D-I-TASSER O75689-D1

D-I-TASSER results for O75689-D1

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

Input Sequence in FASTA format

>O75689 (119 residues)
MAKERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIPQVSKVKSV
RLDAWEEAQVEFMASHGNDAARARFESKVPSFYYRPTPSDCQLLREQWIRAKYERQEFI

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAKERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIPQVSKVKSVRLDAWEEAQVEFMASHGNDAARARFESKVPSFYYRPTPSDCQLLREQWIRAKYERQEFI
Prediction	CCHHHHHHHHHHHHCCCCCCCCCCCCCCCCSSSSCCCSSSHHHHHHHHHCCCCCCSSSSSCCCCCCHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCC
Confidence	95799999999982869883467999999648842657762654788745899763676037877768999999982289999999738877889998787999999999999513569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAKERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIPQVSKVKSVRLDAWEEAQVEFMASHGNDAARARFESKVPSFYYRPTPSDCQLLREQWIRAKYERQEFI
Prediction	85673453045027467143004153562422102100000230243137233233043134440344233203323343024203442475444154724463125104513564578
	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

CCHHHHHHHHHHHHCCCCCCCCCCCCCCCCSSSSCCCSSSHHHHHHHHHCCCCCCSSSSSCCCCCCHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCC
MAKERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIPQVSKVKSVRLDAWEEAQVEFMASHGNDAARARFESKVPSFYYRPTPSDCQLLREQWIRAKYERQEFI

2d9lA

0.24

7.33

1.33

DEthreader

-GSSGLKMLRDMTGLPHNRKCFDCDQRGPTYVNMTVGSFVCTSCSGSLRGLNPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDSS-AIPDF-RDPQKVKEFLQEKYEKKRWY

3jueA1

0.40

0.39

11.40

3.67

SPARKS-K

----VGHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKPGPSCSRQEKEAWIHAKYVEKKFL

2b0oF1

0.32

0.31

9.37

1.58

MapAlign

---LTKLLIAEVKSRPGNSQCCDCGAADPTWLSTNLGVLTCIQCSGVHRELVRFSRMQSLTLDLLGPSELLLALNMGNTSFNEVMEAQLSHGGPKPSAESDMGTRRDYIMAKYVEHRFA

2b0oF

0.34

0.33

9.82

1.16

CEthreader

---LTKLLIAEVKSRPGNSQCCDCGAADPTWLSTNLGVLTCIQCSGVHRELGRFSRMQSLTLDLLGPSELLLALNMGNTSFNEVMEAQLPSGGPKPSAESDMGTRRDYIMAKYVEHRFA

3fm8C1

1.00

28.00

2.59

MUSTER

MAKERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIPQVSKVKSVRLDAWEEAQVEFMASHGNDAARARFESKVPSFYYRPTPSDCQLLREQWIRAKYERQEFI

3fm8C

1.00

28.00

3.01

HHsearch

MAKERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIPQVSKVKSVRLDAWEEAQVEFMASHGNDAARARFESKVPSFYYRPTPSDCQLLREQWIRAKYERQEFI

3fm8C1

1.00

28.00

1.93

FFAS-3D

MAKERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIPQVSKVKSVRLDAWEEAQVEFMASHGNDAARARFESKVPSFYYRPTPSDCQLLREQWIRAKYERQEFI

3fm8C1

1.00

28.00

1.58

EigenThreader

MAKERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIPQVSKVKSVRLDAWEEAQVEFMASHGNDAARARFESKVPSFYYRPTPSDCQLLREQWIRAKYERQEFI

3fm8C

1.00

28.00

2.38

CNFpred

MAKERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIPQVSKVKSVRLDAWEEAQVEFMASHGNDAARARFESKVPSFYYRPTPSDCQLLREQWIRAKYERQEFI

3jueA

0.39

0.38

11.18

1.33

DEthreader

----VGHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVAMAVKKPGPSCSRQEKEAWIHAKYVEKKLA

(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	0.8564

(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	3fm8C1	0.93	1.29	1.000	1.000	model1_3fm8C1.pdb.gz
2	1dcqA	0.93	0.93	0.328	0.975	model1_1dcqA.pdb.gz
3	3lvqE1	0.92	1.27	0.333	0.983	model1_3lvqE1.pdb.gz
4	3jueA1	0.89	1.34	0.400	0.966	model1_3jueA1.pdb.gz
5	2d9lA	0.89	1.87	0.229	0.992	model1_2d9lA.pdb.gz
6	2crrA	0.87	1.51	0.405	0.958	model1_2crrA.pdb.gz
7	2owaA	0.77	2.16	0.308	0.899	model1_2owaA.pdb.gz
8	2crwA	0.74	2.20	0.346	0.874	model1_2crwA.pdb.gz
9	3o47A1	0.73	2.23	0.343	0.857	model1_3o47A1.pdb.gz
10	1u5kA2	0.36	4.40	0.098	0.613	model1_1u5kA2.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:0098772	0.66	molecular function regulator
GO:0008047	0.64	enzyme activator activity
GO:0005096	0.61	GTPase activator 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	0.79	biological regulation
GO:0050789	0.63	regulation of biological process
GO:0009987	0.62	cellular process
GO:0044699	0.61	single-organism process
GO:0050794	0.60	regulation of cellular 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	0.98	cell part
GO:0044424	0.95	intracellular part
GO:0044444	0.72	cytoplasmic part
GO:0016020	0.63	membrane
GO:0044446	0.53	intracellular organelle part
GO:0043226	0.53	organelle
GO:0043229	0.52	intracellular organelle
GO:0043227	0.50	membrane-bounded organelle

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	3f6tB	0.470	4.29	0.081	0.807	2.6.1.1	NA
2	0.060	2o0rA	0.467	4.26	0.062	0.790	2.6.1.-	NA
3	0.060	2wk8B	0.436	4.21	0.031	0.714	2.3.-.-	NA
4	0.060	1pg8A	0.491	4.37	0.067	0.824	4.4.1.11	NA
5	0.060	1n8pA	0.490	4.37	0.086	0.824	4.4.1.1	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	0.60	3mdbC	0.932	1.32	0.992	1.000	0.33	IP9	complex1.pdb.gz	31,33,34,42
2	0.17	3lvqE	0.918	1.27	0.333	0.983	0.17	UUU	complex2.pdb.gz	32,33,45,46,57,74,76,77,78
3	0.10	1ce8A	0.518	3.91	0.086	0.790	0.26	IMP	complex3.pdb.gz	23,38,44,55,57
4	0.02	1a9xG	0.508	4.16	0.102	0.815	0.25	ADP	complex4.pdb.gz	35,36,48,114
5	0.01	1jdbE	0.511	4.02	0.093	0.807	0.40	PO4	complex5.pdb.gz	23,41,43,44
6	0.01	1jdbB	0.508	4.16	0.102	0.815	0.31	GLN	complex6.pdb.gz	50,51,52
7	0.01	1a9x1	0.517	3.93	0.078	0.790	0.38	III	complex7.pdb.gz	36,40,78
8	0.01	1ynuA	0.388	4.74	0.026	0.731	0.12	PY4	complex8.pdb.gz	19,20,44,97
9	0.01	2zy3A	0.424	4.67	0.085	0.773	0.18	PLP	complex9.pdb.gz	46,112,113
10	0.01	1c3oA	0.517	3.92	0.078	0.790	0.35	GLN	complex10.pdb.gz	37,60,78

	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.