D-I-TASSER O95393-D2

D-I-TASSER results for O95393-D2

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

Input Sequence in FASTA format

>O95393 (106 residues)
KGNYCKRTPLYIDFKEIGWDSWIIAPPGYEAYECRGVCNYPLAEHLTPTKHAIIQALVHL
KNSQKASKACCVPTKLEPISILYLDKGVVTYKFKYEGMAVSECGCR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| KGNYCKRTPLYIDFKEIGWDSWIIAPPGYEAYECRGVCNYPLAEHLTPTKHAIIQALVHLKNSQKASKACCVPTKLEPISILYLDKGVVTYKFKYEGMAVSECGCR
Prediction	CCCCCSSSSSSSSSCCCCCCCSSSCCCCSSCSCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCSSCCSSSSSSSCCCSSSSSSSCCSSSSSSSCC
Confidence	9984279989974111498641655993041501475687765567876414566667773887689988247411136899996899499999289587320268
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| KGNYCKRTPLYIDFKEIGWDSWIIAPPGYEAYECRGVCNYPLAEHLTPTKHAIIQALVHLKNSQKASKACCVPTKLEPISILYLDKGVVTYKFKYEGMAVSECGCR
Prediction	8764044360313055142551133154132330323143433753444321313332444445533410032353441300112576413345155031644728
	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 AttentionPotential. 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

CCCCCSSSSSSSSSCCCCCCCSSSCCCCSSCSCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCSSCCSSSSSSSCCCSSSSSSSCCSSSSSSSCC
KGNYCKRTPLYIDFKEIGWDSWIIAPPGYEAYECRGVCNYPLAEHLTPTKHAIIQALVHLKNSQKASKACCVPTKLEPISILYLDKGVVTYKFKYEGMAVSECGCR

1waqA

0.49

0.47

13.71

1.33

DEthreader

-A-RCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDS-NNVVYKQYEDMVVESCGCR

1zkzA

0.65

18.58

4.58

SPARKS-K

AGSHCQKTSLRVNFEDIGWDSWIIAPKEYEAYECKGGCFFPLADDVTPTKHAIVQTLVHLKFPTKVGKACCVPTKLSPISVLYKDMGVPTLKYHYEGMSVAECGCR

6sf1B

1.00

0.98

27.47

1.05

MapAlign

--NYCKRTPLYIDFKEIGWDSWIIAPPGYEAYECRGVCNYPLAEHLTPTKHAIIQALVHLKNSQKASKACCVPTKLEPISILYLDKGVVTYKFKYEGMAVSECGCR

6sf1B

1.00

0.98

27.47

0.93

CEthreader

--NYCKRTPLYIDFKEIGWDSWIIAPPGYEAYECRGVCNYPLAEHLTPTKHAIIQALVHLKNSQKASKACCVPTKLEPISILYLDKGVVTYKFKYEGMAVSECGCR

4n1dA

0.48

0.47

13.73

3.56

MUSTER

-KSSCKRHPLYVDFNLIGWGSWIIYPKQYNAYRCEGECPNPVGEEFHPTNHAYIQSLLKRYQPHRVPSTCCVPTELSAISMLYLDENEKVVLKNYQDMVVEGCGCR

3rjrA

0.35

0.33

9.87

3.04

HHsearch

TEKNCCVRQLYIDFRDLGW-KWIHEPKGYHANFCLGPCPYIWSL---DTQYSKVLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRKPKVE-QLSNMIVRSCKCS

6sf1B

1.00

0.98

27.47

1.80

FFAS-3D

--NYCKRTPLYIDFKEIGWDSWIIAPPGYEAYECRGVCNYPLAEHLTPTKHAIIQALVHLKNSQKASKACCVPTKLEPISILYLDKGVVTYKFKYEGMAVSECGCR

1zkzA

0.61

0.60

17.29

0.95

EigenThreader

AGSHCQKTSLRVNFEDIGWDSWIIAPKEYEAYECKGGCFFPLADDVTPTKHAIVQTLVHLKFPTKVGKACCVPTKLSPISVLYKDMGVPTLKYHYEGMSVECGCR-

4mplA

0.65

18.58

3.56

CNFpred

AGSHCQKTSLRVNFEDIGWDSWIIAPKEYEAYECKGGCFFPLADDVTPTKHAIVQTLVHLKFPTKVGKACCVPTKLSPISVLYKDDGVPTLKYHYEGMSVAECGCR

6sf1B

0.86

0.80

22.58

1.17

DEthreader

-N-YCKRTPLYIDFKIGWDSWII-APPGYEAYECRGVCNYPLAEHLTPTKHAIIQALVHLKN-SQASKACCVPTKLEPISILYLD--V-VTYKKYEGMAVSECGCR

(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	0.8034

(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 AttentionPotential, 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	6sf1B	0.95	0.76	1.000	0.981	model1_6sf1B.pdb.gz
2	1zkzA	0.91	1.24	0.651	1.000	model1_1zkzA.pdb.gz
3	4n1dA	0.91	1.16	0.500	0.981	model1_4n1dA.pdb.gz
4	2qcqB	0.90	1.46	0.400	0.981	model1_2qcqB.pdb.gz
5	1m4uL	0.89	1.50	0.476	0.981	model1_1m4uL.pdb.gz
6	3bmpA	0.88	1.49	0.558	0.972	model1_3bmpA.pdb.gz
7	2pjyA	0.82	1.72	0.370	0.934	model1_2pjyA.pdb.gz
8	2b0uA	0.80	2.37	0.390	0.981	model1_2b0uA.pdb.gz
9	3hh2A	0.76	2.37	0.378	0.915	model1_3hh2A.pdb.gz
10	3rjrA2	0.70	2.34	0.359	0.859	model1_3rjrA2.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:0005102	0.98	receptor binding
GO:0005160	0.94	transforming growth factor beta receptor binding
GO:0005125	0.79	cytokine 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	0.98	regulation of cellular process
GO:0044699	0.96	single-organism process
GO:0032502	0.90	developmental process
GO:0009987	0.90	cellular process
GO:0048522	0.89	positive regulation of cellular process
GO:0044767	0.89	single-organism developmental process
GO:0019222	0.89	regulation of metabolic process
GO:0080090	0.88	regulation of primary metabolic process
GO:0060255	0.88	regulation of macromolecule metabolic process
GO:0044763	0.88	single-organism cellular process
GO:0031323	0.88	regulation of cellular metabolic process
GO:0048583	0.87	regulation of response to stimulus
GO:0007165	0.87	signal transduction
GO:0031325	0.86	positive regulation of cellular metabolic process
GO:0010604	0.86	positive regulation of macromolecule metabolic process
GO:0023051	0.83	regulation of signaling
GO:0010646	0.83	regulation of cell communication
GO:0048869	0.82	cellular developmental process
GO:0009967	0.82	positive regulation of signal transduction
GO:0051247	0.81	positive regulation of protein metabolic process
GO:0001932	0.81	regulation of protein phosphorylation
GO:0048856	0.80	anatomical structure development
GO:0001934	0.80	positive regulation of protein phosphorylation
GO:0043408	0.78	regulation of MAPK cascade
GO:0090092	0.76	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0043067	0.76	regulation of programmed cell death
GO:0042981	0.75	regulation of apoptotic process
GO:0010862	0.75	positive regulation of pathway-restricted SMAD protein phosphorylation
GO:0010556	0.71	regulation of macromolecule biosynthetic process
GO:0060395	0.70	SMAD protein signal transduction
GO:0007167	0.69	enzyme linked receptor protein signaling pathway
GO:0007178	0.68	transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0048468	0.66	cell development
GO:0031326	0.65	regulation of cellular biosynthetic process
GO:0006355	0.64	regulation of transcription, DNA-templated
GO:0006357	0.56	regulation of transcription from RNA polymerase II promoter

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:0044421	0.97	extracellular region part
GO:0005615	0.92	extracellular space
GO:0044464	0.66	cell part
GO:0044424	0.52	intracellular 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	0.565	1lx5A	0.904	1.12	0.476	0.972	2.7.11.30	5,10,32,34,36,38,71,73,76,100,103
2	0.496	1ktzA	0.667	1.78	0.395	0.764	2.7.11.30	5,10,31,34,71,73,76,78,98,100,103
3	0.159	2gooA	0.885	1.23	0.559	0.962	2.7.11.30	5,7,10,29,34,36,71,73,76,79,98,103
4	0.060	1fo4A	0.435	4.96	0.068	0.849	1.17.1.4	NA
5	0.060	2fr7A	0.433	4.14	0.043	0.708	1.14.-.-	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	0.33	2h643	0.898	1.29	0.558	0.981	1.56	III	complex1.pdb.gz	16,17,19,22,81,95,98
2	0.33	2h620	0.876	1.57	0.563	0.972	1.58	III	complex2.pdb.gz	10,19,31,32,33,50,51,54,55,57,66,67,70,72,73,76,96,97,98,100,106
3	0.33	2goo6	0.885	1.23	0.559	0.962	1.52	III	complex3.pdb.gz	6,40,41,42,43,44,45,48,50,53,57
4	0.29	1lx51	0.904	1.12	0.476	0.972	1.42	III	complex4.pdb.gz	11,25,26,27,28,79,80,82,84,90,92,94,101
5	0.08	1nys0	0.657	1.70	0.481	0.755	1.18	III	complex5.pdb.gz	69,70,72,96,97,106
6	0.07	1s4y1	0.628	3.03	0.402	0.840	1.04	III	complex6.pdb.gz	10,17,19,22,29,32,33,70,72,81,97,98,100,106
7	0.03	2x1wA	0.442	3.74	0.158	0.708	1.08	UUU	complex7.pdb.gz	73,74,75,76,78,98,100

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.