D-I-TASSER Q86YJ6-D3

D-I-TASSER results for Q86YJ6-D3

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

Input Sequence in FASTA format

>Q86YJ6 (183 residues)
LVEVVVPTGAAGNLAAGYIAQKIGLPIRLVVAVNRNDIIHRTVQQGDFSLSEAVKSTLAS
AMDIQVPYNMERVFWLLSGSDSQVTRALMEQFERTQSVNLPKELHSKLSEAVTSVSVSDE
AITQTMGRCWDENQYLLCPHSAVAVNYHYQQIDRQQPSTPRCCLAPASAAKFPEAVLAAG
LTP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| LVEVVVPTGAAGNLAAGYIAQKIGLPIRLVVAVNRNDIIHRTVQQGDFSLSEAVKSTLASAMDIQVPYNMERVFWLLSGSDSQVTRALMEQFERTQSVNLPKELHSKLSEAVTSVSVSDEAITQTMGRCWDENQYLLCPHSAVAVNYHYQQIDRQQPSTPRCCLAPASAAKFPEAVLAAGLTP
Prediction	CSSSSSCCCCHHHHHHHHHHHHHCCCCSSSSSSCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCSSSCHHHHHHHHHHCCSSSCCHHHHHHHHHHHHHHHCCSCCCCHHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCHHHHHHHCCCC
Confidence	979997289389999999999919980699984797417999971971358653335686100356332999999996996999999999999709856089999999963313532899999999999998191448837999999999999639998199994578010499999974899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| LVEVVVPTGAAGNLAAGYIAQKIGLPIRLVVAVNRNDIIHRTVQQGDFSLSEAVKSTLASAMDIQVPYNMERVFWLLSGSDSQVTRALMEQFERTQSVNLPKELHSKLSEAVTSVSVSDEAITQTMGRCWDENQYLLCPHSAVAVNYHYQQIDRQQPSTPRCCLAPASAAKFPEAVLAAGLTP
Prediction	703000022120001003003303230200000241330241164241445551453313313233232020001101442153035005404763515036501530343031220227202500340076341030000000020034226656551200000001222136003504668
	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                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSSSCCCCHHHHHHHHHHHHHCCCCSSSSSSCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCSSSCHHHHHHHHHHCCSSSCCHHHHHHHHHHHHHHHCCSCCCCHHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCHHHHHHHCCCC
LVEVVVPTGAAGNLAAGYIAQKIGLPIRLVVAVNRNDIIHRTVQQGDFSLSEAVKSTLASAMDIQVPYNMERVFWLLSGSDSQVTRALMEQFERTQSVNLPKELHSKLSEAVTSVSVSDEAITQTMGRCWDENQYLLCPHSAVAVNYHYQQIDRQQPSTPRCCLAPASAAKFPEAVLAAGLTP

1kl7A

0.31

9.40

1.33

DEthreader

KVKFVVPSGNFGDILAGYFAKKGLPIEKLAIATNENDILDRFLKSGLYERSDKVAATLSPA-DILISSNFERLLWYLAREDAGIVNNWFQELKTNGKFQVDKSIIEGASKDFTSERVSNEETSETIKKIYESPHYILDPHTAVGVCATERLIAKNDKSIQYISLSTAHPAKFADAVNNALYSF

4f4fA1

0.32

9.54

2.06

SPARKS-K

AVSFTVPTGNFGDIFAGYVAKRMGLPIQLIIATNDNDILSRTLESGAYEMRGV-AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSAGRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKAS---GTAPMVVLATAHPAKFPDAVKAACGVE

4f4fA1

0.33

0.32

9.68

1.13

MapAlign

AVSFTVPTGNFGDIFAGYVAKRMGLPIQLIIATNDNDILSRTLESGAYEMR-GVAQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSAGRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKA---SGTAPMVVLATAHPAKFPDAVKAACGVE

4f4fA

0.33

0.32

9.68

0.79

CEthreader

AVSFTVPTGNFGDIFAGYVAKRMGLPIQLIIATNDNDILSRTLESGAYEMRG-VAQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSAGRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKA---SGTAPMVVLATAHPAKFPDAVKAACGVE

4f4fA1

0.33

0.32

9.68

1.21

MUSTER

AVSFTVPTGNFGDIFAGYVAKRMGLPIQLIIATNDNDILSRTLESGAYEMR-GVAQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSAGRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKA---SGTAPMVVLATAHPAKFPDAVKAACGVE

4f4fA1

0.33

0.32

9.68

2.37

HHsearch

AVSFTVPTGNFGDIFAGYVAKRMGLPIELIIATNDNDILSRTLESGAYEMRG-VAQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSAGRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKAS---GTAPMVVLATAHPAKFPDAVKAACGVE

4f4fA1

0.34

0.33

9.97

2.14

FFAS-3D

-VSFTVPTGNFGDIFAGYVAKRMGLPIQLIIATNDNDILSRTLESGAYEMR-GVAQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSAGRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREK---ASGTAPMVVLATAHPAKFPDAVKAAGVEP

4f4fA

0.33

0.32

9.52

1.27

EigenThreader

AVSFTVPTGNFGDIFAGYVAKRMGLPIQLIIATNDNDILSRTLESG----AYEMAQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSAGRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKA---SGTAPMVVLATAHPAKFPDAVKAACGVE

1kl7A

0.33

10.00

1.71

CNFpred

KVKFVVPSGNFGDILAGYFAKKMGLPIKLAIATNENDILDRFLKSGLYERSDKVAATLSPAMDILISSNFERLLWYLARKAGEIVNNWFQELKTNGKFQVDKSIIEGASKDFTSERVSNEETSETIKKIYESSHYILDPHTAVGVCATERLIAKDNKSIQYISLSTAHPAKFADAVNNALSGF

1kl7A2

0.31

9.40

1.33

DEthreader

KVKFVVPSGNFGDILAGYFAKKGLPIEKLAIATNENDILDRFLKSGLYERSDKVAATLSPA-DILISSNFERLLWYLAREDAGIVNNWFQELKTNGKFQVDKSIIEGASKDFTSERVSNEETSETIKKIYESPHYILDPHTAVGVCATERLIAKNDKSIQYISLSTAHPAKFADAVNNALYSF

(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	0.8382

(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	1kl7A	0.96	0.90	0.331	0.989	model1_1kl7A.pdb.gz
2	4f4fA	0.94	1.02	0.330	0.978	model1_4f4fA.pdb.gz
3	3v7nA1	0.83	1.64	0.268	0.896	model1_3v7nA1.pdb.gz
4	1vb3A	0.78	1.66	0.359	0.836	model1_1vb3A.pdb.gz
5	1v7cA	0.70	2.27	0.192	0.792	model1_1v7cA.pdb.gz
6	2d1fA	0.70	2.21	0.171	0.787	model1_2d1fA.pdb.gz
7	2zsjA	0.69	2.24	0.185	0.787	model1_2zsjA.pdb.gz
8	1e5xA	0.60	2.55	0.198	0.705	model1_1e5xA.pdb.gz
9	1wvgA	0.40	5.11	0.057	0.650	model1_1wvgA.pdb.gz
10	3el3A2	0.36	5.64	0.050	0.639	model1_3el3A2.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:0030170	1.00	pyridoxal phosphate binding
GO:0004795	1.00	threonine synthase 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:0009088	1.00	threonine biosynthetic 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:0044424	1.00	intracellular part
GO:0005737	0.99	cytoplasm
GO:0044444	0.64	cytoplasmic part

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	2rhgB	0.653	2.72	0.101	0.787	4.2.1.20	NA
2	0.060	1uiqD	0.700	2.24	0.192	0.792	4.2.3.1	12,64
3	0.060	1tzmC	0.569	3.29	0.072	0.716	3.5.99.7	NA
4	0.060	1x1qA	0.617	3.04	0.121	0.765	4.2.1.20	NA
5	0.060	1d6sA	0.679	2.44	0.146	0.787	2.5.1.47 4.2.99.8	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:

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
	1	0.49	1kl7A	0.973	0.90	0.333	1.000	1.01	PLP	complex1.pdb.gz	8,9,10,11,12,13,61,62,140,166,167

	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.