D-I-TASSER Q9H306-D1

D-I-TASSER results for Q9H306-D1

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

Input Sequence in FASTA format

>Q9H306 (261 residues)
MKRLLLLFLFFITFSSAFPLVRMTENEENMQLAQAYLNQFYSLEIEGNHLVQSKNRSLID
DKIREMQAFFGLTVTGKLDSNTLEIMKTPRCGVPDVGQYGYTLPGWRKYNLTYRIINYTP
DMARAAVDEAIQEGLEVWSKVTPLKFTKISKGIADIMIAFRTRVHGRCPRYFDGPLGVLG
HAFPPGPGLGGDTHFDEDENWTKDGAGFNLFLVAAHEFGHALGLSHSNDQTALMFPNYVS
LDPRKYPLSQDDINGIQSIYG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MKRLLLLFLFFITFSSAFPLVRMTENEENMQLAQAYLNQFYSLEIEGNHLVQSKNRSLIDDKIREMQAFFGLTVTGKLDSNTLEIMKTPRCGVPDVGQYGYTLPGWRKYNLTYRIINYTPDMARAAVDEAIQEGLEVWSKVTPLKFTKISKGIADIMIAFRTRVHGRCPRYFDGPLGVLGHAFPPGPGLGGDTHFDEDENWTKDGAGFNLFLVAAHEFGHALGLSHSNDQTALMFPNYVSLDPRKYPLSQDDINGIQSIYG
Prediction	CCHHHHHHHHHHHHHHCCCCCCCCCCCHCHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCHHHHHHHHHHHHHHHHHCCCCSSSSCCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCC
Confidence	924999999999998227788778882119999999999389999887643345568999999999999299975447999999861888899775555667788777764126740799999899999999999999802785179806899754899851578887777778776333114787776772554575576668874068888887652552688899866544662226888778899999999999729
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MKRLLLLFLFFITFSSAFPLVRMTENEENMQLAQAYLNQFYSLEIEGNHLVQSKNRSLIDDKIREMQAFFGLTVTGKLDSNTLEIMKTPRCGVPDVGQYGYTLPGWRKYNLTYRIINYTPDMARAAVDEAIQEGLEVWSKVTPLKFTKISKGIADIMIAFRTRVHGRCPRYFDGPLGVLGHAFPPGPGLGGDTHFDEDENWTKDGAGFNLFLVAAHEFGHALGLSHSNDQTALMFPNYVSLDPRKYPLSQDDINGIQSIYG
Prediction	433000211120120100102455564622630350054022044754544545445403510340163160523441355025314443133442444334433043341332023204513463034104400420262030313424544210201012220232122133321330231233433303120323230234432210110031301100003134333100101033343551503510140036258
	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                 160                 180                 200                 220                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHCCCCCCCCCCCHCHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCHHHHHHHHHHHHHHHHHCCCCSSSSCCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCC
MKRLLLLFLFFITFSSAFPLVRMTENEENMQLAQAYLNQFYSLEIEGNHLVQSKNRSLIDDKIREMQAFFGLTVTGKLDSNTLEIMKTPRCGVPDVGQYGYTLPGWRKYNLTYRIINYTPDMARAAVDEAIQEGLEVWSKVTPLKFTKISKGIADIMIAFRTRVHGRCPRYFDGPLGVLGHAFPPGPGLGGDTHFDEDENWTKDGAGFNLFLVAAHEFGHALGLSHSNDQTALMFPNYVSLDPRKYPLSQDDINGIQSIYG

1slmA

0.60

0.50

14.39

1.17

DEthreader

-------------------------------LVQKYLENYYDLKKD--------S-GPVVKKIREMQKFLGLEVTGKLDSDTLEVMRKPRCGVPDVGH-R-GIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHG-DFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTLTRFRLSQDDINGIQSLYG

2mzeA

0.46

0.42

12.30

3.14

SPARKS-K

---------------LPLPQEAGGMSELQWEQAQDYLKRFYLYDSETKN------ANSLEAKLKEMQKFFGLPITGMLNSRVIEIMQKPRCGVPDVAEYFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDS-YPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWDGSSLGINFLYAATHALGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYG

1l6jA

0.47

0.39

11.38

1.24

MapAlign

--------------------------LTDRQLAEEYLYRYGYT---------------LGPALLLLQKQLSLPETGELDSATLKAMRTPRCGVPDLGRFQTFDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEH-GDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLPDQGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYR-FTEGPP-LHKDDVNGIRHLYG

1l6jA2

0.46

0.40

11.73

0.97

CEthreader

----------------VLFPGDLRTNLTDRQLAEEYLYRYGYT---------------LGPALLLLQKQLSLPETGELDSATLKAMRTPRCGVPDLGRFQTFELKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGY-PFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGDQGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRF--TEGPPLHKDDVNGIRHLYG

1su3B

0.58

0.47

13.43

2.09

MUSTER

-----------------------------VDLVQKYLEKYYNLKSG-----------PVVEKLKQMQEFFGLKVTGKPDAETLKVMKQPRCGVPDVA------PRWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRDN-SPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSG--DVQLAQDDIDGIQAIYG

1l6jA

0.47

0.41

11.94

3.75

HHsearch

---------------VLFPGDLR-TNLTDRQLAEEYLYRYGYT---------------LGPALLLLQKQLSLPETGELDSATLKAMRTPRCGVPDLGRFQTFDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGY-PFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGDQGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTE--GPPLHKDDVNGIRHLYG

2mzeA

0.38

0.35

10.33

2.65

FFAS-3D

-----------------LPLPQEGMSELQWEQAQDYLKRFYLYDSETK------NANSLEAKLKEMQKFFGLPITGMLNSRVIEIMQKPRCGVPDVYSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHALGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYG

2mzeA

0.38

0.35

10.43

1.43

EigenThreader

---------------LPLPQEAGGMSELQWEQAQDYLKRFYLYDSETKN------ANSLEAKLKEMQKFFGLPITMLNSRVIEIMQKPRCGVPDVAEYSLFPNSPKWTSKVVTYRIVYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHG-DSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTGSSLGINFLYAATHALGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYG

1su3A

0.58

0.47

13.42

2.62

CNFpred

-------------------------------LVQKYLEKYYNLK------------GPVVEKLKQMQEFFGLKVTGKPDAETLKVMKQPRCGVPDVA------PRWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRD-NSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSG--DVQLAQDDIDGIQAIYG

1gxdA

0.52

0.45

13.07

1.17

DEthreader

---------------------------TDKELAVQYLNTFYGCP-KESCNL--FV-LK--DTLKKMQKFFGLPQTGDLDQNTIETMRKPRCGNPDVANYNPRKPKWDKNQITYRIIGYTPDLDPETVDDAFARAFQVWSDVTPLRFSRIHDGEADIMINFGRWEHG-DGYPFDGKDGLLAHAFAPGTGVGGDSHFDDDELWTLEGQGYSLFLVAAHAFGHAMGLEHSQDPGALMAPIYT-YTKNF-RLSQDDIKGIQELYG

(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	0.7445

(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	2mzeA	0.83	2.05	0.462	0.912	model1_2mzeA.pdb.gz
2	1slmA	0.83	0.80	0.595	0.843	model1_1slmA.pdb.gz
3	1gxdA	0.82	1.70	0.488	0.870	model1_1gxdA.pdb.gz
4	1l6jA2	0.81	1.19	0.458	0.831	model1_1l6jA2.pdb.gz
5	1su3B	0.79	0.95	0.571	0.812	model1_1su3B.pdb.gz
6	4fu4A1	0.60	1.88	0.561	0.628	model1_4fu4A1.pdb.gz
7	1bzsA	0.60	1.86	0.573	0.628	model1_1bzsA.pdb.gz
8	3ba0A	0.59	1.01	0.582	0.605	model1_3ba0A.pdb.gz
9	1rm8A	0.59	1.14	0.481	0.605	model1_1rm8A.pdb.gz
10	1buvM	0.59	1.35	0.463	0.609	model1_1buvM.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:0070011	0.99	peptidase activity, acting on L-amino acid peptides
GO:0008237	0.97	metallopeptidase activity
GO:0004175	0.97	endopeptidase activity
GO:0004222	0.95	metalloendopeptidase activity
GO:0046872	0.89	metal ion binding
GO:0004252	0.88	serine-type endopeptidase activity
GO:0008270	0.87	zinc ion binding
GO:0005509	0.80	calcium ion 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:0044699	0.98	single-organism process
GO:0009987	0.97	cellular process
GO:0044763	0.96	single-organism cellular process
GO:0071704	0.92	organic substance metabolic process
GO:0044707	0.91	single-multicellular organism process
GO:0044238	0.91	primary metabolic process
GO:0043170	0.91	macromolecule metabolic process
GO:0019538	0.90	protein metabolic process
GO:0016043	0.90	cellular component organization
GO:0030198	0.89	extracellular matrix organization
GO:0006508	0.89	proteolysis
GO:0022617	0.88	extracellular matrix disassembly
GO:0044710	0.87	single-organism metabolic process
GO:0009056	0.87	catabolic process
GO:0030574	0.86	collagen catabolic process
GO:0065007	0.83	biological regulation
GO:0050789	0.81	regulation of biological process
GO:0050794	0.78	regulation of cellular process
GO:0048518	0.70	positive regulation of biological process
GO:0048522	0.68	positive regulation of cellular process
GO:0032502	0.66	developmental process
GO:0044767	0.63	single-organism developmental process
GO:0050896	0.59	response to stimulus
GO:0051128	0.57	regulation of cellular component organization
GO:0051130	0.54	positive regulation of cellular component organization
GO:0044087	0.54	regulation of cellular component biogenesis
GO:0032461	0.53	positive regulation of protein oligomerization
GO:0048583	0.52	regulation of response to stimulus
GO:0048519	0.50	negative regulation of biological process
GO:0006928	0.50	movement of cell or subcellular component

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	0.77	cell part
GO:0044421	0.60	extracellular region part
GO:0044424	0.59	intracellular part
GO:0005576	0.41	extracellular region
GO:0044444	0.39	cytoplasmic part
GO:0005615	0.33	extracellular space
GO:0043226	0.32	organelle
GO:0043227	0.31	membrane-bounded organelle
GO:0016020	0.30	membrane

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	0.625	1q3aB	0.598	0.85	0.597	0.609	3.4.24.22	217,234
2	0.620	1bzsA	0.598	1.86	0.573	0.628	3.4.24.34	217,234
3	0.616	2jsdA	0.579	1.56	0.547	0.609	3.4.24.-	217,234
4	0.614	1gkcA	0.589	1.12	0.506	0.605	3.4.24.35	217,234
5	0.575	1bqqM	0.585	1.35	0.463	0.609	3.4.24.80	217,234

	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	0.51	1slnA	0.605	1.72	0.598	0.628	1.60	INH	complex1.pdb.gz	177,179,180,212,213,216,217,220,226,233,235,236,237,238
2	0.44	1b3dB	0.604	1.68	0.598	0.628	1.67	CA	complex2.pdb.gz	173,174,176,178,196,199
3	0.42	1d5jB	0.603	1.74	0.598	0.628	1.60	MM3	complex3.pdb.gz	178,179,180,213,216,217,220,226,238
4	0.41	1biwA	0.602	1.56	0.591	0.625	1.69	CA	complex4.pdb.gz	154,155,188,189,190,192
5	0.36	1gkcA	0.589	1.12	0.506	0.605	1.67	ZN	complex5.pdb.gz	216,220,226
6	0.34	1umsA	0.507	2.92	0.535	0.602	1.10	UUU	complex6.pdb.gz	173,177,178,216,226,235,236,237,238,239
7	0.30	1eakA	0.820	1.73	0.492	0.866	1.76	CA	complex7.pdb.gz	154,155,186,188,190
8	0.29	1c3i0	0.600	1.85	0.579	0.628	1.68	III	complex8.pdb.gz	115,116,117,118,119,120,122,124,164,165,166
9	0.29	2usnA	0.598	1.86	0.579	0.628	1.53	IN8	complex9.pdb.gz	104,181,182,183,184,190,216,217,220,225,226
10	0.29	1eakC	0.829	1.49	0.492	0.866	1.45	CA	complex10.pdb.gz	173,174,175,176,177,178,196,199

	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.