D-I-TASSER Q12860-D1

D-I-TASSER results for Q12860-D1

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

Input Sequence in FASTA format

>Q12860 (95 residues)
MKMWLLVSHLVIISIFPEWVEHINDTEVDIGSDLYWPCVATGKPIPTIRWLKNGYAYHKG
ELRLYDVTFENAGMYQCIAENTYGAIYANAELKIL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MKMWLLVSHLVIISIFPEWVEHINDTEVDIGSDLYWPCVATGKPIPTIRWLKNGYAYHKGELRLYDVTFENAGMYQCIAENTYGAIYANAELKIL
Prediction	CSSSSSSSSSSSSCCCCSSSSCCCCSSSSCCCCSSSSSSSSSSCCCSSSSSSCCSSCCCCSSSSCCCCHHHCSSSSSSSSSCCCSSSSSSSSSSC
Confidence	96999999999991298898667748990993199999996418988999989999479819992677344689999999778389999999989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MKMWLLVSHLVIISIFPEWVEHINDTEVDIGSDLYWPCVATGKPIPTIRWLKNGYAYHKGELRLYDVTFENAGMYQCIAENTYGAIYANAELKIL
Prediction	54040404240305124502540563415445604041404662504045334454157440404604561544331404363442303030415
	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

                   |                   |                   |                   |

SS
Seq

CSSSSSSSSSSSSCCCCSSSSCCCCSSSSCCCCSSSSSSSSSSCCCSSSSSSCCSSCCCCSSSSCCCCHHHCSSSSSSSSSCCCSSSSSSSSSSC
MKMWLLVSHLVIISIFPEWVEHINDTEVDIGSDLYWPCVATGKPIPTIRWLKNGYAYHKGELRLYDVTFENAGMYQCIAENTYGAIYANAELKIL

6efzA

0.27

8.39

1.50

DEthreader

TDPMKSQVGYLDVVVPPDILDTSTDMVIREGSNVTLKCAATGSPTPTITWRRGGVAYNGSFLTIAKVNRLNMGAYLCIASNGIPTVSKRVMLIVH

1u2hA

0.29

0.25

7.68

1.17

SPARKS-K

-------------KAPPTFKVSLMDQSVREGQDVIMSIRVQGEPKPVVSWLRNRQPVRPCRLRILAAERGDAGFYTCKAVNEYGARQCEARLEVR

1cs6A

0.29

0.25

7.68

0.47

MapAlign

-------------QYAPSIKAKFADTYALTGQMVTLECFAFGNPVPQIKWRKLSKWLSSPLLHIQNVDFEDEGTYECEAENIKGRDTYQGRIIIH

3pxjA1

0.34

0.29

8.83

0.28

CEthreader

------------AAHPPEIIRKPQNQGVRVGGVASFYCAARGDPPPSIVWRKNGKKVGISILRIEPVRARDDAPYECVAENGVGAVSADATLTIY

5e4iA4

0.60

0.52

14.78

1.20

MUSTER

--------------TYPHWVQKLNDTQLDSGSPLQWECKATGKPRPTYRWLKNGAPLLNGILAIQSVNQSDAGMYQCLAENKYGAIYASAELKIL

3p3yA

0.27

0.26

8.09

0.45

HHsearch

MG-SIRHTISVRVKAAPYWLDEPKNLILAPGEDGRLVCRANGNPKPTVQWMVNGEPLQGDTIIFRDTQISSRAVYQCNTSNEHGYLLANAFVSVL

6eg0B3

0.17

0.15

4.82

1.64

FFAS-3D

---------------PPMITVQNQLIGAVEGKGVTLDCESEAYPKSINYWTRERGEIVPPRLHINPLTQAEFGSYRCVAKNSLGDTDGTIKLYRI

2e7cA

0.17

5.55

0.42

EigenThreader

GSSGTLAQPVTIREIPPKIRLPLQTYIRKVGEQLNLVVPFQGKPRPQVVWTKGGAPLSDTVFFVRQAARSDSGEYELSVQIENMKDTATIRIRVV

5e4iA

0.53

15.20

1.68

CNFpred

SRGKNSFRGQLQIFTYPHWVQKLNDTQLDSGSPLQWECKATGKPRPTYRWLKNG-DTVNGILAIQSVNQSDAGMYQCLAENKYGAIYASAELKIL

5eo9B

0.24

7.54

1.50

DEthreader

TDPMKSQIGFLDVVIPPDFISTSSDVIVPEGSSVRLTCRARGYPEPIVTWRRDGPSFRGEVLKLSKISRNEMGSYLCIASNGVPSVSKRISLSIH

(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	0.8129

(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	4cbpA	0.85	1.77	0.258	0.979	model1_4cbpA.pdb.gz
2	3jxaB	0.82	1.16	0.379	0.884	model1_3jxaB.pdb.gz
3	1cs6A	0.82	1.50	0.453	0.895	model1_1cs6A.pdb.gz
4	3lafA	0.81	1.64	0.274	0.895	model1_3lafA.pdb.gz
5	5e5uB	0.81	2.13	0.221	0.916	model1_5e5uB.pdb.gz
6	5uv6A	0.81	1.43	0.202	0.884	model1_5uv6A.pdb.gz
7	3s97C	0.81	2.52	0.232	0.937	model1_3s97C.pdb.gz
8	5e4iA	0.81	1.37	0.505	0.884	model1_5e4iA.pdb.gz
9	5lf5A	0.81	1.35	0.274	0.895	model1_5lf5A.pdb.gz
10	3pxhA	0.81	1.19	0.305	0.863	model1_3pxhA.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:0004872	0.43	receptor activity
GO:0042802	0.41	identical protein binding
GO:0004888	0.40	transmembrane signaling receptor activity
GO:0046983	0.33	protein dimerization activity
GO:0042803	0.32	protein homodimerization activity
GO:0097367	0.30	carbohydrate derivative 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:0044699	0.83	single-organism process
GO:0009987	0.79	cellular process
GO:0044763	0.76	single-organism cellular process
GO:0032502	0.69	developmental process
GO:0044767	0.65	single-organism developmental process
GO:0065007	0.61	biological regulation
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	0.91	cell part
GO:0044424	0.51	intracellular part
GO:0044425	0.48	membrane part
GO:0031224	0.43	intrinsic component of membrane
GO:0016021	0.42	integral component of membrane
GO:0044459	0.41	plasma membrane part
GO:0044444	0.37	cytoplasmic part
GO:0043226	0.36	organelle
GO:0016020	0.36	membrane
GO:0044422	0.34	organelle part
GO:0031226	0.34	intrinsic component of plasma membrane
GO:0005886	0.33	plasma membrane
GO:0005887	0.32	integral component of plasma membrane
GO:0097458	0.31	neuron 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	0.268	1u2hA	0.785	1.36	0.293	0.863	2.7.11.1	51,53
2	0.226	2dm7A	0.645	2.41	0.188	0.832	2.7.11.1	61
3	0.190	2edwA	0.670	2.13	0.175	0.821	2.7.11.1	38,61
4	0.167	2bk8A	0.714	1.75	0.200	0.842	2.7.11.1	91
5	0.122	2wwmD	0.763	1.61	0.262	0.874	2.7.11.1	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	0.05	1tlk0	0.789	1.69	0.250	0.884	0.86	III	complex1.pdb.gz	15,18,41,43,45,47,48,49
2	0.05	1gl41	0.728	1.68	0.241	0.832	1.01	III	complex2.pdb.gz	44,46,47,49,54,55,78,80,81,82,84,85
3	0.05	2fdb1	0.798	1.83	0.242	0.895	0.61	III	complex3.pdb.gz	14,15,42,43,44,45,46,47,49,51,53,56,78,80,81,82,87
4	0.04	1kn4L	0.689	1.65	0.195	0.810	0.61	PDE	complex4.pdb.gz	21,39,41
5	0.04	1wcbL	0.691	1.66	0.182	0.810	0.68	PE1	complex5.pdb.gz	47,49,80,81,83,84
6	0.03	1indH	0.627	2.40	0.156	0.800	1.00	EOT	complex6.pdb.gz	16,41,43,85
7	0.03	1q72H	0.647	2.41	0.139	0.832	0.66	COC	complex7.pdb.gz	44,46,80,81,84

	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.