D-I-TASSER Q9Y6K0-D1

D-I-TASSER results for Q9Y6K0-D1

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

Input Sequence in FASTA format

>Q9Y6K0 (204 residues)
MSGHRSTRKRCGDSHPESPVGFGHMSTTGCVLNKLFQLPTPPLSRHQLKRLEEHRYQSAG
RSLLEPLMQGYWEWLVRRVPSWIAPNLITIIGLSINICTTILLVFYCPTATEQAPLWAYI
ACACGLFIYQSLDAIDGKQARRTNSSSPLGELFDHGCDSLSTVFVVLGTCIAVQLGVSVC
NQIASHLHIHVFRIKVSTAHSNHH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSGHRSTRKRCGDSHPESPVGFGHMSTTGCVLNKLFQLPTPPLSRHQLKRLEEHRYQSAGRSLLEPLMQGYWEWLVRRVPSWIAPNLITIIGLSINICTTILLVFYCPTATEQAPLWAYIACACGLFIYQSLDAIDGKQARRTNSSSPLGELFDHGCDSLSTVFVVLGTCIAVQLGVSVCNQIASHLHIHVFRIKVSTAHSNHH
Prediction	CCCCCCHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	998653244415789888754456785323456530344688899999889972344799873487998899999997136779626999999999999999998364446788745899999999999998750399987219999436777776349999999999999983353399999999999999999999997519
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSGHRSTRKRCGDSHPESPVGFGHMSTTGCVLNKLFQLPTPPLSRHQLKRLEEHRYQSAGRSLLEPLMQGYWEWLVRRVPSWIAPNLITIIGLSINICTTILLVFYCPTATEQAPLWAYIACACGLFIYQSLDAIDGKQARRTNSSSPLGELFDHGCDSLSTVFVVLGTCIAVQLGVSVCNQIASHLHIHVFRIKVSTAHSNHH
Prediction	874544245326545554454344257423314532634354037731640461304254321023003200420042024313121001311321320010000112324443231111121321331331100001101334432310210113001300120321111113333333132233333311000002223446
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
MSGHRSTRKRCGDSHPESPVGFGHMSTTGCVLNKLFQLPTPPLSRHQLKRLEEHRYQSAGRSLLEPLMQGYWEWLVRRVPSWIAPNLITIIGLSINICTTILLVFYCPTATEQAPLWAYIACACGLFIYQSLDAIDGKQARRTNSSSPLGELFDHGCDSLSTVFVVLGTCIAVQLGVSVCNQIASHLHIHVFRIKVSTAHSNHH

5d92D

0.13

0.09

3.05

0.83

DEthreader

------------------------------------------------------SLIGSGSLNARGLFAAIFLPIARLLAWGVSPDAVTVVGTLGVMAGALIFYPMG------Q---LFWGTVVITVFVF-SDIIDGLMARLLFREGPWGAFLDSYLDRVGDSSVFTGIVWFGNIAILALICLVLSSLVSYSKARAEGLG----

4o6mA2

0.14

0.09

3.18

1.42

SPARKS-K

------------------------------------------------------------DGWIARENRKVSLRISRLLATSVTPNQITVFSFFLSLVGSALFLLNSY--------LTTLLAGVIIQLHSIIDGCDGEIARLKFMESKYGAWLDGVLDRYSDFIIVFSITYVLSVYWIIGFLAAFASLMIAYTGDKFVAAYMRT

4o6mA

0.12

4.14

1.08

MapAlign

LIILEPVLILERDLLLEGRKILVSDGFTVGYFFGGDFRTVFDGNLQSSIEKYLSLSSLIDGWIAREINRKVSLRISRLLATSVTPNQITVFSFFLSLVGSALFL--------LNSYLTTLLAGVIIQLHSIIDGCDGEIARLKFMESKYGAWLDGVLDRYSDFIIVFSITYVLSYWIIGFLAAFASLMIAYTGDKFVAAYMRTY

4o6mA

0.13

0.12

4.27

0.89

CEthreader

GFTVGYFFGGDFRTVFDGNLQSSIEKYLSLNNLESYEIWAIKLSNDNLKTAEKLLLSSLIDGWIARENRKVSLRISRLLADSVTPNQITVFSFFLSLVGSALFLLNS--------YLTTLLAGVIIQLHSIIDGCDGEIARLKFMESKYGAWLDGVLDRYSDFIIVFSITYVLSVYWIIGFLAAFASLMIAYTGDKFVAAYMRT

4o6mA2

0.15

0.10

3.32

0.94

MUSTER

-----------------------------------------------------------DGWIAREINRKVSLRISRLLATSVTPNQITVFSFFLSLVGSALFLLNS--------YLTTLLAGVIIQLHSIIDGCDGEIARLKFMESKYGAWLDGVLDRYSDFIIVFSITYVLSASNPVYWIIGFLAAFASLMIAYTGDKRTYS

4o6mA

0.13

0.12

4.27

3.45

HHsearch

LELLLEGKILVSDGFTVGDGNLSSIKYLSLNNLESYEIWAIKLSNDNLKTAEKLLLSSLIDGWIARINRKVSLRISRLADTSVTPNQITVFSFFLSLVGSALFLLNS--------YLTTLLAGVIIQLHSIIDGCDGEIARLKFMESKYGAWLDGVLDRYSDFIIVFSITYVLSASNPWIIGFLALMIAYTGDKFVAAYMRTYS

4o6mA

0.17

0.13

4.17

1.44

FFAS-3D

------------------------------------------LSNDNLKTAEKLLLSSLIDGWIARINRKVSLRISRLADTSVTPNQITVFSFFLSLVGSALFL--------LNSYLTTLLAGVIIQLHSIIDGCDGEIARLKFMESKYGAWLDGVLDRYSDFIIVFSITYVLSASNPVYWIIGFLAAFASLMIAYTGD-----

4o6mA

0.11

3.86

1.18

EigenThreader

ELSLEEAEERDLLLEGRFRTVFDGNLQSSIEKYLSLNNLESNDNLKTAEKLLLSS--LIDGWIAREIRKVSLRISRLLADTSVTPNQITVFSFFLSLVGSALFLL--------NSYLTTLLAGVIIQLHSIIDGCDGEIARLKFMESKYGAWLDGVLDRYSDFIIVFSITYVLSASNPFLAAFASLMIAYTGDKFVAAYMRTYS

4o6mA

0.17

0.13

4.19

0.96

CNFpred

------------------------------------------LSNDNLKTAEKLLLSSL-GWIAREINRKVSLRISRLLDTSVTPNQITVFSFFLSLVGSALFLLN--------SYLTTLLAGVIIQLHSIIDGCDGEIARLKFMESKYGAWLDGVLDRYSDFIIVFSITYVLSASNPVYWIIGFLAAFASLMIAYTGDKFVAA

4o6mA

0.14

0.09

3.02

0.83

DEthreader

--------------------------------------------------------SLIDGWIAREINRKVSLRISRLLDTSVTPNQITVFSFFLSLVGSALFL-L-------NSYLTTLLAGVIIQLHSIIDGCDGEIARLKFMESKYGAWLDGVLDRYSDFIIVFSITYVLSVYWIGFLAAFALM-AY--DK-VA--M----

(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	0.6746

(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	4o6mA	0.60	2.94	0.107	0.691	model1_4o6mA.pdb.gz
2	6wm5A	0.56	3.66	0.148	0.701	model1_6wm5A.pdb.gz
3	4mndA	0.55	2.99	0.089	0.652	model1_4mndA.pdb.gz
4	5d92D	0.54	3.32	0.088	0.662	model1_5d92D.pdb.gz
5	6nbqD	0.53	4.67	0.029	0.814	model1_6nbqD.pdb.gz
6	6hznA	0.52	4.77	0.080	0.789	model1_6hznA.pdb.gz
7	7a23I	0.52	4.93	0.032	0.814	model1_7a23I.pdb.gz
8	6tjvD	0.52	4.78	0.063	0.794	model1_6tjvD.pdb.gz
9	6vp9B	0.52	5.34	0.045	0.833	model1_6vp9B.pdb.gz
10	7a23M	0.51	4.82	0.035	0.804	model1_7a23M.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:0016772	0.96	transferase activity, transferring phosphorus-containing groups
GO:0016780	0.92	phosphotransferase activity, for other substituted phosphate groups
GO:0017169	0.75	CDP-alcohol phosphatidyltransferase 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:0008152	0.93	metabolic process
GO:0009058	0.84	biosynthetic process
GO:0044699	0.83	single-organism process
GO:0006629	0.75	lipid metabolic process
GO:0006644	0.71	phospholipid metabolic process
GO:0090407	0.67	organophosphate biosynthetic process
GO:0044249	0.67	cellular biosynthetic process
GO:0008610	0.67	lipid biosynthetic process
GO:0046474	0.64	glycerophospholipid biosynthetic process
GO:0006656	0.52	phosphatidylcholine 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:0044444	0.99	cytoplasmic part
GO:0016020	0.66	membrane
GO:0044425	0.63	membrane part
GO:0044446	0.62	intracellular organelle 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	1hcuB	0.437	5.81	0.043	0.784	3.2.1.113	NA
2	0.060	1dl2A	0.444	5.49	0.071	0.770	3.2.1.113	NA
3	0.060	1tazA	0.497	4.80	0.050	0.755	3.1.4.17	75
4	0.060	1vncA	0.443	5.41	0.041	0.716	1.11.1.10	NA
5	0.060	3lxuX	0.439	5.15	0.070	0.686	3.4.14.10	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	0.12	1xlzB	0.505	4.57	0.069	0.750	0.45	FIL	complex1.pdb.gz	94,96,136,137,140,157
2	0.02	3rkoN	0.499	5.18	0.080	0.819	0.77	LFA	complex2.pdb.gz	92,93,96,132,133,136
3	0.01	1xlzA	0.506	4.50	0.069	0.745	0.50	FIL	complex3.pdb.gz	92,133,136,137,140,154
4	0.01	3jsiA	0.501	4.78	0.031	0.765	0.42	WTC	complex4.pdb.gz	136,137,140,149,155,156
5	0.01	2pw3A	0.496	4.66	0.069	0.745	0.48	CMP	complex5.pdb.gz	136,140,157
6	0.01	1tbbA	0.497	4.59	0.069	0.740	0.46	ROL	complex6.pdb.gz	95,133,134,137,159
7	0.01	1xmyA	0.503	4.54	0.069	0.745	0.45	ROL	complex7.pdb.gz	136,137,149,157
8	0.01	2qynA	0.496	4.60	0.069	0.740	0.43	NPV	complex8.pdb.gz	92,136,140,147
9	0.01	3k3hA	0.501	4.76	0.031	0.765	0.46	BYE	complex9.pdb.gz	132,133,136,156,157
10	0.01	2qykA	0.459	5.14	0.057	0.745	0.41	NPV	complex10.pdb.gz	92,136,140

	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.