D-I-TASSER A6ND91-D2

D-I-TASSER results for A6ND91-D2

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

Input Sequence in FASTA format

>A6ND91 (158 residues)
GALWGAEDIRRLDAAGGLRSLRVTMATHPDGFRLEGPLAAAHSPGPCTVLYEGPVRGLCP
FAPRNSNTMAAAALAAPSLGFDGVIGVLVADTSLTDMHVVDVELSGPRGPTGRSFAVHTR
RENPAEPGAVTGSATVTAFWQSLLACCQLPSRPGIHLC

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| GALWGAEDIRRLDAAGGLRSLRVTMATHPDGFRLEGPLAAAHSPGPCTVLYEGPVRGLCPFAPRNSNTMAAAALAAPSLGFDGVIGVLVADTSLTDMHVVDVELSGPRGPTGRSFAVHTRRENPAEPGAVTGSATVTAFWQSLLACCQLPSRPGIHLC
Prediction	CCCCCHHHHHHHHHHCCCSSSSSSSSSCHHHCCCCCCCCCCCCCCCCSSSSSCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCSSSSSSSCCCCCCCSSSSSSSSCCCCCCCSSSSSSCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCSSSC
Confidence	95112899999986199418999985091550766421112468887799972799999877542669999999845579763599999889887625999999728876412698412799987666513799999999999999835899963649
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| GALWGAEDIRRLDAAGGLRSLRVTMATHPDGFRLEGPLAAAHSPGPCTVLYEGPVRGLCPFAPRNSNTMAAAALAAPSLGFDGVIGVLVADTSLTDMHVVDVELSGPRGPTGRSFAVHTRRENPAEPGAVTGSATVTAFWQSLLACCQLPSRPGIHLC
Prediction	61111041033027445054030303131501524542253654743100041404500630242011000000104413264030201001634531303030415446343504343346235643332032003200310240274673411112
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCHHHHHHHHHHCCCSSSSSSSSSCHHHCCCCCCCCCCCCCCCCSSSSSCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCSSSSSSSCCCCCCCSSSSSSSSCCCCCCCSSSSSSCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCSSSC
GALWGAEDIRRLDAAGGLRSLRVTMATHPDGFRLEGPLAAAHSPGPCTVLYEGPVRGLCPFAPRNSNTMAAAALAAPSLGFDGVIGVLVADTSLTDMHVVDVELSGPRGPTGRSFAVHTRRENPAEPGAVTGSATVTAFWQSLLACCQLPSRPGIHLC

1j5pA2

0.22

0.17

5.39

1.00

DEthreader

GAIGGLDVLSSIKD--FVKNVRIETIKPPKS-L-----G--LDLKGKTVVFEGSVEEASKLFPRNINVASTIGL-I-VG-FEKVKVTIVADPAMD-HNIHIVRISSAI------GNYEFKIENI------S-MLTVYSILRT-LRN-LE------IFG

1j5pA2

0.22

0.18

5.58

1.85

SPARKS-K

GAIGGLDVLSSIKDFV--KNVRIETIKPPKSLGLDL--------KGKTVVFEGSVEEASKLFPRNINVASTIGLIVGF---EKVKVTIVADPAMD-HNIHIVRISSAIGN------YEFKIENI-------SMLTVYSILRTLRNLESKIIFG-----

2dc1A

0.20

0.15

4.86

1.45

MapAlign

GAIGGLDAIFSAS--ELIEEIVLTTRKNWRQF------------GRKGVIFEGSASEAAQKFPKNLNVAATLSIAS-GK-D--VKVRLVADE-V-EENIHEILVRGEF------GEMEIRVRNRPMNPKTSYLAALSVTRILRNLK------------

1j5pA2

0.22

0.18

5.58

1.72

CEthreader

GAIGGLDVLSSIKD--FVKNVRIETIKPPKSLG--------LDLKGKTVVFEGSVEEASKLFPRNINVASTIGLIVG---FEKVKVTIVADPAMD-HNIHIVRISSAIG------NYEFKIENI-------SMLTVYSILRTLRNLESKIIFG-----

1j5pA2

0.24

0.19

5.92

1.61

MUSTER

GAIGGLDVLSSIKDF--VKNVRIETIKPPKSLGLD--------LKGKTVVFEGSVEEASKLFPRNINVASTIGLIV---GFEKVKVTIVADPAMD-HNIHIVRISSAI------GNYEFKIENI-------SMLTVYSILRTLRNLESKII--G----

2dc1A2

0.21

0.17

5.41

5.37

HHsearch

GAIGGLDAIFSA-S-ELIEEIVLTTRKNWRQFG------------RKGVIFEGSASEAAQKFPKNLNVAATLSIA--SG--KDVKVRLVAD-EVE-ENIHEILVRGEFGE------MEIRVRNRPMRNPKTSYLAALSVTRILRNLKE-----GLVV-

1j5pA2

0.23

0.18

5.55

1.77

FFAS-3D

GAIGGLDVLSSIKD--FVKNVRIETIKPPKSLGL--------DLKGKTVVFEGSVEEASKLFPRNINVASTIGLI---VGFEKVKVTIVADPAMDH-NIHIVRISSAIGNYEFKI-------------ENISMLTVYSILRTLRNLES----------

1j5pA2

0.21

0.16

5.24

1.18

EigenThreader

GAIGGLDVLSSIKDF--VKNVRIETIKPPKSLG--------LDLKGKTVVFEGSVEEASKLFPRNINVASTIGLIVG---FEKVKVTIVADP-AMDHNIHIVRISSAI------GNYEFKIENIS-----MLTVYSILRTLRNLESKIIFG-------

1j5pA

0.22

0.18

5.58

1.55

CNFpred

GAIGGLDVLSSIK--DFVKNVRIETIKPPKSLGLDL--------KGKTVVFEGSVEEASKLFPRNINVASTIGLIVG---FEKVKVTIVADPAMD-HNIHIVRISSA------IGNYEFKIENI-------SMLTVYSILRTLRNLESKIIFG-----

1j5pA

0.22

0.17

5.39

1.00

DEthreader

GAIGGLDVLSSIKD--FVKNVRIETIKPPKS-L-----G--LDLKGKTVVFEGSVEEASKLFPRNINVASTIGL-I-VG-FEKVKVTIVADPAMD-HNIHIVRISSAI------GNYEFKIENI------S-MLTVYSILRT-LRN-LE------IFG

(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	0.8353

(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	1j5pA	0.71	2.15	0.222	0.791	model1_1j5pA.pdb.gz
2	2dc1A2	0.69	2.23	0.208	0.791	model1_2dc1A2.pdb.gz
3	6ir4A2	0.59	4.12	0.134	0.861	model1_6ir4A2.pdb.gz
4	6k36A	0.58	4.17	0.127	0.861	model1_6k36A.pdb.gz
5	2axqA3	0.57	4.31	0.118	0.835	model1_2axqA3.pdb.gz
6	3abiA	0.54	4.10	0.051	0.791	model1_3abiA.pdb.gz
7	2ep7B	0.52	4.00	0.088	0.785	model1_2ep7B.pdb.gz
8	1wu2A	0.38	4.84	0.083	0.608	model1_1wu2A.pdb.gz
9	1v9lA2	0.35	5.01	0.135	0.627	model1_1v9lA2.pdb.gz
10	4zm6A3	0.34	5.04	0.055	0.570	model1_4zm6A3.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:0003824	0.91	catalytic activity
GO:0016740	0.82	transferase activity
GO:0004514	0.81	nicotinate-nucleotide diphosphorylase (carboxylating) 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	0.94	cellular process
GO:0071704	0.92	organic substance metabolic process
GO:0044699	0.92	single-organism process
GO:0044237	0.92	cellular metabolic process
GO:0044763	0.91	single-organism cellular process
GO:0044710	0.91	single-organism metabolic process
GO:1901360	0.90	organic cyclic compound metabolic process
GO:0044238	0.90	primary metabolic process
GO:0006807	0.90	nitrogen compound metabolic process
GO:0006725	0.90	cellular aromatic compound metabolic process
GO:1901575	0.89	organic substance catabolic process
GO:1901564	0.89	organonitrogen compound metabolic process
GO:0044712	0.89	single-organism catabolic process
GO:0044281	0.89	small molecule metabolic process
GO:0044248	0.89	cellular catabolic process
GO:0006139	0.89	nucleobase-containing compound metabolic process
GO:1901576	0.88	organic substance biosynthetic process
GO:0044711	0.88	single-organism biosynthetic process
GO:0044249	0.88	cellular biosynthetic process
GO:0019674	0.87	NAD metabolic process
GO:0019359	0.87	nicotinamide nucleotide biosynthetic process
GO:0006082	0.84	organic acid metabolic process
GO:0043649	0.83	dicarboxylic acid catabolic process
GO:0034213	0.82	quinolinate catabolic process
GO:0009435	0.81	NAD biosynthetic 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	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0005737	0.95	cytoplasm
GO:0044444	0.61	cytoplasmic 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	0.067	1j5pA	0.710	2.15	0.222	0.791	1.4.1.21	NA
2	0.066	2dc1A	0.688	2.37	0.198	0.797	1.4.1.21	NA
3	0.060	1szjG	0.523	3.78	0.079	0.772	1.2.1.12	21,100
4	0.060	2cvoA	0.542	3.89	0.070	0.759	1.2.1.38	NA
5	0.060	2pkqT	0.531	3.73	0.109	0.772	1.2.1.13	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	0.09	1j5p0	0.710	2.15	0.222	0.791	0.65	III	complex1.pdb.gz	3,4,5,6,7,8,10,11,12,17,74,75,107,108,116,117,118,119,120,121,122,123,134,137,138,141,145
2	0.02	1qxsA	0.532	3.78	0.107	0.778	0.56	S70	complex2.pdb.gz	25,27,32,34,88,90
3	0.01	1rm0A	0.572	3.81	0.075	0.797	0.43	D6P	complex3.pdb.gz	4,24,74,85,101,121

	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.