D-I-TASSER Q9H347-D1

D-I-TASSER results for Q9H347-D1

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

Input Sequence in FASTA format

>Q9H347 (96 residues)
MAKGGEALPQGSPAPVQDPHLIKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQ
LVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MAKGGEALPQGSPAPVQDPHLIKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR
Prediction	CCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCSSSSSCCCCSHHHHHHHHHHHHCCCHHHSSSSSCCSSCCCCCCHHHCCCCCCCSSSSSSSCCCC
Confidence	997788899999987899975999998699929999799991999999999997989789145446855699993799099999599999827999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MAKGGEALPQGSPAPVQDPHLIKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR
Prediction	756647444744547455553030302147542404045623043035203744714263020114133044653056260675200000134588
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCSSSSSCCCCSHHHHHHHHHHHHCCCHHHSSSSSCCSSCCCCCCHHHCCCCCCCSSSSSSSCCCC
MAKGGEALPQGSPAPVQDPHLIKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR

3q3fA

0.28

0.26

7.97

1.33

DEthreader

----KSG-RSWLIYKTTDHYGGQIFVKTLTKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG-

6jh0D2

0.23

0.19

5.88

2.03

SPARKS-K

----------------NSNDPLSILVRNNKGSIAYEVWLTQTVAELKQQVCQQEHVQADLFWLTFEGKPMEDKHQLGEYGLTPQCTVFMNLRLR--

1v5oA

0.17

0.14

4.44

0.53

MapAlign

-------------------SGMLITVYCVEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLDDHCSLGSYGLKDGDMVVLLQKDN--

1wx7A

0.95

0.91

25.43

0.34

CEthreader

----GSSGSSGSPAPVQDPHLIKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR

1wx7A

0.95

0.91

25.43

1.62

MUSTER

----GSSGSSGSPAPVQDPHLIKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR

1a5rA

0.19

6.06

1.17

HHsearch

MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG

1j8cA

0.64

0.61

17.55

1.70

FFAS-3D

MAENGESSGQGSAAAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIK----

5b83A

0.27

8.31

0.77

EigenThreader

IQDKEGIPPDQNIQKESLRGGMQIFVKTLTGKTTLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

1wx7A

0.95

0.91

25.43

1.76

CNFpred

----GSSGSSGSPAPVQDPHLIKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR

5b83A

0.28

0.25

7.65

1.33

DEthreader

------TGK-HLVLRL-G--GMQIFVKTLTKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGP

(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	0.7818

(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	1wx7A	0.79	1.68	0.930	0.854	model1_1wx7A.pdb.gz
2	5b83A	0.79	1.84	0.250	0.865	model1_5b83A.pdb.gz
3	2kanA	0.78	2.14	0.225	0.896	model1_2kanA.pdb.gz
4	1v5oA	0.77	1.55	0.159	0.854	model1_1v5oA.pdb.gz
5	3q3fA	0.77	2.03	0.260	0.906	model1_3q3fA.pdb.gz
6	1wx8A	0.76	2.12	0.359	0.885	model1_1wx8A.pdb.gz
7	7jtkk	0.75	2.05	0.097	0.906	model1_7jtkk.pdb.gz
8	5chfA	0.73	1.12	0.263	0.792	model1_5chfA.pdb.gz
9	6jh0D	0.73	1.52	0.191	0.802	model1_6jh0D.pdb.gz
10	2fazA	0.73	0.91	0.203	0.771	model1_2fazA.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:1901363	0.62	heterocyclic compound binding
GO:0097159	0.62	organic cyclic compound binding
GO:0003676	0.58	nucleic acid binding
GO:0003723	0.51	RNA 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:0009987	0.95	cellular process
GO:0071704	0.90	organic substance metabolic process
GO:0044238	0.89	primary metabolic process
GO:0043170	0.89	macromolecule metabolic process
GO:0044237	0.88	cellular metabolic process
GO:0044260	0.87	cellular macromolecule metabolic process
GO:0019538	0.86	protein metabolic process
GO:0065007	0.81	biological regulation
GO:0050789	0.80	regulation of biological process
GO:0050794	0.79	regulation of cellular process
GO:0019222	0.74	regulation of metabolic process
GO:0080090	0.72	regulation of primary metabolic process
GO:0060255	0.72	regulation of macromolecule metabolic process
GO:0031323	0.72	regulation of cellular metabolic process
GO:0006508	0.68	proteolysis
GO:0044265	0.67	cellular macromolecule catabolic process
GO:0044267	0.66	cellular protein metabolic process
GO:0006511	0.66	ubiquitin-dependent protein catabolic process
GO:0048519	0.65	negative regulation of biological process
GO:0032268	0.65	regulation of cellular protein metabolic process
GO:0006464	0.65	cellular protein modification process
GO:0044699	0.64	single-organism process
GO:0030162	0.63	regulation of proteolysis
GO:1903050	0.61	regulation of proteolysis involved in cellular protein catabolic process
GO:0048522	0.61	positive regulation of cellular process
GO:0016043	0.61	cellular component organization
GO:0048523	0.60	negative regulation of cellular process
GO:0061136	0.59	regulation of proteasomal protein catabolic process
GO:0050896	0.59	response to stimulus
GO:0048583	0.58	regulation of response to stimulus
GO:0032434	0.58	regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0031325	0.57	positive regulation of cellular metabolic process
GO:0010604	0.57	positive regulation of macromolecule metabolic process
GO:0080134	0.56	regulation of response to stress
GO:0045862	0.56	positive regulation of proteolysis
GO:0032446	0.56	protein modification by small protein conjugation
GO:0006996	0.56	organelle organization
GO:1903052	0.55	positive regulation of proteolysis involved in cellular protein catabolic process
GO:0048584	0.55	positive regulation of response to stimulus
GO:0044763	0.55	single-organism cellular process
GO:0034641	0.55	cellular nitrogen compound metabolic process
GO:0009892	0.55	negative regulation of metabolic process
GO:0080135	0.54	regulation of cellular response to stress
GO:0031324	0.54	negative regulation of cellular metabolic process
GO:0006950	0.54	response to stress
GO:0032436	0.53	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0016567	0.53	protein ubiquitination
GO:0010605	0.53	negative regulation of macromolecule metabolic process
GO:1901360	0.52	organic cyclic compound metabolic process
GO:0046483	0.52	heterocycle metabolic process
GO:0043161	0.52	proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0031399	0.52	regulation of protein modification process
GO:0010941	0.52	regulation of cell death
GO:0006725	0.52	cellular aromatic compound metabolic process
GO:0090304	0.51	nucleic acid metabolic process
GO:0065009	0.51	regulation of molecular function
GO:0042981	0.51	regulation of apoptotic process
GO:0009966	0.51	regulation of signal transduction
GO:1903071	0.50	positive regulation of ER-associated ubiquitin-dependent protein catabolic process
GO:0033554	0.50	cellular response to stress

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:0043226	0.89	organelle
GO:0043229	0.88	intracellular organelle
GO:0043231	0.87	intracellular membrane-bounded organelle
GO:0044444	0.82	cytoplasmic part
GO:0005634	0.75	nucleus
GO:0044446	0.71	intracellular organelle part
GO:0032991	0.66	macromolecular complex
GO:0005737	0.62	cytoplasm
GO:0044428	0.58	nuclear part
GO:0016020	0.57	membrane
GO:0005829	0.57	cytosol

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	0.133	2nptD	0.593	2.74	0.101	0.802	2.7.11.25	NA
2	0.066	2o2vA	0.543	2.63	0.101	0.719	2.7.12.2	74
3	0.060	2i6kA	0.510	3.64	0.024	0.750	5.3.3.2	NA
4	0.060	1hx3B	0.480	3.52	0.000	0.708	5.3.3.2	33
5	0.060	1mp8A	0.357	4.64	0.038	0.688	2.7.10.2 2.7.1.112	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	0.29	3a9kA	0.718	0.97	0.324	0.760	0.99	III	complex1.pdb.gz	62,64,67,88,90
2	0.28	1aar0	0.718	1.32	0.320	0.771	1.24	III	complex2.pdb.gz	29,64,67,68,69,88,90,91,92
3	0.20	2c7n1	0.713	0.87	0.333	0.750	1.45	III	complex3.pdb.gz	27,28,29,62,64,65,66,67,69,83,84,86,88,90,91,93,94
4	0.18	2d3gA	0.708	0.79	0.338	0.740	1.16	III	complex4.pdb.gz	29,62,64,65,66,67,69,86,88,90
5	0.04	2d071	0.700	1.31	0.173	0.781	1.03	III	complex5.pdb.gz	21,30,31,32,33,34,35,36,37,45,53,54

	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.