D-I-TASSER Q70J99-D5

D-I-TASSER results for Q70J99-D5

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

Input Sequence in FASTA format

>Q70J99 (117 residues)
GIAKHIQKLVGVRESVLPEDAILPLMKFLEVELCYMNTNLVQENFSSLLTLLWTHTLTVL
VEAAASQRSSSLASNRLKIALQNLEICFHAEGCGLPPKALHTATFQALQRDLELQAA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| GIAKHIQKLVGVRESVLPEDAILPLMKFLEVELCYMNTNLVQENFSSLLTLLWTHTLTVLVEAAASQRSSSLASNRLKIALQNLEICFHAEGCGLPPKALHTATFQALQRDLELQAA
Prediction	CHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCHHHHHHHHHHHHHCC
Confidence	867888876238876787899999999999999999999619999999999999999999999606899738999999999999999724788999887255589999999877409
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| GIAKHIQKLVGVRESVLPEDAILPLMKFLEVELCYMNTNLVQENFSSLLTLLWTHTLTVLVEAAASQRSSSLASNRLKIALQNLEICFHAEGCGLPPKALHTATFQALQRDLELQAA
Prediction	834521441343466343650032015214620430353024600430043005301420352157655445115303400520241042545414374163740540363054378
	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

                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCHHHHHHHHHHHHHCC
GIAKHIQKLVGVRESVLPEDAILPLMKFLEVELCYMNTNLVQENFSSLLTLLWTHTLTVLVEAAASQRSSSLASNRLKIALQNLEICFHAEGCGLPPKALHTATFQALQRDLELQAA

4y21A

0.21

6.77

1.33

DEthreader

SFQPHIEECVRQDSQVDADNVLQPIMDLLDSNLTLFAKICEKTVLKRVLKELWKLVMNTMERTVLPPAKSLTQCAVVELALDTIKQYFHAGGVGLKKTFLKSPDLQSLRYALSLYTQ

3swhA2

0.18

5.83

1.51

SPARKS-K

HIEECVRQMGDISVAQDADNVLQPIMDLLDSNLTLFAKICEKTVLKRVLKELWKLVMNTMERTIVFSKLKPKQCAVVELALDTIKQYFHAGGVGLKKTFLESPDLQSLRYALSLY--

3swhA1

0.10

0.09

3.50

0.89

MapAlign

VSRDFLHGALQTSEHALFSCSVVDVFSQLNQSFEIIKKGHYMRRFAKTISNVLLQYADIVSKDFASYCEKEKVPCILMNNTQQLRVQLEMFEAMLKE-LQ--VKLNNVLDELSHVF-

4y21A3

0.18

5.85

0.80

CEthreader

HIEECVRQMGDISVAQDADNVLQPIMDLLDSNLTLFAKICEKTVLKRVLKELWKLVMNTMERTIVLKSLTPKQCAVVELALDTIKQYFHAGGVGLKKTFLESPDLQSLRYALSLYTQ

5ue8A

0.20

0.19

6.02

1.06

MUSTER

HIEECVRQMGDILSQVDADNVLQPIMDLLDSNLTLFAKICEKTVLKRVLKELWKLVMNTMERTI-------KQCAVVELALDTIKQYFHAGGVGLKKTFLKSPDLQSLRYALSLYTQ

5ue8A2

0.19

0.18

5.79

2.71

HHsearch

HIEECVRQMGDILSAQDADNVLQPIMDLLDSNLTLFAKICEKTVLKRVLKELWKLVMNTMERTI-------KQCAVVELALDTIKQYFHAGGVGLKKTFLKSPDLQSLRYALSLYTQ

4y21A3

0.18

5.84

1.57

FFAS-3D

-IEECVRQMGCSSVAQDADNVLQPIMDLLDSNLTLFAKICEKTVLKRVLKELWKLVMNTMERTIVLPSLTPKQCAVVELALDTIKQYFHAGGVGLKKTFLESPDLQSLRYALSLYTQ

4y21A3

0.19

6.08

1.02

EigenThreader

HIEECVRQMGDILSQVDADNVLQPIMDLLDSNLTLFAKICEKTVLKRVLKELWKLVMNTMERTIVLKSLTPKQCAVVELALDTIKQYFHAGGVGLKKTFLEKSDLQSLRYALSLYTQ

3swhA

0.19

0.18

5.80

0.81

CNFpred

HIEECVRQMGDIL--QDADNVLQPIMDLLDSNLTLFAKICEKTVLKRVLKELWKLVMNTMERTIVLPPE-PKQCAVVELALDTIKQYFHAGGVGLKKTFLESPDLQSLRYALSLY--

4y21A3

0.22

0.21

6.76

1.33

DEthreader

F-QPHIEECVRQDSQVDADNVLQPIMDLLDSNLTLFAKICEKTVLKRVLKELWKLVMNTMERTVLPPAKSLTKQCVVELALDTIKQYFHAGGVGLKKTFLKSPDLQSLRYALSLYTQ

(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	0.7949

(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	4y21A	0.89	1.63	0.197	1.000	model1_4y21A.pdb.gz
2	3swhA2	0.87	1.48	0.191	0.957	model1_3swhA2.pdb.gz
3	3hr0A	0.80	1.95	0.125	0.957	model1_3hr0A.pdb.gz
4	4l8tA	0.78	2.35	0.142	0.957	model1_4l8tA.pdb.gz
5	6ku0A	0.78	2.33	0.088	0.966	model1_6ku0A.pdb.gz
6	2f6hX2	0.74	2.48	0.152	0.940	model1_2f6hX2.pdb.gz
7	3wb8A2	0.74	2.50	0.102	0.923	model1_3wb8A2.pdb.gz
8	3mmiA	0.71	2.60	0.072	0.949	model1_3mmiA.pdb.gz
9	4j5mA1	0.63	3.41	0.118	0.940	model1_4j5mA1.pdb.gz
10	3j7jC	0.52	4.34	0.038	0.855	model1_3j7jC.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:0019899	0.86	enzyme binding
GO:0017137	0.85	Rab GTPase 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:0065007	0.84	biological regulation
GO:0050789	0.79	regulation of biological process
GO:0050794	0.77	regulation of cellular process
GO:0051179	0.75	localization
GO:0044699	0.74	single-organism process
GO:0006810	0.74	transport
GO:0044765	0.68	single-organism transport
GO:0046903	0.66	secretion
GO:0009987	0.63	cellular process
GO:0051049	0.54	regulation of transport
GO:0048583	0.54	regulation of response to stimulus
GO:0048518	0.54	positive regulation of biological process
GO:0048522	0.53	positive regulation of cellular process
GO:0044763	0.53	single-organism cellular process
GO:0051050	0.52	positive regulation of transport
GO:0050776	0.52	regulation of immune response
GO:0032386	0.52	regulation of intracellular transport
GO:0017157	0.52	regulation of exocytosis
GO:0002684	0.52	positive regulation of immune system process
GO:1903307	0.51	positive regulation of regulated secretory pathway
GO:0043304	0.51	regulation of mast cell degranulation

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:0044444	1.00	cytoplasmic part
GO:0043231	1.00	intracellular membrane-bounded organelle
GO:0070382	0.90	exocytic vesicle
GO:0005773	0.80	vacuole
GO:0030141	0.79	secretory granule
GO:0005764	0.79	lysosome
GO:0033093	0.78	Weibel-Palade body

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	7reqB	0.556	3.65	0.040	0.846	5.4.99.2	109
2	0.060	3kvnX	0.564	3.49	0.070	0.821	3.1.1.1	NA
3	0.060	3dsxA	0.529	3.42	0.085	0.803	2.5.1.60	NA
4	0.060	2d0tB	0.558	4.53	0.087	0.923	1.13.11.52	NA
5	0.060	3c5wA	0.531	3.10	0.044	0.778	3.1.3.16	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	0.02	3rkoM	0.582	3.98	0.087	0.983	0.33	CA7	complex1.pdb.gz	81,89,93,94
2	0.02	3m1cA	0.569	4.25	0.074	0.880	0.32	XYL	complex2.pdb.gz	29,32,91,93
3	0.01	2dqmA	0.570	4.04	0.083	0.914	0.20	BES	complex3.pdb.gz	26,29,33,49,93,94
4	0.01	3b34A	0.569	3.94	0.083	0.906	0.17	PHE	complex4.pdb.gz	29,50,94
5	0.01	2zxgA	0.571	4.06	0.093	0.914	0.13	S23	complex5.pdb.gz	83,86,87,91
6	0.01	3rkoN	0.571	4.26	0.078	0.957	0.28	LFA	complex6.pdb.gz	85,88,89
7	0.01	1g9aA	0.567	3.98	0.026	0.880	0.20	BAB	complex7.pdb.gz	50,51,53,54
8	0.01	1tyg4	0.399	3.67	0.051	0.615	0.17	III	complex8.pdb.gz	85,88,89,90
9	0.01	3perB	0.584	3.38	0.045	0.872	0.32	PO4	complex9.pdb.gz	37,91,94
10	0.01	1f31A	0.570	3.80	0.026	0.863	0.37	UUU	complex10.pdb.gz	45,46,91,93,95

	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.