D-I-TASSER P13637-D1

D-I-TASSER results for P13637-D1

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

Input Sequence in FASTA format

>P13637 (166 residues)
MGDKKDDKDSPKKNKGKERRDLDDLKKEVAMTEHKMSVEEVCRKYNTDCVQGLTHSKAQE
ILARDGPNALTQALVIREGEKMQVNAEEVVVGDLVEIKGGDRVPADLRIISAHGCKVDNS
SLTGESEPQTRSPDCTHDNPLETRNITFFSTNCVEGTARGVVVATG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGDKKDDKDSPKKNKGKERRDLDDLKKEVAMTEHKMSVEEVCRKYNTDCVQGLTHSKAQEILARDGPNALTQALVIREGEKMQVNAEEVVVGDLVEIKGGDRVPADLRIISAHGCKVDNSSLTGESEPQTRSPDCTHDNPLETRNITFFSTNCVEGTARGVVVATG
Prediction	CCCCCCCCCCCCCCCCCHHHHHHHHHCCHSHHHHHCCHHHHHHHHHHCHSSSSSHHHHHHHHHHHHHCCCCCCSSSSCCSSSSSSHHHCCCCCSSSSCCCCSSCCCSSSSSSCCSSSSCCCCCCCCCCSCCCCCCCCCCCCCCCCSSSCCCSSSSSSSSSSSSSCC
Confidence	9988766555432334114209887352011322231999999984130000014999999999981099811999899899995243788829999379733141799993691566011247875403666666788554553787275178725899999459
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGDKKDDKDSPKKNKGKERRDLDDLKKEVAMTEHKMSVEEVCRKYNTDCVQGLTHSKAQEILARDGPNALTQALVIREGEKMQVNAEEVVVGDLVEIKGGDRVPADLRIISAHGCKVDNSSLTGESEPQTRSPDCTHDNPLETRNITFFSTNCVEGTARGVVVATG
Prediction	8365567565466655555541550453131432513033013313220001211430450053047223540302154553504065002130030333231103010020561413103234123215243632674323330000011301433030103238
	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                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCHHHHHHHHHCCHSHHHHHCCHHHHHHHHHHCHSSSSSHHHHHHHHHHHHHCCCCCCSSSSCCSSSSSSHHHCCCCCSSSSCCCCSSCCCSSSSSSCCSSSSCCCCCCCCCCSCCCCCCCCCCCCCCCCSSSCCCSSSSSSSSSSSSSCC
MGDKKDDKDSPKKNKGKERRDLDDLKKEVAMTEHKMSVEEVCRKYNTDCVQGLTHSKAQEILARDGPNALTQALVIREGEKMQVNAEEVVVGDLVEIKGGDRVPADLRIISAHGCKVDNSSLTGESEPQTRSPDCTHDNPLETRNITFFSTNCVEGTARGVVVATG

3kdpA

0.78

0.64

18.23

1.17

DEthreader

-----------------------------SMDDHKLSLDELHRKYGTDLSRGLTPARAAEILARDGPNAVQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTG

3kdpA2

0.71

0.64

18.31

3.12

SPARKS-K

-----------AKKERDMDELKKEVSMD----DHKLSLDELHRKYGTDLSRGLTPARAAEILARDGPNAPQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTG

3ba6A2

0.33

0.27

8.14

1.42

MapAlign

------------------------------EAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNEPEMGKVYRAKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSLRVDQSILTGESVSVIKHTEPVRAVNQDKKNMLFSGTNIAAGKALGIVATTG

3ba6A2

0.33

0.27

8.14

1.23

CEthreader

-----------------------------MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNEPEMGKVYRADRVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSLRVDQSILTGESVSVIKHTEPVRAVNQDKKNMLFSGTNIAAGKALGIVATTG

3kdpA2

0.75

0.69

19.45

2.34

MUSTER

---------------AKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTPARAAEILARDGPMVPQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTG

3ixzA

0.65

0.58

16.68

2.55

HHsearch

----------------KRKEKLENMKKEMEINDHQLSVAELEQKYQTSATKGLSASLAAELLLRDGPNALRQATVIRDGDKFQINADQLVVGDLVEMKGGDRVPADIRILQAQGRKVDNSSLTGESEPQTRSPECTHESPLETRNIAFFSTMCLEGTAQGLVVNTG

3ixzA2

0.48

13.85

2.10

FFAS-3D

LLRDGPNALRPPRGTPEYVKFARQLAGGLQCLMWVAAAILIAVVVVTGCFGYYQEFKSTNIIASFKNLVPQQATVIRDGDKFQINADQLVVGDLVEMKGGDRVPADIRILQAQGRKVDNSSLTGESEPQTRSPECTHESPLETRNIAFFSTMCLEGTAQGLVVNTG

3kdpA2

0.73

0.66

18.80

1.38

EigenThreader

--AKKERDMDELKKEV-------------SMDDHKLSLDELHRKYGTDLSRGLTPARAAEILARDGPNAPQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTG

5yluA

0.56

0.48

13.70

2.78

CNFpred

----------------------GDLTTDDNLYLALALIAVVVVTGCFGY---YQEFKSTNIIASFKNLVPQQATVIRDGDKFQINADQLVVGDLVEMKGGDRVPADIRILQAQGCKVDNSSLTGESEPQTRSPECTHESPLETRNIAFFSTMCLEGTAQGLVVNTG

3kdpA2

0.78

0.64

18.23

1.17

DEthreader

-----------------------------SMDDHKLSLDELHRKYGTDLSRGLTPARAAEILARDGPNAVQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTG

(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	0.7837

(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	3kdpA2	0.81	1.66	0.715	0.849	model1_3kdpA2.pdb.gz
2	3ixzA	0.80	1.88	0.613	0.849	model1_3ixzA.pdb.gz
3	3ba6A2	0.77	1.49	0.343	0.825	model1_3ba6A2.pdb.gz
4	6xmpA2	0.69	3.29	0.181	0.868	model1_6xmpA2.pdb.gz
5	6a69A	0.69	2.26	0.290	0.795	model1_6a69A.pdb.gz
6	6rohA	0.60	2.77	0.178	0.699	model1_6rohA.pdb.gz
7	6k7gA	0.59	2.82	0.267	0.687	model1_6k7gA.pdb.gz
8	1mhsA1	0.58	3.49	0.250	0.741	model1_1mhsA1.pdb.gz
9	7bspA	0.58	2.68	0.216	0.675	model1_7bspA.pdb.gz
10	6lcpA1	0.58	2.59	0.216	0.669	model1_6lcpA1.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:0022892	1.00	substrate-specific transporter activity
GO:0043492	0.99	ATPase activity, coupled to movement of substances
GO:0019829	0.98	cation-transporting ATPase activity
GO:0022890	0.85	inorganic cation transmembrane transporter activity
GO:0015662	0.85	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism
GO:0046873	0.76	metal ion transmembrane transporter activity
GO:0015077	0.52	monovalent inorganic cation transmembrane transporter 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:0044699	0.93	single-organism process
GO:0065007	0.92	biological regulation
GO:0044763	0.91	single-organism cellular process
GO:0098771	0.89	inorganic ion homeostasis
GO:0030003	0.89	cellular cation homeostasis
GO:0006875	0.79	cellular metal ion homeostasis
GO:0006812	0.69	cation transport
GO:0034220	0.64	ion transmembrane transport
GO:0098662	0.62	inorganic cation transmembrane transport
GO:1902600	0.61	hydrogen ion transmembrane transport
GO:0030004	0.61	cellular monovalent inorganic cation homeostasis
GO:0030001	0.58	metal ion transport
GO:0090662	0.52	ATP hydrolysis coupled transmembrane transport
GO:0015988	0.52	energy coupled proton transmembrane transport, against electrochemical gradient
GO:0071805	0.51	potassium ion transmembrane transport
GO:0071436	0.51	sodium ion export
GO:0055078	0.51	sodium ion homeostasis
GO:0055075	0.51	potassium ion homeostasis

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	0.99	cell part
GO:0044425	0.97	membrane part
GO:0016021	0.96	integral component of membrane
GO:0044424	0.95	intracellular part
GO:0044459	0.92	plasma membrane part
GO:0005887	0.88	integral component of plasma membrane
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0016020	0.67	membrane

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	3ixzA	0.802	1.88	0.613	0.849	3.6.3.10	118
2	0.060	1mo7A	0.272	6.13	0.030	0.572	3.6.3.9	77
3	0.060	1h3gA	0.348	5.78	0.044	0.645	3.2.1.54	55
4	0.060	3kaoA	0.428	5.15	0.092	0.741	4.1.2.40	112
5	0.060	1yifA	0.428	5.08	0.055	0.747	3.2.1.37	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	2voyE	0.122	2.53	0.071	0.145	0.44	III	complex1.pdb.gz	97,118,120
	2	0.01	2voyB	0.118	2.67	0.065	0.139	0.54	III	complex2.pdb.gz	49,53,61,65,66

	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.