D-I-TASSER P41240-D2

D-I-TASSER results for P41240-D2

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

Input Sequence in FASTA format

>P41240 (104 residues)
TKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSCDGKVEHYRIMYH
ASKLSIDEEVYFENLMQLVEHYTSDADGLCTRLIKPKVMEGTVA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| TKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSCDGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTSDADGLCTRLIKPKVMEGTVA
Prediction	CCCCCCCCCCCCCCHHHHHHHHCCCCCCSSSSSCCCCCCCCSSSSSSSCCSSSSSSSSSSCCSSSSCCCCCSCCHHHHHHHHHHCCCCCCSSCCCSSCCCCCCC
Confidence	98432887289999999999972799980999827899992999999899899999998299699859831299999999984487998235572104789999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| TKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSCDGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTSDADGLCTRLIKPKVMEGTVA
Prediction	87367354133714274035305757503000020554421000002377402001023575312037634173474256114644441424534124466568
	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

CCCCCCCCCCCCCCHHHHHHHHCCCCCCSSSSSCCCCCCCCSSSSSSSCCSSSSSSSSSSCCSSSSCCCCCSCCHHHHHHHHHHCCCCCCSSCCCSSCCCCCCC
TKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSCDGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTSDADGLCTRLIKPKVMEGTVA

4fl2A

0.28

8.51

1.33

DEthreader

S-ANHLPFFFGNITREEAEDYLVGMSDGLYLLRQSR-NYLGFALSVAHGRKAHHYTIERENGTYAIAGGRTHASPADLCHYHSQESDGLVCLLKKPFNRQVQPY

1jwoA

0.57

0.53

15.21

2.83

SPARKS-K

--LSLMPWFHGKISGQEAVQQLQPPEDGLFLVRESARHPGDYVLCVSFGRDVIHYRVLHRDGHLTIDEAVFFCNLMDMVEHYSKDKGAICTKLVRPKRK-----

2dlyA

0.40

0.38

11.06

0.74

MapAlign

--LQAEPWFFGAIKRADAEKQLLYNQTGAFLIRESESQKGDFSLSVLDEGVVKHYRIRRLEGGFFLTRRKVFSTLNEFVNYYTTTSDGLCVKLEKPCLK-----

2dlyA

0.38

11.12

0.49

CEthreader

RSLQAEPWFFGAIKRADAEKQLLYNQTGAFLIRESESQKGDFSLSVLDEGVVKHYRIRRLEGGFFLTRRKVFSTLNEFVNYYTTTSDGLCVKLEKPCLKIQVSG

1k9aB3

0.98

27.48

2.05

MUSTER

TKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSCEGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTTDADGLCTRLIKPKVMEGTVA

1k9aB

0.98

27.48

1.37

HHsearch

TKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSCEGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTTDADGLCTRLIKPKVMEGTVA

1k9aB3

0.98

0.97

27.21

1.90

FFAS-3D

TKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSCEGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTTDADGLCTRLIKPKVMEGTV-

3hhmB1

0.26

8.00

1.02

EigenThreader

MSLQNAEWYWGDISREEVNEKLRDTADGTFLVRDAS-TKGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLKLDVKLLYPVSKYQQQV

3eazA

0.99

0.95

26.66

2.03

CNFpred

TKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSSDGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTSDADGLCTRLIKPKVME----

4fl2A1

0.28

8.51

1.33

DEthreader

S-ANHLPFFFGNITREEAEDYLVGMSDGLYLLRQSR-NYLGFALSVAHGRKAHHYTIERENGTYAIAGGRTHASPADLCHYHSQESDGLVCLLKKPFNRQVQPY

(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	0.8141

(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	2ozoA1	0.91	1.43	0.298	1.000	model1_2ozoA1.pdb.gz
2	1a81A	0.91	1.44	0.320	0.990	model1_1a81A.pdb.gz
3	4fl2A	0.91	1.33	0.304	0.981	model1_4fl2A.pdb.gz
4	2ptkA	0.90	1.61	0.394	0.981	model1_2ptkA.pdb.gz
5	1k9aB	0.90	1.77	0.923	0.981	model1_1k9aB.pdb.gz
6	2dlyA	0.90	1.53	0.379	0.990	model1_2dlyA.pdb.gz
7	1jwoA	0.89	0.72	0.531	0.923	model1_1jwoA.pdb.gz
8	1nrvA	0.89	0.90	0.289	0.933	model1_1nrvA.pdb.gz
9	4tziA	0.88	1.30	0.333	0.952	model1_4tziA.pdb.gz
10	1qcfA	0.88	1.68	0.327	0.981	model1_1qcfA.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:0003824	0.73	catalytic activity
GO:0005102	0.72	receptor binding
GO:0016740	0.66	transferase activity
GO:0016773	0.65	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.65	kinase activity
GO:0004672	0.63	protein kinase activity
GO:0004713	0.62	protein tyrosine kinase activity
GO:0004715	0.60	non-membrane spanning protein tyrosine kinase 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:0050789	0.95	regulation of biological process
GO:0050794	0.94	regulation of cellular process
GO:0009987	0.83	cellular process
GO:0044699	0.80	single-organism process
GO:0007165	0.79	signal transduction
GO:0008152	0.75	metabolic process
GO:0071704	0.74	organic substance metabolic process
GO:0007166	0.74	cell surface receptor signaling pathway
GO:0044763	0.73	single-organism cellular process
GO:0044238	0.73	primary metabolic process
GO:0044237	0.73	cellular metabolic process
GO:0007169	0.68	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0043170	0.67	macromolecule metabolic process
GO:0044260	0.66	cellular macromolecule metabolic process
GO:0006796	0.64	phosphate-containing compound metabolic process
GO:0050896	0.61	response to stimulus
GO:0016310	0.61	phosphorylation
GO:0019538	0.59	protein metabolic process
GO:0002376	0.59	immune system process
GO:0006464	0.58	cellular protein modification process
GO:0006950	0.57	response to stress
GO:0048869	0.56	cellular developmental process
GO:0042127	0.56	regulation of cell proliferation
GO:0006468	0.56	protein phosphorylation
GO:0018108	0.54	peptidyl-tyrosine phosphorylation
GO:0006955	0.54	immune response
GO:0045087	0.53	innate immune response
GO:0038083	0.53	peptidyl-tyrosine autophosphorylation
GO:0030154	0.52	cell differentiation
GO:0048583	0.50	regulation of response to stimulus

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:0044424	0.95	intracellular part
GO:0044425	0.72	membrane part
GO:0044459	0.64	plasma membrane part
GO:0031234	0.60	extrinsic component of cytoplasmic side 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	0.482	1lkkA	0.855	1.52	0.381	0.933	2.7.10.2	8,15,19,35,52,54,66,75,79,89,96
2	0.474	1h9oA	0.813	1.70	0.327	0.904	2.7.10.1	NA
3	0.396	2yu7A	0.813	1.97	0.298	0.942	3.1.3.48	8,10,34,58,75,96
4	0.089	1csyA	0.794	2.28	0.451	0.962	2.7.10.2	6,8,10,13,15,19,42,52,54,56,66,75,79,89,96
5	0.071	1fyrA	0.566	1.89	0.269	0.635	2.7.10.1	8,15,19,22,28,30,35,44,46,52,54

	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	0.69	1a08B	0.879	0.94	0.417	0.923	1.49	III	complex1.pdb.gz	15,33,35,36,37,43,54,55,56,88
2	0.53	1shdA	0.857	0.88	0.419	0.894	1.40	III	complex2.pdb.gz	15,33,43,53,54,55,56,58,66,67,87,88,89
3	0.43	1o4oA	0.882	1.13	0.408	0.942	1.15	HPS	complex3.pdb.gz	33,35,36,43,56
4	0.08	1o4oA	0.882	1.13	0.408	0.942	0.88	HPS	complex4.pdb.gz	53,88,89,90

	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.