

1lvaA1

0.17

5.50

0.91

SPARKS-K

IQEHREGLDWQEAATRASLSLEETRKLLQSAAAGQV

3mtnA

0.44

0.11

3.25

0.40

CNFpred

-------QDAQEFLKL--------------------

2wqtT

0.11

3.97

0.83

DEthreader

LPCLGHPNAAVWLARKMAS-LGEPLRDIILTGALGI

6w09A3

0.09

0.08

3.17

0.71

MapAlign

-ELLSVTLESASAKLRVLYQGNNVTVSAYVRAMN--

1t0cA

0.13

0.11

3.83

0.95

MUSTER

--EAEDLQVGQ----VELGGGPGAGSLQPLALEGSL

6o16A3

0.28

8.50

0.35

HHsearch

AKFLLEGQVFRKLASFKSCLSSPSTMLKTWARLQPR

1ml5n

0.03

1.75

0.39

CEthreader

KGQVVKAVVVRTKRGVRRPDGSYIRFDENACVIIRD

(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	0.5982

(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	6j9wA	0.49	3.30	0.086	0.917	model1_6j9wA.pdb.gz
2	7dmeA2	0.49	3.36	0.088	0.917	model1_7dmeA2.pdb.gz
3	4bxdA	0.49	2.09	0.094	0.889	model1_4bxdA.pdb.gz
4	6dtqA	0.49	3.08	0.057	0.889	model1_6dtqA.pdb.gz
5	3au2A	0.49	1.72	0.059	0.722	model1_3au2A.pdb.gz
6	3ib6A	0.48	2.46	0.059	0.833	model1_3ib6A.pdb.gz
7	1bwqA	0.48	3.08	0.091	0.861	model1_1bwqA.pdb.gz
8	2c4nA2	0.46	2.76	0.091	0.889	model1_2c4nA2.pdb.gz
9	1zjjB2	0.43	2.92	0.029	0.861	model1_1zjjB2.pdb.gz
10	2hx1A2	0.42	2.89	0.088	0.917	model1_2hx1A2.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:0097159	0.85	organic cyclic compound binding
GO:1901363	0.84	heterocyclic compound binding
GO:0003676	0.82	nucleic acid binding
GO:0042134	0.80	rRNA primary transcript binding
GO:0003824	0.51	catalytic 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:0044260	1.00	cellular macromolecule metabolic process
GO:0016042	1.00	lipid catabolic process
GO:1901576	0.81	organic substance biosynthetic process
GO:0044249	0.81	cellular biosynthetic process
GO:0006139	0.81	nucleobase-containing compound metabolic process
GO:0006363	0.80	termination of RNA polymerase I transcription
GO:0006361	0.80	transcription initiation from RNA polymerase I promoter

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:0005811	1.00	lipid particle
GO:0044444	0.88	cytoplasmic part
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0016020	0.84	membrane
GO:0044425	0.82	membrane part
GO:0005634	0.81	nucleus
GO:0005901	0.80	caveola
GO:0005739	0.80	mitochondrion
GO:0005737	0.80	cytoplasm

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	2cfmA	0.396	2.84	0.083	0.694	6.5.1.1	NA
2	0.060	1xfbA	0.436	3.48	0.057	0.889	4.1.2.13	NA
3	0.060	1akaA	0.446	2.93	0.125	0.778	2.6.1.1	NA
4	0.060	1ahuA	0.451	3.13	0.171	0.972	1.1.3.38 1.1.3.13	NA
5	0.060	2p8uA	0.474	2.80	0.000	0.917	2.3.3.10	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	1eexB	0.459	3.21	0.029	0.917	0.11	COY	complex1.pdb.gz	8,20,24,27,28
2	0.01	1gl9B	0.457	2.74	0.114	0.917	0.11	ANP	complex2.pdb.gz	21,22,23
3	0.01	2dvhA	0.466	3.06	0.061	0.917	0.22	HEC	complex3.pdb.gz	5,8,13,16,17
4	0.01	2f3c1	0.396	3.05	0.032	0.861	0.24	III	complex4.pdb.gz	7,8,9,13,14,15
5	0.01	1vyh3	0.467	3.01	0.118	0.861	0.11	III	complex5.pdb.gz	6,7,8,17
6	0.01	2flqB	0.357	3.68	0.056	0.806	0.25	ARG	complex6.pdb.gz	5,7,16
7	0.01	3a9fA	0.459	2.83	0.000	0.861	0.31	HEC	complex7.pdb.gz	16,19,20,22

	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.