D-I-TASSER Q9Y5S8-D2

D-I-TASSER results for Q9Y5S8-D2

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

Input Sequence in FASTA format

>Q9Y5S8 (272 residues)
QKVVITKVVMHPSKVLELQMNKRGFSMEVGQYIFVNCPSISLLEWHPFTLTSAPEEDFFS
IHIRAAGDWTENLIRAFEQQYSPIPRIEVDGPFGTASEDVFQYEVAVLVGAGIGVTPFAS
ILKSIWYKFQCADHNLKTKKIYFYWICRETGAFSWFNNLLTSLEQEMEELGKVGFLNYRL
FLTGWDSNIVGHAALNFDKATDIVTGLKQKTSFGRPMWDNEFSTIATSHPKSVVGVFLCG
PRTLAKSLRKCCHRYSSLDPRKVQFYFNKENF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| QKVVITKVVMHPSKVLELQMNKRGFSMEVGQYIFVNCPSISLLEWHPFTLTSAPEEDFFSIHIRAAGDWTENLIRAFEQQYSPIPRIEVDGPFGTASEDVFQYEVAVLVGAGIGVTPFASILKSIWYKFQCADHNLKTKKIYFYWICRETGAFSWFNNLLTSLEQEMEELGKVGFLNYRLFLTGWDSNIVGHAALNFDKATDIVTGLKQKTSFGRPMWDNEFSTIATSHPKSVVGVFLCGPRTLAKSLRKCCHRYSSLDPRKVQFYFNKENF
Prediction	CSSSSSSSSSSCCCSSSSSSSCCCCCCCCCSSSSSSSCCCCCCCCCCSSSSSCCCCCSSSSSSSSCCCCCHHHHHHHHHCCCCCCSSSSSCCCCCCCCCCCCCCSSSSSSCCCCHHHHHHHHHHHHHHHHHCCCCCCCCSSSSSSSCCCHHHHHHHHHHHHHHHHHHHHHCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCSSSSSSSCCHHHHHHHHHHHHHHCCCCCCCSSSSSSSSCC
Confidence	93899999995799799999289998689708999947877754477357745899979999997899458999999854788847998589999865523489099996263677899999999987640244566635999985089899999999999999988862777269999998258876432211111123454445421012689779999999999668963899995992899999999999689888831899987239
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| QKVVITKVVMHPSKVLELQMNKRGFSMEVGQYIFVNCPSISLLEWHPFTLTSAPEEDFFSIHIRAAGDWTENLIRAFEQQYSPIPRIEVDGPFGTASEDVFQYEVAVLVGAGIGVTPFASILKSIWYKFQCADHNLKTKKIYFYWICRETGAFSWFNNLLTSLEQEMEELGKVGFLNYRLFLTGWDSNIVGHAALNFDKATDIVTGLKQKTSFGRPMWDNEFSTIATSHPKSVVGVFLCGPRTLAKSLRKCCHRYSSLDPRKVQFYFNKENF
Prediction	75230140232264002020445705130001000001323331111002000245420000011343203300400342344313020201101022424523200000011100000000221033144443324323020201044451041035005402730573543220302000124465343443244534431143142332203230451054016534532000000014410530150046244556440302014238
	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

CSSSSSSSSSSCCCSSSSSSSCCCCCCCCCSSSSSSSCCCCCCCCCCSSSSSCCCCCSSSSSSSSCCCCCHHHHHHHHHCCCCCCSSSSSCCCCCCCCCCCCCCSSSSSSCCCCHHHHHHHHHHHHHHHHHCCCCCCCCSSSSSSSCCCHHHHHHHHHHHHHHHHHHHHHCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCSSSSSSSCCHHHHHHHHHHHHHHCCCCCCCSSSSSSSSCC
QKVVITKVVMHPSKVLELQMNKRGFSMEVGQYIFVNCPSISLLEWHPFTLTSAPEEDFFSIHIRAAGDWTENLIRAFEQQYSPIPRIEVDGPFGTASEDVFQYEVAVLVGAGIGVTPFASILKSIWYKFQCADHNLKTKKIYFYWICRETGAFSWFNNLLTSLEQEMEELGKVGFLNYRLFLTGWDSNIVGHAALNFDKATDIVTGLKQKTSFGRPMWDNEFSTIATSHPKSVVGVFLCGPRTLAKSLRKCCHRYSSLDPRKVQFYFNKENF

5o0xA

0.40

0.36

10.62

1.33

DEthreader

EPTFVVNASLLPSKVLGLQVQRPSFNYQPGDYLFIKCPGISKFEWHPFTISSAPEPDVLTLHIRAVGSWTGKLYQLIREQRLPGVPVYIDGPYGTPSTHIFESKYAILICAGIGVTPFASILKSILHRNQQNPAKMPLKKVHFYWLNREQKAFEWFVELLSKIEAEDT----NNLFDLNLYLT----------LI----TGL-K----SRTKTGRPDWEEIFKDVAKQHAPDNVEVFFCGPTGLALQLRHLCTK-Y-G----FGYRKENFPW

5o0xA

0.44

0.39

11.51

1.85

SPARKS-K

EPTFVVNASLLPSKVLGLQVQPQSFNYQPGDYLFIKCPGISKFEWHPFTISSAPMPDVLTLHIRAVGSWTGKLYQLIREQRLPGVPVYIDGPYGTPSTHIFESKYAILICAGIGVTPFASILKSILHRNQQNPAKMPLKKVHFYWLNREQKAFEWFVELLSKIEAEDTN----NLFDLNLYLTLI-------------------TGLKSRTKTGRPDWEEIFKDVAKQHAPDNVEVFFCGPTGLALQLRHLCTKYG--------FGYRKENF

7d3eA

0.35

0.34

10.10

1.13

MapAlign

VEISVVKAELLPSGVTHLRFQRPGFEYKSGQWVRIACLALGTTEYHPFTLTSAPHEDTLSLHIRAAGPWTTRLREIYS--APTYPKLYLDGPFGEGHQEWHKFEVSVLVGGGIGVTPFASILKDLVFKSS-VSCQVFCKKIYFIWVTRTQRQFEWLADIIREVEEND----HQDLVSVHIYITQRTMLYICERHFQKVLNRSLFTGLRSITHFGRPPFEPFFNSLQEVHPQVKIGVFSCGPPGMTKNVEKACQLI--NRQDRTHFSHHYENF

7d3eA

0.35

0.33

10.00

0.67

CEthreader

VEISVVKAELLPSGVTHLRFQRPQFEYKSGQWVRIACLALGTTEYHPFTLTSAPHEDTLSLHIRAAGPWTTRLREIYSAPTYP--KLYLDGPFGEGHQEWHKFEVSVLVGGGIGVTPFASILKDLVFKSSVS-CQVFCKKIYFIWVTRTQRQFEWLADIIREVEEND----HQDLVSVHIYITQLAEKFDLRTTMQKVLNRSLFTGLRSITHFGRPPFEPFFNSLQEVHPQRKIGVFSCGPPGMTKNVEKACQLINR--QDRTHFSHHYENF

5o0xA

0.45

0.40

11.61

1.64

MUSTER

EPTFVVNASLLPSKVLGLQVQRQSFNYQPGDYLFIKCPGISKFEWHPFTISSAPEPDVLTLHIRAVGSWTGKLYQLIREQRLPGVPVYIDGPYGTPSTHIFESKYAILICAGIGVTPFASILKSILHRNQQNPAKMPLKKVHFYWLNREQKAFEWFVELLSKIEAED----TNNLFDLNLYLT-------------------LITGLKSRTKTGRPDWEEIFKDVAKQHAPDNVEVFFCGPTGLALQLRHLCTKYG--------FGYRKENF

6wxrA

0.37

0.32

9.60

1.89

HHsearch

VEISVVKAELLPSGVTHLRFQRQGFEYKSGQWVRIACLALGTTEYHPFTLTSAPHEDTLSLHIRAAGPWTTRLREIYSP--PRYPKLYLDGPFGEGHQEWHKFEVSVLVGGGIGVTPFASILKDLVFKSSVS----CCKKIYFIWVTRTQRQFEWLADIIREVEEND----RQDLVSVHIYITQLAEK----------------FDLR-----GRPPFEPFFNSLQEVHPQ-KIGVFSCGPPGMTKNVEKACQLINRQ----THFSHHYENF

5o0xA

0.44

0.39

11.51

2.41

FFAS-3D

EPTFVVNASLLPSKVLGLQVQPQSFNYQPGDYLFIKCPGISKFEWHPFTISSAPMPDVLTLHIRAVGSWTGKLYQLIRSQSLPGVPVYIDGPYGTPSTHIFESKYAILICAGIGVTPFASILKSILHRNQQNPAKMPLKKVHFYWLNREQKAFEWFVELLSKIEAE----DTNNLFDLNLYLT-------------------LITGLKSRTKTGRPDWEEIFKDVAKQHAPDNVEVFFCGPTGLALQLRHLCTKYG--------FGYRKENF

5o0xA

0.33

0.30

9.04

1.23

EigenThreader

EPTFVVNASLLPSKVLGLQVQRPSFNYQPGDYLFIKCPGISKFEWHPFTISAPEMPDVLTLHIRAVGSWTGKLYQLIREQQSLPGVPVYIDGPYTPSTHIFESKYAILICAGIGVTPFASILKSILHRNQQNPAKMPLKKVHFYWLNREQKAFEWFVELLSKIEAED----TNNLFDLNLYLT-----------------LITGLKSRTKTGRPD-WEEIFKDVAKQHAPDNVEVFFCGP-TGLALQLRHLCTKYGFGYRKENF---PWLEL

5o0xA

0.45

0.40

11.61

1.97

CNFpred

EPTFVVNASLLPSKVLGLQVQRPSFNYQPGDYLFIKCPGISKFEWHPFTISSAPEPDVLTLHIRAVGSWTGKLYQLIREQRLPGVPVYIDGPYGTPSTHIFESKYAILICAGIGVTPFASILKSILHRNQQNPAKMPLKKVHFYWLNREQKAFEWFVELLSKIEAEDT----NNLFDLNLYLT-------------------LITGLKSRTKTGRPDWEEIFKDVAKQHAPDNVEVFFCGPTGLALQLRHLCTKY--------GFGYRKENF

7d3eA

0.33

0.32

9.60

1.33

DEthreader

VEISVVKAELLPSGVTHLRFQRPGFEYKSGQWVRIACLALGTTEYHPFTLTSAPHEDTLSLHIRAAGPWTTRLREIYS-APTYP-KLYLDGPFGEGHQEWHKFEVSVLVGGGIGVTPFASILKDLVFKSSVSCQ-VFCKKIYFIWVTRTQRQFEWLADIIREVEENDH---Q-DLVSVHIYITQAKFDLRTTMLYIERHFKLNRSGLRSITHFGRPPFEPFFNSLQEVHPVRKIGVFSCGPPGMTKNVEKACQLINRQD-THFSHHYENF--

(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	0.8794

(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	7d3eA	0.87	2.40	0.338	0.967	model1_7d3eA.pdb.gz
2	5o0xA	0.85	1.36	0.416	0.893	model1_5o0xA.pdb.gz
3	6wxrA2	0.78	2.11	0.349	0.864	model1_6wxrA2.pdb.gz
4	2bf4A	0.76	2.93	0.112	0.882	model1_2bf4A.pdb.gz
5	1gvhA	0.76	2.36	0.143	0.849	model1_1gvhA.pdb.gz
6	6t1tA	0.75	3.00	0.113	0.875	model1_6t1tA.pdb.gz
7	2bgjA	0.75	3.05	0.136	0.864	model1_2bgjA.pdb.gz
8	2qtzA	0.75	3.09	0.147	0.875	model1_2qtzA.pdb.gz
9	1tllA	0.74	2.98	0.093	0.864	model1_1tllA.pdb.gz
10	5gxuA	0.74	3.16	0.101	0.868	model1_5gxuA.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	0.95	catalytic activity
GO:0016491	0.94	oxidoreductase activity
GO:0016651	0.73	oxidoreductase activity, acting on NAD(P)H
GO:0050664	0.72	oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor
GO:0016175	0.50	superoxide-generating NADPH oxidase 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	0.89	cellular process
GO:0044699	0.86	single-organism process
GO:0050896	0.84	response to stimulus
GO:0065007	0.81	biological regulation
GO:0008152	0.75	metabolic process
GO:0050789	0.72	regulation of biological process
GO:0044237	0.72	cellular metabolic process
GO:0050794	0.67	regulation of cellular process
GO:0072593	0.59	reactive oxygen species metabolic process
GO:0032502	0.56	developmental process
GO:0044767	0.53	single-organism developmental process
GO:0006950	0.53	response to stress
GO:0044763	0.52	single-organism cellular process
GO:0042221	0.52	response to chemical

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	0.97	cell part
GO:0044424	0.74	intracellular part
GO:0016020	0.70	membrane
GO:0044444	0.61	cytoplasmic part
GO:0044425	0.61	membrane part
GO:0043226	0.55	organelle
GO:0043227	0.54	membrane-bounded organelle
GO:0044459	0.52	plasma membrane part
GO:0032991	0.51	macromolecular complex

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	0.289	1fdrA	0.729	2.96	0.157	0.842	1.18.1.2	NA
2	0.287	2bgjA	0.750	3.05	0.136	0.864	1.18.1.2	NA
3	0.285	3fpkA	0.735	3.03	0.146	0.853	1.18.1.2	NA
4	0.283	1a8pA	0.741	3.07	0.128	0.860	1.18.1.2	NA
5	0.273	1qfjD	0.692	2.94	0.200	0.805	1.5.1.29 1.16.1.3	32,47,110

	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	0.39	2vnhA	0.745	3.03	0.148	0.860	0.86	NAP	complex1.pdb.gz	111,148,183,184,243,244,246
2	0.17	3es9B	0.733	3.14	0.102	0.864	0.80	NAP	complex2.pdb.gz	112,113,147,148,182,243,247,271
3	0.04	2qdxA	0.736	3.08	0.137	0.857	0.89	FAD	complex3.pdb.gz	32,46,47,48,49,62,65,67,68,69,70,113,116,268,271

	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.