D-I-TASSER P31415-D1

D-I-TASSER results for P31415-D1

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

Input Sequence in FASTA format

>P31415 (157 residues)
MSATDRMGPRAVPGLRLALLLLLVLGTPKSGVQGQEGLDFPEYDGVDRVINVNAKNYKNV
FKKYEVLALLYHEPPEDDKASQRQFEMEELILELAAQVLEDKGVGFGLVDSEKDAAVAKK
LGLTEVDSMYVFKGDEVIEYDGEFSADTIVEFLLDVL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSATDRMGPRAVPGLRLALLLLLVLGTPKSGVQGQEGLDFPEYDGVDRVINVNAKNYKNVFKKYEVLALLYHEPPEDDKASQRQFEMEELILELAAQVLEDKGVGFGLVDSEKDAAVAKKLGLTEVDSMYVFKGDEVIEYDGEFSADTIVEFLLDVL
Prediction	CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCSSSCCCHHHHHHHHHCCSSSSSSSCCCCCCHHHCHHHHHHHHHHHHHHHHHCCCCCSSSSSSCCHHHHHHHHHCCCCCCSSSSSSCCSSSSCCCCCCHHHHHHHHHHHC
Confidence	9864556642254337999999999998641132335677664798737993716599999749779999859997556554112236899999998602469649999573258899982996465599997996873489889899999999869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSATDRMGPRAVPGLRLALLLLLVLGTPKSGVQGQEGLDFPEYDGVDRVINVNAKNYKNVFKKYEVLALLYHEPPEDDKASQRQFEMEELILELAAQVLEDKGVGFGLVDSEKDAAVAKKLGLTEVDSMYVFKGDEVIEYDGEFSADTIVEFLLDVL
Prediction	7534542334213413333333233321133234556261363445630150356104500663410001000104404633452523540262036215757030020205515600652706522001003675426062614362005103525
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCSSSCCCHHHHHHHHHCCSSSSSSSCCCCCCHHHCHHHHHHHHHHHHHHHHHCCCCCSSSSSSCCHHHHHHHHHCCCCCCSSSSSSCCSSSSCCCCCCHHHHHHHHHHHC
MSATDRMGPRAVPGLRLALLLLLVLGTPKSGVQGQEGLDFPEYDGVDRVINVNAKNYKNVFKKYEVLALLYHEPPEDDKASQRQFEMEELILELAAQVLEDKGVGFGLVDSEKDAAVAKKLGLTEVDSMYVFKGDEVIEYDGEFSADTIVEFLLDVL

3f8uA

0.12

0.10

3.63

1.17

DEthreader

-----------YWRNRVMMVAKKFLHQFDGLKRYLKSEPIPESN-DGPVKVVVAENFDEINNENKDVLIEFYAPW-----CG-HCKNLEPKYKELGEKLSKDPIVIAKMDATANDVP-SPYEVRGFPTIYFSPAKNPKKYEGGRELSDFISYLQREA

2pptA

0.16

0.15

4.89

1.53

SPARKS-K

MGAKMAESLRLTCLACGQANKVPSDRLAAGPKCGICGAGLITGK----VAGIDPAILARAERDDLPLLVDFWAPWCG------PCRQMAPQFQAAAATLA-GQVRLAKIDTQAHPAVAGRHRIQGIPAFILFHKGELARAAGARPASELVGFVRGKL

2l5lA

0.16

0.11

3.60

0.50

MapAlign

--------------------------------------------GNGKVIHLTKAEFLKVYEGDKPAIVDFYADW------CGPCKMVAPILDELAKEYD-GQIVIYKVDTEKEQELAGAFGIRSIPSILFIPMEGPEMAQGAMPKASFKKAIDFLL

2dmlA

0.21

0.16

5.06

0.36

CEthreader

------------------------------GSSGSSGAVSGLYSSSDDVIELTPSNFNREVISDGLWLVEFYAPWCGH------CQRLTPEWKKAATALKDV-VKVGAVNADKHQSLGGQYGVQGFPTIKIFGKNKPEDYQGGRTGEAIVDAALSAL

3trqA

0.96

0.75

21.08

1.14

MUSTER

----------------------------------EEGLDFPEYDGVDRVINVNAKNYKNVFKKYEVLALLYHEPPEDDKASQRQFEMEELILELAAQVLEDKGVGFGLVDSEKDAAVAKKLGLTEEDSIYVFKEDEVIEYDGEFSADTLVEFLLDVL

5xf7A

0.16

0.11

3.83

1.00

HHsearch

-----------------------------------HITKPVHILEERSLLVLTPAGLTQMLNQTRFLMVLFHNPSSKQRNLAEEL-------GKAVEIMGKNGIGFGKVDITIEKELQQEFGITKAPELKLFFEGNPISCKGVVESAALVVWLRRQI

3v1wA1

0.97

0.65

18.21

2.00

FFAS-3D

-----------------------------------EGLDFPEYDGVDRVINVNAKNYKNVFKKYEVLALLYHEPPEDDKASQRQFEMEELILELAAQVLEDKGVGFGLVDSEKDAAVAKKLGLTEEDSIYVFKEDEVIEY-----------------

3idvA

0.12

0.11

4.06

0.87

EigenThreader

DKDYAPWCGHCKQFAPEYEKIANILKDKDPPIFDVSGYPPDWTPPPEVTLVLTKENFDEVVNDADIILVEFYAPWCG------HCKKLAPEYEKAAKELSKPPIPLAKVDATAETDLAKRFDVSGYPTLKIFRKGRPYDYNGPREKYGIVDYMIEQS

5creA

1.00

0.77

21.58

1.53

CNFpred

------------------------------------GLDFPEYDGVDRVINVNAKNYKNVFKKYEVLALLYHEPPEDDKASQRQFEMEELILELAAQVLEDKGVGFGLVDSEKDAAVAKKLGLTEVDSMYVFKGDEVIEYDGEFSADTIVEFLLDVL

3idvA1

0.17

0.12

3.99

1.00

DEthreader

-----------------------------------D-DLEVKE--ENGVLVLNDANFDNFVADKDTVLLEFYAPW-----CG-HCKQFAPEYEKIANILKDKPIPVAKIDATSASVLASRFDVSGYPTIKILKKGQAVDYEGSRTQEEIVAKVREVS

(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	0.731

(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	3v1wA	0.75	1.45	0.926	0.777	model1_3v1wA.pdb.gz
2	1sjiA	0.72	1.65	0.554	0.764	model1_1sjiA.pdb.gz
3	3boaA1	0.57	2.51	0.159	0.681	model1_3boaA1.pdb.gz
4	2dj1A	0.57	2.09	0.158	0.669	model1_2dj1A.pdb.gz
5	3uemA	0.56	2.87	0.122	0.681	model1_3uemA.pdb.gz
6	2r2jA	0.54	2.61	0.127	0.643	model1_2r2jA.pdb.gz
7	2k18A1	0.53	2.23	0.139	0.618	model1_2k18A1.pdb.gz
8	3ec3A1	0.48	3.02	0.112	0.624	model1_3ec3A1.pdb.gz
9	4x3mA2	0.36	3.47	0.150	0.510	model1_4x3mA2.pdb.gz
10	2qaeA1	0.32	5.20	0.036	0.560	model1_2qaeA1.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:0046872	0.85	metal ion binding
GO:0005509	0.84	calcium ion 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:0065008	1.00	regulation of biological quality
GO:0050789	0.97	regulation of biological process
GO:0060341	0.96	regulation of cellular localization
GO:0051924	0.96	regulation of calcium ion transport
GO:0050794	0.96	regulation of cellular process
GO:0010880	0.95	regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
GO:0051239	0.89	regulation of multicellular organismal process
GO:0044699	0.89	single-organism process
GO:0019722	0.88	calcium-mediated signaling
GO:0009987	0.88	cellular process
GO:0006942	0.88	regulation of striated muscle contraction
GO:0044763	0.85	single-organism cellular process
GO:0016043	0.81	cellular component organization
GO:0051258	0.80	protein polymerization
GO:0031032	0.73	actomyosin structure organization
GO:0045214	0.72	sarcomere organization
GO:0014809	0.64	regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion
GO:0050896	0.53	response to stimulus
GO:0023051	0.50	regulation of signaling

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:0044424	1.00	intracellular part
GO:0044444	0.98	cytoplasmic part
GO:0044422	0.94	organelle part
GO:0044446	0.90	intracellular organelle part
GO:0044432	0.87	endoplasmic reticulum part
GO:0043226	0.72	organelle
GO:0043229	0.70	intracellular organelle
GO:0043227	0.70	membrane-bounded organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0005783	0.63	endoplasmic reticulum
GO:0016529	0.62	sarcoplasmic reticulum
GO:0070013	0.53	intracellular organelle lumen
GO:0033018	0.51	sarcoplasmic reticulum lumen

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	0.088	1aiuA	0.536	2.43	0.130	0.637	1.8.4.10	NA
2	0.077	1syrA	0.522	2.69	0.149	0.643	1.8.1.8	NA
3	0.069	1nswA	0.538	2.66	0.165	0.656	1.8.1.9	NA
4	0.067	1wmjA	0.529	2.79	0.150	0.656	1.8.4.8	NA
5	0.067	1t00A	0.541	2.91	0.157	0.681	1.8.1.8	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	0.16	1a8y0	0.747	1.18	0.934	0.771	0.79	III	complex1.pdb.gz	42,43,44,45,47,80,83,84,86,87,89,90,98,101,146,147,150,151
2	0.03	1mdiA	0.530	2.41	0.130	0.637	0.43	III	complex2.pdb.gz	74,75,111,112,113,115,118,119
3	0.03	1x9m1	0.540	2.52	0.167	0.650	0.62	III	complex3.pdb.gz	111,115,118,119,124,125,126,140,141,144,148,151,152,155,156
4	0.02	2o8v2	0.537	2.63	0.171	0.656	0.49	III	complex4.pdb.gz	108,123,124,125,129,140
5	0.02	1cqgA	0.531	2.41	0.130	0.637	0.45	III	complex5.pdb.gz	108,129,139,140,141
6	0.02	1mdkA	0.530	2.41	0.130	0.637	0.41	III	complex6.pdb.gz	108,109,110,124,125,126,127,141
7	0.02	1ovn0	0.549	2.65	0.104	0.675	0.56	III	complex7.pdb.gz	58,60,63,64,65,103

	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.