D-I-TASSER O60256-D1

D-I-TASSER results for O60256-D1

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

Input Sequence in FASTA format

>O60256 (163 residues)
MFCVTPPELETKMNITKGGLVLFSANSNSSCMELSKKIAERLGVEMGKVQVYQEPNRETR
VQIQESVRGKDVFIIQTVSKDVNTTIMELLIMVYACKTSCAKSIIGVIPYFPYSKQCKMR
KRGSIVSKLLASMMCKAGLTHLITMDLHQKEIQGFFNIPVDNL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MFCVTPPELETKMNITKGGLVLFSANSNSSCMELSKKIAERLGVEMGKVQVYQEPNRETRVQIQESVRGKDVFIIQTVSKDVNTTIMELLIMVYACKTSCAKSIIGVIPYFPYSKQCKMRKRGSIVSKLLASMMCKAGLTHLITMDLHQKEIQGFFNIPVDNL
Prediction	CCCCCCCCCCCCCCCCCCCSSSSSSCCCCCHHHHHHHHHHHHCCCCSSSSSSSCCCCCSSSSSCCCCCCCSSSSSSCCCCCCCHHHHHHHHHHHHHHHHCCCSSSSSSCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCSSSSSCCCCHHHCCCCCCSCCCC
Confidence	9867798776677789998799982699984999999999979973447999749981899857766798299997299986558999999999999936985899943666433456678876039999999998199989997188667748177806889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MFCVTPPELETKMNITKGGLVLFSANSNSSCMELSKKIAERLGVEMGKVQVYQEPNRETRVQIQESVRGKDVFIIQTVSKDVNTTIMELLIMVYACKTSCAKSIIGVIPYFPYSKQCKMRKRGSIVSKLLASMMCKAGLTHLITMDLHQKEIQGFFNIPVDNL
Prediction	7435444626551446543010000112453450043007317152151315425421130305550443200000012433142102112113004424043000000001123334344333221320032134340100000001264036217133637
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCSSSSSSCCCCCHHHHHHHHHHHHCCCCSSSSSSSCCCCCSSSSSCCCCCCCSSSSSSCCCCCCCHHHHHHHHHHHHHHHHCCCSSSSSSCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCSSSSSCCCCHHHCCCCCCSCCCC
MFCVTPPELETKMNITKGGLVLFSANSNSSCMELSKKIAERLGVEMGKVQVYQEPNRETRVQIQESVRGKDVFIIQTVSKDVNTTIMELLIMVYACKTSCAKSIIGVIPYFPYSKQCKMRKRGSIVSKLLASMMCKAGLTHLITMDLHQKEIQGFFNIPVDNL

5t3oA1

0.41

0.36

10.48

1.33

DEthreader

---------------P---LLIFSGQS---NRPLAQAIAEALGLPLGKSTTLRFANDNLFVRYEESLREGDVFIVQSFVPPVQDHLMELLMMVDAAKGASAARVTAVIPYFSYARSDKKDPRISITARLIADLLQTAGADRVLTMTLHSPQVHGFFKIPVDHL

5t3oA1

0.42

0.36

10.64

2.38

SPARKS-K

------------------PLLIFSGQSN---RPLAQAIAEALGLPLGKSTTLRFANDNLFVRYEESLREGDVFIVQSFVPPVQDHLMELLMMVDAAKGASAARVTAVIPYFSYARSDKKAPRISITARLIADLLQTAGADRVLTMTLHSPQVHGFFKIPVDHL

4s2uA

0.41

0.36

10.48

0.84

MapAlign

-----------------PDMKLFAGNA---TPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVARVPITAKVVADFLSSVGVDRVLTVDLHAEQIQGFFDVPVDNV

4s2uA1

0.41

0.36

10.48

0.70

CEthreader

-----------------PDMKLFAGNA---TPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVARVPITAKVVADFLSSVGVDRVLTVDLHAEQIQGFFDVPVDNV

2c4kA1

0.74

0.66

18.78

2.59

MUSTER

------------------GYRVFSANSTAACTELAKRITERLGAELGKSVVYQETNGETRVEIKESVRGQDIFIIQTIPRDVNTAVMELLIMAYALKTACARNIIGVIPYFPYSKQSKMRKRGSIVCKLLASMLAKAGLTHIITMDLHQKEIQGFFSFPVDNL

1dkrB

0.46

0.42

12.18

2.75

HHsearch

-----------SNQYGDKNLKIFSLNS---NPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKASREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHL

2c4kA1

0.74

0.66

18.61

2.26

FFAS-3D

-------------------YRVFSANSTAACTELAKRITERLGAELGKSVVYQETNGETRVEIKESVRGQDIFIIQTIPRDVNTAVMELLIMAYALKTACARNIIGVIPYFPYSKQSKMRKRGSIVCKLLASMLAKAGLTHIITMDLHQKEIQGFFSFPVDNL

1dkrB

0.45

0.41

12.01

0.78

EigenThreader

-----------SNQYGDKNLKIFSLNS---NPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHL

2c4kA

0.74

0.66

18.78

1.97

CNFpred

------------------GYRVFSANSTAACTELAKRITERLGAELGKSVVYQETNGETRVEIKESVRGQDIFIIQTIPRDVNTAVMELLIMAYALKTACARNIIGVIPYFPYSKQSKMRKRGSIVCKLLASMLAKAGLTHIITMDLHQKEIQGFFSFPVDNL

5t3oA

0.40

0.35

10.31

1.33

DEthreader

---------------P---LLIFSGQS---NRPLAQAIAEALGLPLGKSTTLRFANDNLFVRYEESLREGDVFIVQSFVPPVQDHLMELLMMVDAAKGASAARVTAVIPYFSYARSDKKDAPISITARLIADLLQTAGADRVLTMTLHSPQVHGFFKIPVDHL

(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	0.905

(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	2c4kA	0.88	0.61	0.745	0.890	model1_2c4kA.pdb.gz
2	5mp7A	0.85	0.87	0.364	0.877	model1_5mp7A.pdb.gz
3	2hcrB1	0.85	0.79	0.521	0.871	model1_2hcrB1.pdb.gz
4	4s2uA1	0.85	1.08	0.406	0.877	model1_4s2uA1.pdb.gz
5	1dkrB1	0.84	1.80	0.456	0.902	model1_1dkrB1.pdb.gz
6	3dahC1	0.84	1.06	0.444	0.871	model1_3dahC1.pdb.gz
7	4twbA1	0.81	1.35	0.191	0.865	model1_4twbA1.pdb.gz
8	1u9yA1	0.78	1.61	0.266	0.853	model1_1u9yA1.pdb.gz
9	3lpnA2	0.59	2.93	0.100	0.730	model1_3lpnA2.pdb.gz
10	1jlrA	0.55	3.00	0.063	0.693	model1_1jlrA.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	0.90	catalytic activity
GO:0016740	0.87	transferase activity
GO:0004749	0.86	ribose phosphate diphosphokinase activity
GO:1901363	0.66	heterocyclic compound binding
GO:0097159	0.66	organic cyclic compound binding
GO:0036094	0.58	small molecule binding
GO:0000166	0.57	nucleotide binding
GO:0035639	0.56	purine ribonucleoside triphosphate binding
GO:0032555	0.56	purine ribonucleotide binding
GO:0032550	0.56	purine ribonucleoside binding
GO:0005524	0.54	ATP 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:0009987	0.91	cellular process
GO:0008152	0.90	metabolic process
GO:0071704	0.87	organic substance metabolic process
GO:0044237	0.87	cellular metabolic process
GO:0044699	0.81	single-organism process
GO:0044238	0.73	primary metabolic process
GO:0006807	0.69	nitrogen compound metabolic process
GO:1901576	0.65	organic substance biosynthetic process
GO:0034641	0.63	cellular nitrogen compound metabolic process
GO:0044710	0.59	single-organism metabolic process
GO:0006139	0.59	nucleobase-containing compound metabolic process
GO:0044281	0.57	small molecule metabolic process
GO:0019637	0.57	organophosphate metabolic process
GO:0006796	0.57	phosphate-containing compound metabolic process
GO:0044763	0.56	single-organism cellular process
GO:0090407	0.54	organophosphate biosynthetic process
GO:1901135	0.50	carbohydrate derivative metabolic 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:0044464	0.95	cell part
GO:0044424	0.89	intracellular part
GO:0044444	0.65	cytoplasmic part
GO:0032991	0.58	macromolecular complex
GO:0043234	0.56	protein complex
GO:1990234	0.53	transferase complex
GO:0061695	0.52	transferase complex, transferring phosphorus-containing groups
GO:0043226	0.52	organelle
GO:0002189	0.51	ribose phosphate diphosphokinase complex

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	2w5fB	0.571	4.06	0.058	0.816	3.2.1.8	127,132
2	0.060	3hg3A	0.578	3.22	0.069	0.755	3.2.1.22	153
3	0.060	3dzcA	0.578	3.27	0.076	0.767	5.1.3.14	NA
4	0.060	1ktbA	0.575	3.25	0.069	0.761	3.2.1.49	146
5	0.060	3dahC	0.841	1.06	0.444	0.871	2.7.6.1	65

	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	0.13	1u9zA	0.787	1.51	0.266	0.853	0.22	R5P	complex1.pdb.gz	96,98,104
2	0.02	1v1bA	0.580	3.74	0.104	0.810	0.21	ATP	complex2.pdb.gz	94,97,98
3	0.02	1v1aA	0.581	3.65	0.105	0.804	0.40	ADP	complex3.pdb.gz	67,69,71
4	0.02	1ofu1	0.575	3.41	0.126	0.767	0.13	III	complex4.pdb.gz	70,71,72,139,141,142,143
5	0.02	1v1aB	0.586	3.56	0.105	0.804	0.24	ADP	complex5.pdb.gz	67,69,71,73,95,96
6	0.01	2vawA	0.583	3.75	0.090	0.797	0.16	GDP	complex6.pdb.gz	135,136,137,138,153,157
7	0.01	1jhqA	0.580	3.69	0.076	0.797	0.24	PMO	complex7.pdb.gz	73,90,138,139,141
8	0.01	1jhaA	0.581	3.68	0.076	0.797	0.24	NIO	complex8.pdb.gz	93,138,139,140
9	0.01	1d0vA	0.580	3.69	0.076	0.797	0.20	NIO	complex9.pdb.gz	138,139,140
10	0.01	2z4tA	0.582	4.04	0.060	0.859	0.31	C5P	complex10.pdb.gz	67,68,71,72,73,74,138,139

	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.