D-I-TASSER Q07325-D1

D-I-TASSER results for Q07325-D1

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

Input Sequence in FASTA format

>Q07325 (125 residues)
MKKSGVLFLLGIILLVLIGVQGTPVVRKGRCSCISTNQGTIHLQSLKDLKQFAPSPSCEK
IEIIATLKNGVQTCLNPDSADVKELIKKWEKQVSQKKKQKNGKKHQKKKVLKVRKSQRSR
QKKTT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MKKSGVLFLLGIILLVLIGVQGTPVVRKGRCSCISTNQGTIHLQSLKDLKQFAPSPSCEKIEIIATLKNGVQTCLNPDSADVKELIKKWEKQVSQKKKQKNGKKHQKKKVLKVRKSQRSRQKKTT
Prediction	CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCSSCCCCCCCCCHHHSSSSSSSCCCCCCCCCSSSSSSCCCCSSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCC
Confidence	97159999999999999986355557887412034115856964610889972999999735899972897896699969999999999999988887632221111345555666783021279
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MKKSGVLFLLGIILLVLIGVQGTPVVRKGRCSCISTNQGTIHLQSLKDLKQFAPSPSCEKIEIIATLKNGVQTCLNPDSADVKELIKKWEKQVSQKKKQKNGKKHQKKKVLKVRKSQRSRQKKTT
Prediction	74321001131120011131323433573304134344540425305504334434506443010103565421022726204400530364445556554554555654464755744566668
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCSSCCCCCCCCCHHHSSSSSSSCCCCCCCCCSSSSSSCCCCSSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCC
MKKSGVLFLLGIILLVLIGVQGTPVVRKGRCSCISTNQGTIHLQSLKDLKQFAPSPSCEKIEIIATLKNGVQTCLNPDSADVKELIKKWEKQVSQKKKQKNGKKHQKKKVLKVRKSQRSRQKKTT

7ay1A

0.09

0.08

3.01

0.83

DEthreader

VIQAEIPPLVHVEGTNSVHSWIHEMIRQELVKVTEFYLSFLPLQTVQRKAQPLL---SMSMR------------CLILLAVGFLLLKG-DDGQN-PEKIFQNCDITLLQFLVTLFCKTAPT-PS-

4zaiA

0.17

0.11

3.66

2.29

SPARKS-K

-------------------MVLEVYYTSLRCRCVQESSVFIPRRFIDRIQILPRGNGCPRKEIIVWKKNKSIVCVDPQAEWIQRMMEVLRKRSSSTLPV--------------------------

1mgsA

0.44

0.22

6.55

0.76

MapAlign

----------------------------LRCQCLQTLQG-IHPKNIQSVNVKSPGPHCAQTEVIATLKNGRKACLNPASPIVKKIIEKMLNS---------------------------------

1mgsA

0.40

0.23

6.85

0.75

CEthreader

----------------------ASVATELRCQCLQTLQG-IHPKNIQSVNVKSPGPHCAQTEVIATLKNGRKACLNPASPIVKKIIEKMLNSDKSN-----------------------------

6ehzA

0.27

0.21

6.40

1.87

MUSTER

----------------------KPVSLSYRCPCRFFES-HIARANVKHLKIL-NTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNKGRREEKVGKKEKIGKKKRQKKRKAAQKRKN---

1ilqA

0.30

0.17

5.10

1.95

HHsearch

-------------------------AKELRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDPKENWVQRVVEKFLKRAENS-----------------------------

1ilqA

0.30

0.17

5.09

1.07

FFAS-3D

--------------------------KELRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDPKENWVQRVVEKFLKRAEN------------------------------

1j9oA

0.13

0.10

3.34

0.75

EigenThreader

----------------------VGSEVSDKRTCVSLTTQRLPVSRIKTYTIT----EGSLRAVIFITKRGLKVCADPQATWVRDVVRSMDRKS---NTRNNMIQTKPT---GTQQSTNTAVTLTG

1icwA

0.28

0.15

4.66

1.42

CNFpred

---------------------------ELRCQCIKTYSKPFHPKFIKELRVIESGPHCANTCIIVKLSDGRELALDPKENWVQRVVEKFLKRAENS-----------------------------

1eotA

0.17

0.10

3.17

0.83

DEthreader

------------------------PASVPTTCCFNLANRKIPLQRLESYRRITSGK-CPQKAVIFKTKLAKDICADPKKKWVQDSMKYLDQKS--PTP--K------------------------

(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	0.6078

(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	4zaiA	0.50	2.04	0.175	0.584	model1_4zaiA.pdb.gz
2	1mgsA	0.50	2.36	0.370	0.576	model1_1mgsA.pdb.gz
3	3p5pA	0.50	3.94	0.093	0.728	model1_3p5pA.pdb.gz
4	1esrA	0.49	1.78	0.187	0.560	model1_1esrA.pdb.gz
5	6mnjA2	0.49	4.60	0.035	0.840	model1_6mnjA2.pdb.gz
6	1o80A	0.49	2.10	0.375	0.560	model1_1o80A.pdb.gz
7	1f2lD	0.49	1.82	0.214	0.560	model1_1f2lD.pdb.gz
8	1eihA	0.49	2.22	0.219	0.576	model1_1eihA.pdb.gz
9	1ilqA	0.48	1.63	0.296	0.544	model1_1ilqA.pdb.gz
10	1eotA	0.48	2.11	0.176	0.552	model1_1eotA.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:0045236	0.98	CXCR chemokine receptor binding
GO:0008009	0.95	chemokine 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:0050794	1.00	regulation of cellular process
GO:0048518	1.00	positive regulation of biological process
GO:0002376	0.97	immune system process
GO:0050896	0.94	response to stimulus
GO:0048522	0.94	positive regulation of cellular process
GO:0040017	0.94	positive regulation of locomotion
GO:0032879	0.93	regulation of localization
GO:0048583	0.92	regulation of response to stimulus
GO:0030335	0.92	positive regulation of cell migration
GO:0048584	0.91	positive regulation of response to stimulus
GO:0042127	0.91	regulation of cell proliferation
GO:0007165	0.91	signal transduction
GO:0002687	0.91	positive regulation of leukocyte migration
GO:0050920	0.90	regulation of chemotaxis
GO:0050921	0.89	positive regulation of chemotaxis
GO:0007186	0.89	G-protein coupled receptor signaling pathway
GO:0006950	0.89	response to stress
GO:1901700	0.88	response to oxygen-containing compound
GO:0010033	0.88	response to organic substance
GO:0019221	0.87	cytokine-mediated signaling pathway
GO:0070098	0.86	chemokine-mediated signaling pathway
GO:0043207	0.86	response to external biotic stimulus
GO:0002690	0.86	positive regulation of leukocyte chemotaxis
GO:0032496	0.85	response to lipopolysaccharide
GO:0006955	0.85	immune response
GO:0006952	0.85	defense response
GO:0006954	0.84	inflammatory response
GO:0009987	0.51	cellular process
GO:0044699	0.50	single-organism 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:0005615	0.98	extracellular space
GO:0044464	0.67	cell 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	2rd0A	0.445	4.38	0.018	0.736	2.7.1.153	63
2	0.060	2e1qA	0.423	4.93	0.105	0.736	1.17.3.2 1.17.1.4	NA
3	0.060	1tz3A	0.420	4.80	0.045	0.768	2.7.1.4	NA
4	0.060	2aw5B	0.458	4.75	0.026	0.792	1.1.1.40	NA
5	0.060	2i6aA	0.455	4.59	0.038	0.800	2.7.1.20	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	0.08	1ilpA	0.482	1.65	0.296	0.544	1.28	III	complex1.pdb.gz	32,34,35,36,37,39,40,41,42,44,45,64,67,71,72,73,74
2	0.04	1icw0	0.494	1.53	0.275	0.552	0.90	III	complex2.pdb.gz	47,48,49,50,51,53,54,61,78,83,86
3	0.04	1nr40	0.449	2.22	0.242	0.528	1.15	III	complex3.pdb.gz	29,32,33,34,35,36,37,47,50,66,70,72,74
4	0.03	1dok0	0.469	1.73	0.181	0.528	1.13	III	complex4.pdb.gz	29,31,34,35,36,37,45,57,64,67,69,71,72,73,74

	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.