D-I-TASSER Q16281-D2

D-I-TASSER results for Q16281-D2

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

Input Sequence in FASTA format

>Q16281 (144 residues)
KTKKKDAIVVDPSSNLYYRWLTAIALPVFYNWYLLICRACFDELQSEYLMLWLVLDYSAD
VLYVLDVLVRARTGFLEQGLMVSDTNRLWQHYKTTTQFKLDVLSLVPTDLAYLKVGTNYP
EVRFNRLLKFSRLFEFFDRTETRT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| KTKKKDAIVVDPSSNLYYRWLTAIALPVFYNWYLLICRACFDELQSEYLMLWLVLDYSADVLYVLDVLVRARTGFLEQGLMVSDTNRLWQHYKTTTQFKLDVLSLVPTDLAYLKVGTNYPEVRFNRLLKFSRLFEFFDRTETRT
Prediction	CCCCCCCSSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCSSSSSCCSSSSCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence	998778857739986677899999999999999998776530447550358999999999999999999822278759989974999999997233167889999789999998633368899999999999999999985179
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| KTKKKDAIVVDPSSNLYYRWLTAIALPVFYNWYLLICRACFDELQSEYLMLWLVLDYSADVLYVLDVLVRARTGFLEQGLMVSDTNRLWQHYKTTTQFKLDVLSLVPTDLAYLKVGTNYPEVRFNRLLKFSRLFEFFDRTETRT
Prediction	855657520010433032321231233333333220010024424663321111213313331220030102220254232032144003203433302110112333331323334323313323333132034005432658
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCSSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCSSSSSCCSSSSCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCC
KTKKKDAIVVDPSSNLYYRWLTAIALPVFYNWYLLICRACFDELQSEYLMLWLVLDYSADVLYVLDVLVRARTGFLEQGLMVSDTNRLWQHYKTTTQFKLDVLSLVPTDLAYLKVGTNYPEVRFNRLLKFSRLFEFFDRTETRT

7lftA

0.62

0.58

16.69

1.33

DEthreader

-------VVIDPSGNTYYNWLFCITLPVMYNWTMVIARACFDELQSDYLEYWLILDYVSDIVYLIDMFVRTRTGYLEQGLLVKEELKLINKYKSNLQFKLDVLSLIPTD-LLYFKLGNYPEIRLNRLLRFSRMFEFFQRTETRT

7lftA1

0.64

0.61

17.45

2.19

SPARKS-K

-------VVIDPSGNTYYNWLFCITLPVMYNWTMVIARACFDELQSDYLEYWLILDYVSDIVYLIDMFVRTRTGYLEQGLLVKEELKLINKYKSNLQFKLDVLSLIPTDLLYFKLGWNYPEIRLNRLLRFSRMFEFFQRTETRT

5u6oA

0.19

6.03

0.97

MapAlign

RVKTAGFWIIHPYSDFRFYWDLIMLIMMVGNLVIIPVGI--TFFTEQTTTPWIIFNVASDTVFLLDLIMNFRTGTV-NSSEIILDKVIKMNYL-KSWFVVDFISSIPVDYIFLIVERFTKILSLLRLLRLSRLIRYIHQWEEIF

7lftA

0.64

0.61

17.45

0.87

CEthreader

-------VVIDPSGNTYYNWLFCITLPVMYNWTMVIARACFDELQSDYLEYWLILDYVSDIVYLIDMFVRTRTGYLEQGLLVKEELKLINKYKSNLQFKLDVLSLIPTDLLYFKLGWNYPEIRLNRLLRFSRMFEFFQRTETRT

5h3oA1

0.30

9.06

1.60

MUSTER

-RKYLANYTQDPSTDNFYYWTCVVTVAYIYNLLFVIARQVFNDLIWHFRMLWVFFDLLMDCVYLIDTFLNYRMGYMDQGLVVREAEKVTKAYWQSKQYRIDGISLIPLDYILGWPIPYLPILRLNRLIRYKRVRNCLERTETRS

1orqC

0.17

0.14

4.58

2.33

HHsearch

----------IGDVMEHPLVELGVSYAALLSVIVVVVECTMQLSGE-YLVRLYLVDLILVIILWADYAYRAYKS------------GDPAGYVK--KTLYEIPALVPAGLLALIEGHLLGLFRLVRLLRFLRILLIISRGSKAI

7lftA1

0.65

0.61

17.44

2.30

FFAS-3D

--------VIDPSGNTYYNWLFCITLPVMYNWTMVIARACFDELQSDYLEYWLILDYVSDIVYLIDMFVRTRTGYLEQGLLVKEELKLINKYKSNLQFKLDVLSLIPTDLLYFKLGWNYPEIRLNRLLRFSRMFEFFQRTETRT

5u6oA1

0.20

0.19

6.23

1.33

EigenThreader

RVKTAGFWIIHPYSDFRFYWDLIMLIMMVGNLVIIPVGITFFTEQ--TTTPWIIFNVASDTVFLLDLIMNFRTGTVN-SSEIILDPKVIKMNYLKSWFVVDFISSIPVDYIFLIVEKGTKILSLLRLLRLSRLIRYIHQWEEIF

5u6oA

0.22

0.21

6.59

1.05

CNFpred

RVKTAGFWIIHPYSDFRFYWDLIMLIMMVGNLVIIPVGITFFTEQT--TTPWIIFNVASDTVFLLDLIMNFRTGTVN-SEIILDPKVIKMNYLKS-WFVVDFISSIPVDYIFLIV-RFTKILSLLRLLRLSRLIRYIHQWEEIF

7lftA1

0.62

0.58

16.69

1.33

DEthreader

-------VVIDPSGNTYYNWLFCITLPVMYNWTMVIARACFDELQSDYLEYWLILDYVSDIVYLIDMFVRTRTGYLEQGLLVKEELKLINKYKSNLQFKLDVLSLIPTD-LLYFKLGNYPEIRLNRLLRFSRMFEFFQRTETRT

(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	0.8133

(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	7lftA1	0.88	1.29	0.625	0.944	model1_7lftA1.pdb.gz
2	5u6oA	0.83	2.30	0.199	0.979	model1_5u6oA.pdb.gz
3	5h3oA1	0.81	2.34	0.252	0.965	model1_5h3oA1.pdb.gz
4	5k7lA3	0.80	2.51	0.223	0.965	model1_5k7lA3.pdb.gz
5	6v1xA	0.76	2.36	0.195	0.924	model1_6v1xA.pdb.gz
6	5va1A	0.74	2.06	0.227	0.854	model1_5va1A.pdb.gz
7	3caxA	0.67	3.24	0.085	0.861	model1_3caxA.pdb.gz
8	7cn0A	0.67	2.07	0.241	0.771	model1_7cn0A.pdb.gz
9	6gy6A	0.67	3.51	0.043	0.903	model1_6gy6A.pdb.gz
10	5u70A1	0.67	3.30	0.093	0.882	model1_5u70A1.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:0022836	1.00	gated channel activity
GO:0005216	1.00	ion channel activity
GO:0005261	0.99	cation channel activity
GO:0022890	0.93	inorganic cation transmembrane transporter activity
GO:0005249	0.92	voltage-gated potassium channel activity
GO:0004872	0.74	receptor activity
GO:0099600	0.73	transmembrane receptor activity
GO:0015276	0.72	ligand-gated ion channel activity
GO:0005221	0.71	intracellular cyclic nucleotide activated cation channel activity
GO:1901363	0.70	heterocyclic compound binding
GO:0097159	0.70	organic cyclic compound binding
GO:0036094	0.70	small molecule binding
GO:0000166	0.69	nucleotide binding
GO:0032555	0.68	purine ribonucleotide binding
GO:0032561	0.66	guanyl ribonucleotide binding
GO:0030551	0.65	cyclic nucleotide binding
GO:0005223	0.65	intracellular cGMP activated cation channel activity
GO:0030553	0.64	cGMP binding
GO:0005222	0.63	intracellular cAMP activated cation channel 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	0.97	biological regulation
GO:0065008	0.92	regulation of biological quality
GO:0042391	0.90	regulation of membrane potential

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	0.99	cell part
GO:0044425	0.99	membrane part
GO:0044459	0.95	plasma membrane part
GO:0016021	0.92	integral component of membrane
GO:0005887	0.91	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	0.067	1q0mD	0.518	3.87	0.053	0.757	1.15.1.1	NA
2	0.066	3gm1B	0.535	3.83	0.050	0.785	2.7.10.2	NA
3	0.066	3g4xA	0.518	3.91	0.061	0.757	1.15.1.1	76
4	0.060	1g4wR	0.478	3.10	0.044	0.625	3.1.3.48	NA
5	0.060	1h2aL	0.546	3.92	0.058	0.771	1.12.2.1	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	0.09	1v54P	0.604	3.45	0.053	0.847	0.22	CDL	complex1.pdb.gz	68,71,72,74
2	0.02	3ny9A	0.589	4.24	0.097	0.889	0.26	CLR	complex2.pdb.gz	70,71,78
3	0.02	3ny9A	0.589	4.24	0.097	0.889	0.31	CLR	complex3.pdb.gz	69,73,81
4	0.01	3ny9A	0.589	4.24	0.097	0.889	0.12	JSZ	complex4.pdb.gz	15,73,76
5	0.01	3dqbA	0.605	3.90	0.071	0.882	0.19	III	complex5.pdb.gz	11,73,82,142
6	0.01	3d4sA	0.587	4.36	0.083	0.896	0.14	TIM	complex6.pdb.gz	15,16,19,20,23,24
7	0.01	3ablP	0.603	3.45	0.060	0.847	0.24	CDL	complex7.pdb.gz	66,70,73,74,80
8	0.01	3rvyB	0.615	3.41	0.057	0.806	0.26	PX4	complex8.pdb.gz	72,73,75,77
9	0.01	2einP	0.605	3.30	0.068	0.819	0.18	CDL	complex9.pdb.gz	68,71,72,75,76
10	0.01	3ag4P	0.603	3.45	0.060	0.847	0.24	CDL	complex10.pdb.gz	66,70,73,80

	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.