D-I-TASSER Q9H4B4-D3

D-I-TASSER results for Q9H4B4-D3

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

Input Sequence in FASTA format

>Q9H4B4 (120 residues)
PQLGILRYFASYMEQHLMKGGDLPSVEEVEVPAPPLLLQWVKTDQALLMLFSDGTVQVNF
YGDHTKLILSGWEPLLVTFVARNRSACTYLASHLRQLGCSPDLRQRLRYALRLLRDRSPA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| PQLGILRYFASYMEQHLMKGGDLPSVEEVEVPAPPLLLQWVKTDQALLMLFSDGTVQVNFYGDHTKLILSGWEPLLVTFVARNRSACTYLASHLRQLGCSPDLRQRLRYALRLLRDRSPA
Prediction	CCSSHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCSSSSSCCCSSSSSSCCCSSSSSSSCCCCSSSSSCCCCSSSSSSCCCCCSSSSSHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC
Confidence	903269999999999976436776656555678713303444186699997199299998268719999479973999991899779998577877199999999999999999986059
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| PQLGILRYFASYMEQHLMKGGDLPSVEEVEVPAPPLLLQWVKTDQALLMLFSDGTVQVNFYGDHTKLILSGWEPLLVTFVARNRSACTYLASHLRQLGCSPDLRQRLRYALRLLRDRSPA
Prediction	843400520451046203633644446566453232023124343100010234303021353322000137441000002674633314044047452375035104202510563278
	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

CCSSHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCSSSSSCCCSSSSSSCCCSSSSSSSCCCCSSSSSCCCCSSSSSSCCCCCSSSSSHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC
PQLGILRYFASYMEQHLMKGGDLPSVEEVEVPAPPLLLQWVKTDQALLMLFSDGTVQVNFYGDHTKLILSGWEPLLVTFVARNRSACTYLASHLRQLGCSPDLRQRLRYALRLLRDRSPA

6mf4A

0.25

0.19

5.94

1.17

DEthreader

--------------------------DEEYHKDDVFLRRYTRYKPFVMFELSDGTFQFNFK-DHHKMAISD-GGKLVTYISPSHESTTYPLVEVLKYGEPSNFREKLTLIKEGLKQKSTI

3fvhA1

0.32

9.54

2.22

SPARKS-K

HLSDMLQQLHSVNASKPSERGLVRPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCP-LMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSS

3fvhA

0.29

0.28

8.63

0.92

MapAlign

-KKITLLKYFRNYMSEHLLKAGANITPREGDELAPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPL-MAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSS

3fvhA

0.37

10.89

0.90

CEthreader

KKITLLKYFRNYMSEHLLKAGANITPREGELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMA-AVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSS

3fvhA

0.37

10.89

1.91

MUSTER

KKITLLKYFRNYMSEHLLKAGANIPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPL-MAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSS

3fvhA

0.36

10.66

3.53

HHsearch

KKITLLKYFRNYMSEHLLKAGANITPREELARL-PYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPL-MAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSS

3fvhA

0.37

10.89

1.74

FFAS-3D

KKITLLKYFRNYMSEHLLKAGAITPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCP-LMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSS

3fvhA

0.30

9.09

1.15

EigenThreader

PNSLMKKITLLKYFRNYMSEHLLKAGANITPRRLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPL-MAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSS

1q4kA

0.36

10.67

1.87

CNFpred

KKITLLKYFRNYMSEHLLKAGANITPREGDLARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPL-MAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSS

3fvhA

0.36

0.28

8.19

1.00

DEthreader

---------------------------DEGEARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLM-AAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSS

(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	0.6922

(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	3fvhA	0.87	2.43	0.319	0.992	model1_3fvhA.pdb.gz
2	4rs6A	0.78	2.90	0.345	0.967	model1_4rs6A.pdb.gz
3	6mf4A	0.69	3.00	0.204	0.858	model1_6mf4A.pdb.gz
4	4n7vA	0.64	2.25	0.088	0.733	model1_4n7vA.pdb.gz
5	5lhxA	0.60	1.49	0.150	0.667	model1_5lhxA.pdb.gz
6	3p24A	0.59	3.14	0.053	0.775	model1_3p24A.pdb.gz
7	4mmhA	0.58	3.80	0.064	0.858	model1_4mmhA.pdb.gz
8	6ljaA3	0.57	3.87	0.018	0.867	model1_6ljaA3.pdb.gz
9	4on1A	0.57	3.13	0.064	0.792	model1_4on1A.pdb.gz
10	4o9xA	0.57	3.86	0.069	0.883	model1_4o9xA.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	0.97	catalytic activity
GO:0016301	0.96	kinase activity
GO:0004674	0.93	protein serine/threonine kinase 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	0.98	cellular process
GO:0065007	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0050794	0.92	regulation of cellular process
GO:0044699	0.91	single-organism process
GO:0022402	0.88	cell cycle process
GO:1903047	0.85	mitotic cell cycle process
GO:0051726	0.83	regulation of cell cycle
GO:0048518	0.81	positive regulation of biological process
GO:0048522	0.80	positive regulation of cellular process
GO:0044260	0.79	cellular macromolecule metabolic process
GO:0044238	0.79	primary metabolic process
GO:0010564	0.79	regulation of cell cycle process
GO:0048519	0.78	negative regulation of biological process
GO:0044763	0.78	single-organism cellular process
GO:0048523	0.77	negative regulation of cellular process
GO:0006464	0.77	cellular protein modification process
GO:0000075	0.77	cell cycle checkpoint
GO:0006468	0.76	protein phosphorylation
GO:0007346	0.75	regulation of mitotic cell cycle
GO:0080090	0.71	regulation of primary metabolic process
GO:0060255	0.71	regulation of macromolecule metabolic process
GO:0044772	0.70	mitotic cell cycle phase transition
GO:0043066	0.70	negative regulation of apoptotic process
GO:0016043	0.70	cellular component organization
GO:0009893	0.70	positive regulation of metabolic process
GO:0010604	0.69	positive regulation of macromolecule metabolic process
GO:0050896	0.68	response to stimulus
GO:0006996	0.68	organelle organization
GO:0051246	0.67	regulation of protein metabolic process
GO:0045786	0.67	negative regulation of cell cycle
GO:0051247	0.66	positive regulation of protein metabolic process
GO:0033554	0.66	cellular response to stress
GO:0007093	0.66	mitotic cell cycle checkpoint
GO:0006974	0.65	cellular response to DNA damage stimulus
GO:0031323	0.63	regulation of cellular metabolic process
GO:1901990	0.61	regulation of mitotic cell cycle phase transition
GO:0045732	0.61	positive regulation of protein catabolic process
GO:0031325	0.60	positive regulation of cellular metabolic process
GO:1902589	0.58	single-organism organelle organization
GO:0032268	0.58	regulation of cellular protein metabolic process
GO:0007017	0.58	microtubule-based process
GO:0007010	0.58	cytoskeleton organization
GO:0007165	0.57	signal transduction
GO:0000226	0.57	microtubule cytoskeleton organization
GO:0051171	0.56	regulation of nitrogen compound metabolic process
GO:0032270	0.56	positive regulation of cellular protein metabolic process
GO:0031326	0.56	regulation of cellular biosynthetic process
GO:0035556	0.55	intracellular signal transduction
GO:0006355	0.55	regulation of transcription, DNA-templated
GO:0006357	0.54	regulation of transcription from RNA polymerase II promoter
GO:1901991	0.52	negative regulation of mitotic cell cycle phase transition
GO:0032436	0.52	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0031324	0.52	negative regulation of cellular metabolic process
GO:0010605	0.52	negative regulation of macromolecule metabolic process
GO:0000122	0.51	negative regulation of transcription from RNA polymerase II promoter
GO:0051128	0.50	regulation of cellular component organization

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:0043229	0.95	intracellular organelle
GO:0044446	0.92	intracellular organelle part
GO:0044430	0.88	cytoskeletal part
GO:0043232	0.87	intracellular non-membrane-bounded organelle
GO:0005815	0.86	microtubule organizing center
GO:0005813	0.83	centrosome
GO:0005737	0.75	cytoplasm
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0044444	0.71	cytoplasmic part
GO:0005634	0.71	nucleus
GO:0032991	0.52	macromolecular complex
GO:0044428	0.51	nuclear 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	0.060	1tlbA	0.486	4.53	0.060	0.842	1.3.3.3	NA
2	0.060	2x1cA	0.476	4.74	0.043	0.817	2.3.1.164	NA
3	0.060	1ftaA	0.511	3.78	0.072	0.742	3.1.3.11	44
4	0.060	3bziA	0.862	2.49	0.319	0.992	2.7.11.21	NA
5	0.060	1jroB	0.486	3.78	0.030	0.717	1.1.1.204	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	2vgrC	0.537	4.03	0.040	0.808	0.16	BLA	complex1.pdb.gz	47,49,51,57

	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.