D-I-TASSER Q6P1A2-D2

D-I-TASSER results for Q6P1A2-D2

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

Input Sequence in FASTA format

>Q6P1A2 (112 residues)
LHSGYLVCFQMEFLIVIVERQAARLIQESPTLSKLAAITVLQPFYYLVQQTIHWLFMGYS
MTAFCLFTWDKWLKVYKSIYFLGHIFFLSLLFILPYIHKAMVPRKEKLKKME

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| LHSGYLVCFQMEFLIVIVERQAARLIQESPTLSKLAAITVLQPFYYLVQQTIHWLFMGYSMTAFCLFTWDKWLKVYKSIYFLGHIFFLSLLFILPYIHKAMVPRKEKLKKME
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Confidence	9501899999999999999999999974712025532836999999999999999997787776665344379999999999999999999999888876347765332259
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| LHSGYLVCFQMEFLIVIVERQAARLIQESPTLSKLAAITVLQPFYYLVQQTIHWLFMGYSMTAFCLFTWDKWLKVYKSIYFLGHIFFLSLLFILPYIHKAMVPRKEKLKKME
Prediction	5130013123312200201440351056264245037441131012311333233333333311030334422400333223222333333333331453335457556788
	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

CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
LHSGYLVCFQMEFLIVIVERQAARLIQESPTLSKLAAITVLQPFYYLVQQTIHWLFMGYSMTAFCLFTWDKWLKVYKSIYFLGHIFFLSLLFILPYIHKAMVPRKEKLKKME

4hpqC

0.06

0.05

2.40

1.17

DEthreader

KSELREIGRNLIEEWSTVLRLVNDMKFWQEITKMR--SH-LD-SKLNEIPTIRKQVENITRQYQTMLVQLKHEEYIS-VFEGISALIQKFKASCLEDIRQTRNLLYAFEYHL

6xkwn3

0.10

3.64

0.49

CEthreader

-TDWTIGHVHSGALGWNGMITFGMLYFLTLWGRSGLYSLKLVSWHFWLATIGIVLYASSMWVSGIMEGTVGAKFPMNVVRGVGGVLYLTGGLIMAYNLWATVAKQPKTANLA

1w27A

0.10

3.64

0.85

EigenThreader

SGMASMVLFEANILAVLAEVMSAIFAEVMQGKPEFTDHLTHKLTSPQWLGPQIEVIRSSTKMIEREINGTPIGVSMDNT-RLAIAAIGKLMFAQFSELVLDYGFKGAEIAMA

5o0tA

0.12

0.11

3.79

0.71

FFAS-3D

---GATLNLNGALILIPMLRHFMTWLRKTTINN-YIPIDESIEFHKLVGQVMFALAIVHTGAHFLNYTTFAQSLFGTKAGISGFLLLLVFIIMWVTAQAPIRKG--------

1gakA

0.06

2.69

0.78

SPARKS-K

VVSRQEQSYVQRGMVNFLDEEMHKLVKRFRDMRWNLGPGFVFLLKKVNRERMMRYCMDYARYSKKILQLKTLTKMGRFVGYRNYGVIRELYADVFRDVQGFPKMTAAMRKYS

6gcs5

0.12

0.11

3.77

0.77

CNFpred

VTAGIYLLLRSANILEYTPTVLFIILWIGLTTLSAGLIAICSNDLKRIIALSTMSQLGMMTIAIGLSAYNLALFHLLGHAFFKALLFMSAGSIIHSIL--------------

4wvmB

0.12

4.07

1.17

DEthreader

STPILRKVRNTLEAIVQVQMRCNDALDD-PTVNLF--T-EVQKKLSDFQKICDDHMSKLQATIAKLIDESALLNLFE--ENSPFN-IESLNMWMEFEEREINVLRMDTKAPA

4g5eA

0.12

4.12

0.66

MapAlign

HYDKWLHYHALIRQSVRAELMAGLAILIT-EHIGTNKIPAVQTRV-AKLIGFHQAMLAHIVASEEGFHYKPNILIYDFGRALYLENFSQMIYELVDLSGRSFLTDWGNRLFV

1wp9A

0.14

0.13

4.60

0.53

MUSTER

DLP--EIYKEVRKLLREMLRDALKPLAETGLLESSSPDIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEI

6bugC

0.09

0.06

2.36

0.90

HHsearch

ITWYYIAYGIFHGIGLVINDAWLRKKKTINKDRKGLKPLPENKWTKALGIFITFNTVMLSFLIFSGF-LNDLWFTK------------------------------------

(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	0.7077

(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	1r8iA	0.68	3.14	0.080	0.946	model1_1r8iA.pdb.gz
2	4iw0A3	0.66	3.16	0.037	0.946	model1_4iw0A3.pdb.gz
3	5ebzA3	0.66	3.20	0.066	0.946	model1_5ebzA3.pdb.gz
4	2rjsB2	0.66	3.14	0.091	0.893	model1_2rjsB2.pdb.gz
5	6sz9D	0.66	3.35	0.056	0.946	model1_6sz9D.pdb.gz
6	1w27A	0.66	3.21	0.082	0.955	model1_1w27A.pdb.gz
7	3qa8A	0.65	3.42	0.057	0.929	model1_3qa8A.pdb.gz
8	6at7B	0.64	3.71	0.036	0.991	model1_6at7B.pdb.gz
9	6cq0A	0.64	3.30	0.046	0.946	model1_6cq0A.pdb.gz
10	4n4jA2	0.63	3.34	0.047	0.911	model1_4n4jA2.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:0016747	1.00	transferase activity, transferring acyl groups other than amino-acyl groups
GO:0008374	0.72	O-acyltransferase activity
GO:0071617	0.67	lysophospholipid acyltransferase activity
GO:0047184	0.56	1-acylglycerophosphocholine O-acyltransferase 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:0009987	0.87	cellular process
GO:0008152	0.87	metabolic process
GO:0044699	0.86	single-organism process
GO:0071704	0.85	organic substance metabolic process
GO:0044238	0.84	primary metabolic process
GO:0044710	0.83	single-organism metabolic process
GO:0044763	0.82	single-organism cellular process
GO:0044237	0.82	cellular metabolic process
GO:0006629	0.81	lipid metabolic process
GO:0044255	0.79	cellular lipid metabolic process
GO:0046486	0.54	glycerolipid metabolic process
GO:0006644	0.54	phospholipid metabolic process
GO:0050789	0.51	regulation of biological 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:0016020	0.94	membrane
GO:0044464	0.84	cell part
GO:0044424	0.78	intracellular part
GO:0044444	0.70	cytoplasmic part
GO:0044446	0.53	intracellular organelle part
GO:0044425	0.52	membrane 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	0.066	1urfA	0.472	2.89	0.092	0.652	2.7.11.13	NA
2	0.060	1jqkF	0.538	4.03	0.093	0.902	1.2.99.2	NA
3	0.060	2uxwA	0.574	3.52	0.045	0.875	1.3.99.-	58
4	0.060	1jswB	0.593	3.61	0.119	0.902	4.3.1.1	NA
5	0.060	1yfeA	0.574	3.56	0.075	0.884	4.2.1.2	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	0.02	1egcC	0.584	3.32	0.108	0.875	0.40	FAD	complex1.pdb.gz	13,15,83,88
2	0.02	2j9tA	0.585	2.74	0.078	0.804	0.67	BO3	complex2.pdb.gz	56,59,79,83
3	0.01	1rke1	0.605	3.69	0.066	0.884	0.47	III	complex3.pdb.gz	2,3,54,55,58,59,61,65,66,78,79,82,85,86,89,93
4	0.01	3gm1B	0.599	3.63	0.056	0.911	0.47	III	complex4.pdb.gz	5,9,57,58,61,65
5	0.01	1zw2A	0.507	3.92	0.020	0.839	0.43	III	complex5.pdb.gz	3,4,7,10,11,14,17,56,63,76,84,87,91
6	0.01	3tj6A	0.504	4.16	0.038	0.866	0.45	III	complex6.pdb.gz	4,11,14,18,21,22,25,84,88,91,94
7	0.01	3s90A	0.497	4.01	0.041	0.839	0.46	III	complex7.pdb.gz	3,6,7,10,13,14,17,21,60,84,88,91,92,95
8	0.01	1ub44	0.246	4.56	0.044	0.446	0.47	III	complex8.pdb.gz	53,57,84,86

	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.