D-I-TASSER Q05932-D1

D-I-TASSER results for Q05932-D1

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

Input Sequence in FASTA format

>Q05932 (136 residues)
MSRARSHLRAALFLAAASARGITTQVAARRGLSAWPVPQEPSMEYQDAVRMLNTLQTNAG
YLEQVKRQRGDPQTQLEAMELYLARSGLQISPELFTKYFWRLYHRLEETKDGSCVSMPPY
FRFLTLMAFHVFLQEK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSRARSHLRAALFLAAASARGITTQVAARRGLSAWPVPQEPSMEYQDAVRMLNTLQTNAGYLEQVKRQRGDPQTQLEAMELYLARSGLQISPELFTKYFWRLYHRLEETKDGSCVSMPPYFRFLTLMAFHVFLQEK
Prediction	CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCSSSSSSCCCSCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCC
Confidence	9547888988788765413678753220100112345567653145555543213228999999999709999943571348755894189999999999999999986402689998189999999999999729
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSRARSHLRAALFLAAASARGITTQVAARRGLSAWPVPQEPSMEYQDAVRMLNTLQTNAGYLEQVKRQRGDPQTQLEAMELYLARSGLQISPELFTKYFWRLYHRLEETKDGSCVSMPPYFRFLTLMAFHVFLQEK
Prediction	7543463044143243444444547444444346452354454514501411103222120022015536354330420221131454403663015103401520473467675421210120030012103648
	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 DeepPotential. 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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCSSSSSSCCCSCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCC
MSRARSHLRAALFLAAASARGITTQVAARRGLSAWPVPQEPSMEYQDAVRMLNTLQTNAGYLEQVKRQRGDPQTQLEAMELYLARSGLQISPELFTKYFWRLYHRLEETKDGSCVSMPPYFRFLTLMAFHVFLQEK

1o5zA1

0.20

0.14

4.48

1.01

SPARKS-K

---------------------------------------HHHMAYLEVLRYLYHKVKPGERISMLLSKLGNPHLEYSTFRERIRLNEEYISEEDVVKIYETMEPILNELDKEEI-FSPSFFEVVTAMAFLYFAEKN

2gcaA1

0.17

0.12

3.86

1.03

MapAlign

------------------------------------------MNYTETVAYIHSFPRLARRILTLLHALGNPQAANAIAHVLEASGLTVIPDAALVNAVAFVRAALERLQQQQADFNVTEFEFITALGYWYFRQR-

1o5zA1

0.25

0.15

4.78

2.22

HHsearch

---------------------------------------HHHMAYLEVLRYLYH--KVKPGLERLLSKLGNPHLEY-----------KRISEEDVVKIYETMEPILNELDK-EEIFSPSFFEVVTAMAFLYFAEKN

2gcaA1

0.12

4.13

1.37

FFAS-3D

-----NYTETVAYIHSFPRLAKTGDHRRILTLLHALGNPQQQGRY-IHVTGTNGKGSAANAIAHVLEASGLTVGLYTSPFERIMIDHEPIPDAALVNAVAFVRAALERLQQQQADFNVTEFEFITALGYWYFRQRQ

1o5zA1

0.23

0.15

4.85

0.83

DEthreader

----------------------------------------HHMAYLEVLRYLYH-KVKPGRISMLLSKLGNPHLEY-KVGSYIRLNEEYISEEDVVKIYETMEPILNELDK-EEIFSPSFFEVVTAMAFLYFAEKN

2gcaA1

0.20

0.14

4.46

0.67

SPARKS-K

------------------------------------------MNYTETVAYIHSFPRLHRRILTLLHALGNPQQAANAIAHVLEASGLTIPDAALVNAVAFVRAALERLQQQQADFNVTEFEFITALGYWYFRQRQ

2gcaA

0.17

0.12

3.86

1.03

MapAlign

------------------------------------------MNYTETVAYIHSFPRLARRILTLLHALGNPQAANAIAHVLEASGLTVIPDAALVNAVAFVRAALERLQQQQADFNVTEFEFITALGYWYFRQR-

1o5zA1

0.21

0.15

4.68

0.84

CEthreader

---------------------------------------HHHMAYLEVLRYLYHKVKPGERISMLLSKLGNPHLHLSTFRERIRLNEEYISEEDVVKIYETMEPILNELDKEEIF-SPSFFEVVTAMAFLYFAEKN

1o5zA1

0.20

0.14

4.48

0.95

MUSTER

---------------------------------------HHHMAYLEVLRYLYHKKPGLERISMLLSKLGNPHLEYSTFRERIRLNEEYISEEDVVKIYETMEPILNELDK-EEIFSPSFFEVVTAMAFLYFAEKN

2gcaA

0.21

0.15

4.66

1.96

HHsearch

------------------------------------------MNYTETVAYIHSFPRLAKDHRRLLHALGNPQQQGRYIAHVLEASGLTIPDAALVNAVAFVRAALERLQQQQADFNVTEFEFITALGYWYFRQRQ

(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	0.614

(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 DeepPotential, 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	2gcaA1	0.58	2.67	0.138	0.691	model1_2gcaA1.pdb.gz
2	1o5zA1	0.55	3.03	0.191	0.691	model1_1o5zA1.pdb.gz
3	2vosA1	0.52	3.18	0.160	0.691	model1_2vosA1.pdb.gz
4	4fr2A	0.38	5.31	0.055	0.684	model1_4fr2A.pdb.gz
5	4i1aA1	0.32	3.93	0.044	0.485	model1_4i1aA1.pdb.gz
6	2abkA1	0.31	4.60	0.061	0.493	model1_2abkA1.pdb.gz
7	1fadA	0.31	4.08	0.023	0.456	model1_1fadA.pdb.gz
8	1w78A1	0.31	5.19	0.041	0.581	model1_1w78A1.pdb.gz
9	3n2aA	0.30	5.59	0.058	0.603	model1_3n2aA.pdb.gz
10	4acqA1	0.30	5.17	0.050	0.551	model1_4acqA1.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:0004326	1.00	tetrahydrofolylpolyglutamate synthase activity
GO:0008841	0.97	dihydrofolate synthase activity
GO:1901363	0.53	heterocyclic compound binding
GO:0097159	0.53	organic cyclic compound 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:0044237	0.99	cellular metabolic process
GO:0044699	0.97	single-organism process
GO:0071704	0.94	organic substance metabolic process
GO:0006807	0.93	nitrogen compound metabolic process
GO:1901360	0.92	organic cyclic compound metabolic process
GO:0046483	0.92	heterocycle metabolic process
GO:0044763	0.92	single-organism cellular process
GO:0006725	0.92	cellular aromatic compound metabolic process
GO:1901564	0.91	organonitrogen compound metabolic process
GO:0034641	0.90	cellular nitrogen compound metabolic process
GO:0044710	0.89	single-organism metabolic process
GO:0044281	0.88	small molecule metabolic process
GO:0009058	0.80	biosynthetic process
GO:0044249	0.79	cellular biosynthetic process
GO:0006082	0.79	organic acid metabolic process
GO:0019752	0.78	carboxylic acid metabolic process
GO:1901605	0.76	alpha-amino acid metabolic process
GO:1901576	0.75	organic substance biosynthetic process
GO:0006760	0.75	folic acid-containing compound metabolic process
GO:1901566	0.74	organonitrogen compound biosynthetic process
GO:0044271	0.74	cellular nitrogen compound biosynthetic process
GO:1901362	0.73	organic cyclic compound biosynthetic process
GO:0019438	0.73	aromatic compound biosynthetic process
GO:0018130	0.73	heterocycle biosynthetic process
GO:0042559	0.71	pteridine-containing compound biosynthetic process
GO:0042398	0.71	cellular modified amino acid biosynthetic process
GO:0009108	0.71	coenzyme biosynthetic process
GO:0044238	0.66	primary metabolic process
GO:0009396	0.65	folic acid-containing compound biosynthetic process
GO:0046900	0.63	tetrahydrofolylpolyglutamate metabolic process
GO:0006536	0.58	glutamate metabolic process
GO:0006139	0.58	nucleobase-containing compound metabolic process
GO:0046901	0.56	tetrahydrofolylpolyglutamate 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:0044424	1.00	intracellular part
GO:0044444	0.99	cytoplasmic part
GO:0044446	0.98	intracellular organelle part
GO:0005759	0.97	mitochondrial matrix

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	3ippB	0.443	5.09	0.068	0.809	2.8.1.1	NA
2	0.060	2vs4A	0.435	4.82	0.048	0.735	2.4.1.87	NA
3	0.060	1ileA	0.430	4.95	0.045	0.757	6.1.1.5	NA
4	0.060	1s4nA	0.431	4.83	0.067	0.713	2.4.1.131	NA
5	0.060	1qh3A	0.428	4.73	0.073	0.750	3.1.2.6	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	2h39A	0.445	5.04	0.047	0.779	0.46	ADQ	complex1.pdb.gz	71,73,74,75,76
	2	0.01	3gdpA	0.443	4.91	0.051	0.787	0.41	UUU	complex2.pdb.gz	63,64,66,71

	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.