D-I-TASSER P43652-D4

D-I-TASSER results for P43652-D4

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

Input Sequence in FASTA format

>P43652 (117 residues)
RAIPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSS
NYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKIPERGQCIINSNKDD

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| RAIPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKIPERGQCIINSNKDD
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCHHHHHHHCCCCC
Confidence	936899999999999998999999968789999999999943799999999999999999999801788899997799999999724443463789986398632899997487899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| RAIPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKIPERGQCIINSNKDD
Prediction	846513630440233163203304623551241231031044236161740350053025115511532224025524611540175365346404611746335343014416688
	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

CCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCHHHHHHHCCCCC
RAIPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKIPERGQCIINSNKDD

5oklA

0.86

24.31

1.33

DEthreader

HFAPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKPERGQCIINSNKDDR

5oklA3

1.00

28.00

2.15

SPARKS-K

RAIPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKIPERGQCIINSNKDD

5oklA

1.00

0.97

27.28

1.24

MapAlign

---PVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKIPERGQCIINSNKDD

5oklA3

1.00

28.00

1.11

CEthreader

RAIPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKIPERGQCIINSNKDD

5oklA3

1.00

28.00

2.15

MUSTER

RAIPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKIPERGQCIINSNKDD

5oklA3

1.00

28.00

3.17

HHsearch

RAIPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKIPERGQCIINSNKDD

5oklA3

1.00

28.00

1.90

FFAS-3D

RAIPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKIPERGQCIINSNKDD

5oklA3

1.00

28.00

1.25

EigenThreader

RAIPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKIPERGQCIINSNKDD

5oklA

1.00

28.00

1.49

CNFpred

RAIPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKIPERGQCIINSNKDD

5oklA3

0.90

0.89

24.99

1.33

DEthreader

RAIPVTQYLKAFSSYQKHVCGALLKFGTKVVHFIYIAILSQKFPKIEFKELISLVEDVSSNYDGCCEGDVVQCIRDTSKVMNHICSKQDSISSKIKECCEKKPERGQCIINSNKD-D

(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	0.957

(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	5oklA3	0.98	0.61	1.000	1.000	model1_5oklA3.pdb.gz
2	7yimA	0.92	1.25	0.436	1.000	model1_7yimA.pdb.gz
3	1n5uA	0.89	1.64	0.402	1.000	model1_1n5uA.pdb.gz
4	1kw2A	0.72	2.89	0.152	0.932	model1_1kw2A.pdb.gz
5	8b4oB	0.59	3.87	0.018	0.906	model1_8b4oB.pdb.gz
6	7qa8A	0.59	4.16	0.055	0.940	model1_7qa8A.pdb.gz
7	3gtdA	0.58	3.94	0.052	0.914	model1_3gtdA.pdb.gz
8	2e9fB	0.58	3.87	0.069	0.897	model1_2e9fB.pdb.gz
9	1j3uA	0.58	3.86	0.070	0.880	model1_1j3uA.pdb.gz
10	3e04D	0.58	3.90	0.026	0.914	model1_3e04D.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:0097159	0.90	organic cyclic compound binding
GO:1901363	0.83	heterocyclic compound binding
GO:0008289	0.63	lipid binding
GO:0043167	0.61	ion binding
GO:0003676	0.54	nucleic acid binding
GO:0030170	0.53	pyridoxal phosphate binding
GO:0019825	0.53	oxygen binding
GO:0015643	0.53	toxic substance binding
GO:0008144	0.53	drug binding
GO:0005504	0.53	fatty acid binding
GO:0003677	0.53	DNA binding
GO:0036094	0.52	small molecule 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:0044699	1.00	single-organism process
GO:0051179	0.90	localization
GO:1902578	0.89	single-organism localization
GO:0065007	0.72	biological regulation
GO:0009987	0.71	cellular process
GO:0050789	0.67	regulation of biological process
GO:0050896	0.65	response to stimulus
GO:0065008	0.64	regulation of biological quality
GO:0044763	0.64	single-organism cellular process
GO:0050794	0.63	regulation of cellular process
GO:0051704	0.62	multi-organism process
GO:0048519	0.60	negative regulation of biological process
GO:0048523	0.57	negative regulation of cellular process
GO:0009605	0.57	response to external stimulus
GO:0031667	0.56	response to nutrient levels
GO:0051716	0.55	cellular response to stimulus
GO:0044764	0.55	multi-organism cellular process
GO:0044419	0.55	interspecies interaction between organisms
GO:0010941	0.55	regulation of cell death
GO:0006950	0.55	response to stress
GO:0051659	0.54	maintenance of mitochondrion location
GO:0043066	0.54	negative regulation of apoptotic process
GO:0019836	0.54	hemolysis by symbiont of host erythrocytes
GO:0009267	0.54	cellular response to starvation

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	0.64	cell part
GO:0044421	0.62	extracellular region part
GO:0005615	0.57	extracellular space
GO:0044424	0.54	intracellular part
GO:0005576	0.51	extracellular region

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	2z36B	0.525	3.55	0.038	0.752	1.-.-.-	33
2	0.060	1rw9A	0.520	3.68	0.009	0.769	4.2.2.5	NA
3	0.060	1k7wD	0.422	4.31	0.058	0.692	4.3.2.1	67
4	0.060	2uvnA	0.538	4.47	0.018	0.863	1.14.-.-	NA
5	0.060	1gu6A	0.550	3.76	0.039	0.778	1.7.2.2	32

	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	0.42	2xvvA	0.908	1.47	0.402	1.000	1.20	9DN	complex1.pdb.gz	19,34,39,42,58,77,80,107
2	0.42	2bxbA	0.937	1.08	0.402	1.000	1.07	OPB	complex2.pdb.gz	16,19,34,38,42,58,62,77,81,107,110
3	0.40	2bxnA	0.895	1.59	0.402	1.000	0.81	IDB	complex3.pdb.gz	18,19,22,31,34,38,39,43,58,62,77,80
4	0.10	1e7cA	0.892	1.62	0.402	1.000	1.14	HLT	complex4.pdb.gz	29,56,59,60,63
5	0.10	2vufB	0.943	1.01	0.402	1.000	0.87	FUA	complex5.pdb.gz	21,31,32,58,59,62,63,66

	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.