D-I-TASSER O14737-D1

D-I-TASSER results for O14737-D1

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

Input Sequence in FASTA format

>O14737 (125 residues)
MADEELEALRRQRLAELQAKHGDPGDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLA
LVKPEKTKAVENYLIQMARYGQLSEKVSEQGLIEILKKVSQQTEKTTTVKFNRRKVMDSD
EDDDY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MADEELEALRRQRLAELQAKHGDPGDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLALVKPEKTKAVENYLIQMARYGQLSEKVSEQGLIEILKKVSQQTEKTTTVKFNRRKVMDSDEDDDY
Prediction	CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCC
Confidence	98399999999999999997255320109999999999999999999389999999846441889999999999999991999998599999999999986166763478873146887553569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MADEELEALRRQRLAELQAKHGDPGDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLALVKPEKTKAVENYLIQMARYGQLSEKVSEQGLIEILKKVSQQTEKTTTVKFNRRKVMDSDEDDDY
Prediction	87474165136433541475456785555554554455424410441035504430431432347305401530241054351654043740350055137646754504051353344655666
	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                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCC
MADEELEALRRQRLAELQAKHGDPGDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLALVKPEKTKAVENYLIQMARYGQLSEKVSEQGLIEILKKVSQQTEKTTTVKFNRRKVMDSDEDDDY

6vmtA

0.25

0.19

5.95

1.17

DEthreader

----------VP-ISEQAQQM-VAKQQAQQERMEALEEQKENMLRAFVSAEGRERLKRIAQVKAGRSQAVEMHIIQAVQRGKMQPPVSDDTVRELLGQMANQEASRSH-----------------

6iqcA

0.32

0.26

7.94

1.60

SPARKS-K

YDDEELEELLRRKAAQEQKRIEEERKRKAELESQKESILRVIL-----TPEARQRLTNIKLVKPEFAESLENQLIALAQSGRIKIPITDEELKQILEQISQQNRRDF------------------

3b9zA

0.03

1.85

0.84

MapAlign

YNYSINILAMLLVGFGFLMVFVRRYGFSATTGTYLVVAQTIVNTLLALC-GATLATYFLSALFIVDMANAALAGGVAIGPVGAFVIG-LLGGAISVVGFVFIQPMLESKAKTIDTCGVHNLHGLP

6vmtA

0.26

0.21

6.41

0.77

CEthreader

-----------VPISEEQAQQMVAKQQAQQERMEALEEQKENMLRAFVSAEGRERLKRIAQVKAGRSQAVEMHIIQAVQRGKMQPPVSDDTVRELLGQMANQEAESRSHI---------------

2cruA

0.89

0.84

23.62

1.81

MUSTER

-GSSGSSGLRRQRLAELQAKHGDPGDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLALVKPEKTKAVENYLIQMARYGQLSEKVSEQGLIEILKKVSQQTEKTTTVKFNRSGPSSG------

2cruA

0.89

0.84

23.62

4.23

HHsearch

-GSSGSSGLRRQRLAELQAKHGDPGDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLALVKPEKTKAVENYLIQMARYGQLSEKVSEQGLIEILKKVSQQTEKTTTVKFNRSGPSSG------

6iqcA

0.36

0.29

8.58

1.82

FFAS-3D

YDDEELEELLRRKAAQEQKRI-----EEERKRKAELESQKESILRVILTPEARQRLTNIKLVKPEFAESLENQLIALAQSGRIKIPITDEELKQILEQISQQNRRD-------------------

2jxnA

0.19

0.18

5.66

0.95

EigenThreader

MDPELQCIRECRLAQLNSGGTNGDRNSGANNGGGENSAPVGAAIANFLEPQALERLSRVALVRRDRAQAVETYLKKLIATNNVTHKITEAEIVSILNGIAKQQNSQNNS-----KIIFE------

2k6bA

0.99

0.89

24.87

1.22

CNFpred

SADEELEALRRQRLAELQAKHGDPGDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLALVKPEKTKAVENYLIQMARYGQLSEKVSEQGLIEILKKVSQQTEKTTTVKFN-------------

6iqcA

0.25

0.21

6.43

1.00

DEthreader

-S---YDDEELEELLRRKAAQEQKRIEEERKRKAELESQKESILRVILTPEARQRLTNIKL-VKEFAESLENQLIALAQSGRIKIPITDEELKQILEQISQQNRRDF------------------

(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	0.7117

(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	6vmtA	0.61	1.64	0.232	0.672	model1_6vmtA.pdb.gz
2	2cruA	0.60	2.77	0.730	0.736	model1_2cruA.pdb.gz
3	6iqcA	0.55	2.32	0.262	0.672	model1_6iqcA.pdb.gz
4	5z4aA	0.53	4.23	0.067	0.872	model1_5z4aA.pdb.gz
5	4rd8A	0.52	3.75	0.063	0.768	model1_4rd8A.pdb.gz
6	4xq7A	0.52	4.30	0.043	0.848	model1_4xq7A.pdb.gz
7	1px5B	0.52	4.47	0.051	0.864	model1_1px5B.pdb.gz
8	6l8hA	0.52	4.04	0.081	0.816	model1_6l8hA.pdb.gz
9	4s3nA	0.50	4.48	0.085	0.848	model1_4s3nA.pdb.gz
10	1zrlA1	0.35	4.66	0.062	0.600	model1_1zrlA1.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:0097367	0.83	carbohydrate derivative binding
GO:0048487	0.82	beta-tubulin binding
GO:0010698	0.82	acetyltransferase activator activity
GO:0008201	0.82	heparin 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	0.94	cellular process
GO:0050896	0.91	response to stimulus
GO:0065007	0.83	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0050794	0.81	regulation of cellular process
GO:0048518	0.79	positive regulation of biological process
GO:0048583	0.78	regulation of response to stimulus
GO:0048522	0.78	positive regulation of cellular process
GO:0051716	0.77	cellular response to stimulus
GO:0048584	0.77	positive regulation of response to stimulus
GO:0043065	0.77	positive regulation of apoptotic process
GO:0080090	0.65	regulation of primary metabolic process
GO:0060255	0.65	regulation of macromolecule metabolic process
GO:0048523	0.65	negative regulation of cellular process
GO:0044699	0.65	single-organism process
GO:0031323	0.65	regulation of cellular metabolic process
GO:0032268	0.64	regulation of cellular protein metabolic process
GO:0031325	0.64	positive regulation of cellular metabolic process
GO:0010604	0.64	positive regulation of macromolecule metabolic process
GO:0010468	0.64	regulation of gene expression
GO:2001235	0.63	positive regulation of apoptotic signaling pathway
GO:0070887	0.63	cellular response to chemical stimulus
GO:0043280	0.63	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0010628	0.63	positive regulation of gene expression
GO:0010033	0.63	response to organic substance
GO:0009719	0.63	response to endogenous stimulus
GO:1903645	0.62	negative regulation of chaperone-mediated protein folding
GO:1903638	0.62	positive regulation of protein import into mitochondrial outer membrane
GO:0090200	0.62	positive regulation of release of cytochrome c from mitochondria
GO:0071560	0.62	cellular response to transforming growth factor beta stimulus
GO:0008285	0.62	negative regulation of cell proliferation
GO:0044763	0.60	single-organism cellular process
GO:0012501	0.55	programmed cell death
GO:0008152	0.50	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:0044424	1.00	intracellular part
GO:0043229	0.95	intracellular organelle
GO:0043227	0.95	membrane-bounded organelle
GO:0005634	0.94	nucleus
GO:0005737	0.79	cytoplasm
GO:0070062	0.65	extracellular exosome

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	1og2A	0.478	4.14	0.035	0.792	1.14.14.1	NA
2	0.060	1n6bA	0.487	4.52	0.043	0.816	1.14.14.1	NA
3	0.060	1r0lC	0.472	4.61	0.081	0.816	1.1.1.267	NA
4	0.060	1vljB	0.486	3.94	0.098	0.736	1.1.1.-	NA
5	0.060	1w27A	0.486	3.98	0.077	0.744	4.3.1.24	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	3hb3A	0.429	5.08	0.065	0.792	0.13	HEA	complex1.pdb.gz	52,53,55,67,71,74,77,78,81

	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.