D-I-TASSER Q9ULI2-D2

D-I-TASSER results for Q9ULI2-D2

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

Input Sequence in FASTA format

>Q9ULI2 (92 residues)
NRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHENFAKMIDEAEVLEFPMVVKNTRGH
RGKAVFLARDKHHLADLSHLIRHEAPYLFQKY

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| NRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHENFAKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKY
Prediction	CCHHHHHHHHCHHHHHHHHHHCCCCCCCSSSSCCHHHHHHHHHHHHHHCCCSSSSSCCCCCCCCSSSSCCHHHHHHHHHHHHCCCCSSSSCC
Confidence	97899999616999999999919899997996283139999999993199889970999985227996999999999999850898799619
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| NRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHENFAKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKY
Prediction	85450032032133024105737042131210334741440252066140000021343341310320534720450163057524100034
	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

                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHCHHHHHHHHHHCCCCCCCSSSSCCHHHHHHHHHHHHHHCCCSSSSSCCCCCCCCSSSSCCHHHHHHHHHHHHCCCCSSSSCC
NRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHENFAKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKY

6dgiA2

0.13

4.51

1.50

DEthreader

CGPEASANSFNKITSKLWYDALDIPNTPYLFLTNTSSIDKAKQAFGHW-GSIFVKAARQGSSVGCYKVTTEDQIAPAIEAAFGSEQVLVEQA

6dgiA2

0.13

4.52

1.65

SPARKS-K

CGPEASANSFNKITSKLWYDALDIPNTPYLFLTNTPSSIDKAKQAFGHWGSIFVKAARQGSSVGCYKVTTEDQIAPAIEAAFGFSQVLVEQA

1bxrA2

0.16

0.15

5.08

0.76

MapAlign

TSPDAIDRAEDRERFQHAVERLKLKQPANATVT---AIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSPVLLDHF

1bxrA2

0.17

0.16

5.37

0.56

CEthreader

TSPDAIDRAEDRERFQHAVERLKLKQPANATVTA---IEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVAPVLLDHF

3k5iC

0.20

6.26

1.31

MUSTER

PSWQAIRTIQNKFNQKEHLRKYGIPMAEHRELVEN-TPAELAKVGEQLGYPLMLKSKTMADGRGNFRVNSQDDIPEALEALK-DRPLYAEKW

1bxrA2

0.18

0.17

5.66

1.06

HHsearch

TSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEM---AVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTASNDAPVLLDHF

4iwxA2

0.31

0.30

9.20

1.49

FFAS-3D

NESVAIARARDKLRSMQLLARQGIDLPVTGIAHSPDDTSDLID--MVGGAPLVVKLVEGTQGIGVVLAETRQAAESVIDAFRGNAHILVQEY

1ehiA2

0.09

3.34

0.90

EigenThreader

APLRGHAVSFDKALTKELLTVNGIRNTKYIVVDPE-SANNWDKIVAELGNIVFVKAANQGSSVGISRVTNAEEYTEALSDSFQDYKVLIEEA

4mamA

0.15

0.14

4.78

1.32

CNFpred

PSAKAIAISQDRLLEKSFMQDHGIATAKFVNID---SLAKLQSAVDDHGLPAILKTRRFGDGKGQFVIRSQEDITKAWDVLKDPDGLIYEAF

6dgiA

0.13

4.51

1.50

DEthreader

CGPEASANSFNKITSKLWYDALDIPNTPYLFLTNTSSIDKAKQAFGHW-GSIFVKAARQGSSVGCYKVTTEDQIAPAIEAAFGSEQVLVEQA

(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	0.8759

(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	6dgiA	0.90	1.13	0.132	0.989	model1_6dgiA.pdb.gz
2	2i8cB	0.89	1.39	0.120	1.000	model1_2i8cB.pdb.gz
3	1ehiA2	0.89	1.57	0.098	1.000	model1_1ehiA2.pdb.gz
4	3i12A	0.88	1.73	0.141	1.000	model1_3i12A.pdb.gz
5	3e5nA2	0.87	1.72	0.130	1.000	model1_3e5nA2.pdb.gz
6	2vpqB2	0.87	1.25	0.202	0.967	model1_2vpqB2.pdb.gz
7	1iowA	0.86	1.67	0.176	0.989	model1_1iowA.pdb.gz
8	3lwbA2	0.85	1.58	0.200	0.978	model1_3lwbA2.pdb.gz
9	4fu0A	0.85	1.94	0.141	1.000	model1_4fu0A.pdb.gz
10	3se7A	0.84	1.40	0.184	0.946	model1_3se7A.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:0072590	1.00	N-acetyl-L-aspartate-L-glutamate ligase activity
GO:0072591	0.70	citrate-L-glutamate ligase 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:0008152	0.93	metabolic process
GO:0071704	0.91	organic substance metabolic process
GO:0044237	0.91	cellular metabolic process
GO:1901576	0.84	organic substance biosynthetic process
GO:0006807	0.84	nitrogen compound metabolic process
GO:0044249	0.83	cellular biosynthetic process
GO:1901564	0.82	organonitrogen compound metabolic process
GO:0044699	0.81	single-organism process
GO:1901566	0.79	organonitrogen compound biosynthetic process
GO:0044763	0.74	single-organism cellular process
GO:0044710	0.73	single-organism metabolic process
GO:0044238	0.73	primary metabolic process
GO:0044281	0.72	small molecule metabolic process
GO:1901135	0.68	carbohydrate derivative metabolic process
GO:0065007	0.67	biological regulation
GO:1901137	0.66	carbohydrate derivative biosynthetic process
GO:0050789	0.65	regulation of biological process
GO:0043170	0.65	macromolecule metabolic process
GO:0050794	0.64	regulation of cellular process
GO:0044260	0.63	cellular macromolecule metabolic process
GO:0065008	0.62	regulation of biological quality
GO:0016043	0.62	cellular component organization
GO:0044711	0.59	single-organism biosynthetic process
GO:0034645	0.59	cellular macromolecule biosynthetic process
GO:0051128	0.58	regulation of cellular component organization
GO:0022603	0.58	regulation of anatomical structure morphogenesis
GO:0009252	0.58	peptidoglycan biosynthetic process
GO:0071555	0.57	cell wall organization
GO:0034641	0.57	cellular nitrogen compound metabolic process
GO:0008360	0.57	regulation of cell shape
GO:0044271	0.51	cellular nitrogen compound 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:0005737	1.00	cytoplasm

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	1vbgA	0.673	2.85	0.152	0.913	2.7.9.1	NA
2	0.060	3mwdA	0.680	2.57	0.094	0.924	2.3.3.8	NA
3	0.060	2i8cB	0.892	1.39	0.120	1.000	6.3.2.4	15
4	0.060	2dwcB	0.762	1.54	0.074	0.880	2.1.2.-	NA
5	0.060	1z2oX	0.741	2.03	0.179	0.913	2.7.1.159	88

	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	0.30	3jzfB	0.837	1.64	0.198	0.989	0.70	JZK	complex1.pdb.gz	12,53,55,56,59,60,61,62,63,64,65,88,90,91,92
	2	0.28	3se7E	0.849	1.41	0.184	0.946	0.60	ATP	complex2.pdb.gz	53,55,60,61,62,65

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.