D-I-TASSER O15229-D3

D-I-TASSER results for O15229-D3

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

Input Sequence in FASTA format

>O15229 (113 residues)
SWFIFQKNMERFLHAIMPSTFIPLYTMVTFSRIRYHEAVQRWHWQKKVINKGLFFLGSLI
AISSTYLLIHYMSPRSFLRLRRPWNWIAHFRNTTCFPAKAVDSLEQISNLISR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| SWFIFQKNMERFLHAIMPSTFIPLYTMVTFSRIRYHEAVQRWHWQKKVINKGLFFLGSLIAISSTYLLIHYMSPRSFLRLRRPWNWIAHFRNTTCFPAKAVDSLEQISNLISR
Prediction	CHHHHHHHHHHHHHHHCCCCSSSCSSSSSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHCCHHHCC
Confidence	90477899999999977775020024687379888999998999999999999999999999999999996475547888536788887334566566653523315044239
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| SWFIFQKNMERFLHAIMPSTFIPLYTMVTFSRIRYHEAVQRWHWQKKVINKGLFFLGSLIAISSTYLLIHYMSPRSFLRLRRPWNWIAHFRNTTCFPAKAVDSLEQISNLISR
Prediction	83230133025301531463213223312146241440353462144004301333133333323221222344421420341141133146223144533532452453268
	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

CHHHHHHHHHHHHHHHCCCCSSSCSSSSSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHCCHHHCC
SWFIFQKNMERFLHAIMPSTFIPLYTMVTFSRIRYHEAVQRWHWQKKVINKGLFFLGSLIAISSTYLLIHYMSPRSFLRLRRPWNWIAHFRNTTCFPAKAVDSLEQISNLISR

5fn0A2

0.26

0.18

5.47

1.37

SPARKS-K

PTYLLERELGQIMAQRQPTRFIPRYSMVTFSRLPYAQAMARGQIQEQLLKFAVADLTSINLDAVEHEVTRCLPPLSHL-----------------------------------

5fn0A2

0.22

0.16

5.02

1.28

MUSTER

PTYLLERELGQIMAQRQPTRFIPRYSMVTFSRLPYAQAMARGQIQEQLLKFAVANHSDLTSINLDAVEHEVTRCLPPLSHL--------------------------------

5fn0A2

0.24

0.16

4.96

3.90

HHsearch

PTYLLERELGQIMAQRQPTRFIPRYSMVTFSRLPYAQAMARGQIQEQLLKFAV-ANHSDLDAV--EHEVRCLPPLSH---------------------L--------------

5fn0A2

0.24

0.15

4.70

1.17

FFAS-3D

--YLLERELGQIMAQRQPTRFIPRYSMVTFSRLPYAQAMARGQIQEQLLKFAVANHSDLTLDAVEHEVTRCLPP---------------------------------------

4d0nB

0.03

1.54

1.00

DEthreader

----------SMSK---Q--LEAWRIDSFLKQQKKDVVKRQEVIYELMQTEFHHVRTLKIMSGYSQGMMADLL--FEQQMVEKPK-QH-QYKVRLLVRLLILVFLQIFASL-Q

6w2rA1

0.11

0.10

3.51

0.77

SPARKS-K

DERRELEKVARKAIEAAREG-------------NTDEVREQLQRALEIARESAVKLALDVALRVAQEAAKRGNKDAIDEAAEVVVRIAEESNNSDALEQALRVLEEIAKAVLK

3jacA

0.02

1.40

0.82

MapAlign

GGGGGGGGGGGGGGGG---GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

3jacA

0.02

1.48

0.48

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

4widA2

0.15

5.05

0.53

MUSTER

TPFQDMRCLFEVANEQFNDTPVPQIVQYAVNSSSLEKFVMLMHTPITMLSDQVRVL-ILYLIDEIVHAIHTNSNQSNGLKPKVRIVINEFHATLMMGIDKMKSLNELREIVND

6lkdA

0.74

0.46

13.04

2.36

HHsearch

RWFLFQRLLDKFLHALMPSTFIPLYTMVAFTRIRYHEAVLRWHWQKKVINRGLFVLGSLVAIGSAYILVH-------------------------------------------

(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	0.5657

(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	5fn0A2	0.58	1.98	0.205	0.655	model1_5fn0A2.pdb.gz
2	1chkA	0.53	4.12	0.038	0.885	model1_1chkA.pdb.gz
3	4ilyB	0.53	4.34	0.038	0.894	model1_4ilyB.pdb.gz
4	6p25A2	0.53	4.07	0.056	0.876	model1_6p25A2.pdb.gz
5	2b0tA	0.53	4.08	0.028	0.867	model1_2b0tA.pdb.gz
6	2x0oA	0.53	4.29	0.046	0.841	model1_2x0oA.pdb.gz
7	1itwA2	0.53	4.14	0.019	0.858	model1_1itwA2.pdb.gz
8	2d05A	0.50	4.43	0.058	0.876	model1_2d05A.pdb.gz
9	1phhA	0.49	4.83	0.028	0.885	model1_1phhA.pdb.gz
10	2w02B	0.48	4.69	0.046	0.823	model1_2w02B.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:0004497	1.00	monooxygenase activity
GO:0016709	0.99	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
GO:1901363	0.98	heterocyclic compound binding
GO:0097159	0.98	organic cyclic compound binding
GO:0036094	0.98	small molecule binding
GO:0004502	0.98	kynurenine 3-monooxygenase activity
GO:0050660	0.97	flavin adenine dinucleotide binding
GO:0016174	0.97	NAD(P)H oxidase 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:0044710	1.00	single-organism metabolic process
GO:1901564	0.99	organonitrogen compound metabolic process
GO:0055086	0.99	nucleobase-containing small molecule metabolic process
GO:0044550	0.99	secondary metabolite biosynthetic process
GO:0019637	0.99	organophosphate metabolic process
GO:0006796	0.99	phosphate-containing compound metabolic process
GO:0006733	0.99	oxidoreduction coenzyme metabolic process
GO:0019674	0.98	NAD metabolic process
GO:0006082	0.98	organic acid metabolic process
GO:0070189	0.97	kynurenine 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:0005741	1.00	mitochondrial outer membrane
GO:0043226	0.63	organelle
GO:0043227	0.62	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	2j1pB	0.439	4.19	0.071	0.708	2.5.1.1 2.5.1.10 2.5.1.29	NA
2	0.060	2zalA	0.425	4.32	0.091	0.717	3.5.1.1	NA
3	0.060	1t09B	0.514	4.53	0.045	0.885	1.1.1.42	NA
4	0.060	3blvC	0.480	4.68	0.076	0.885	1.1.1.41	21
5	0.060	1t09A	0.515	4.52	0.045	0.885	1.1.1.42	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:

No Binding sites was predicted

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

	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.