D-I-TASSER Q9Y689-D1

D-I-TASSER results for Q9Y689-D1

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

Input Sequence in FASTA format

>Q9Y689 (179 residues)
MGILFTRIWRLFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNT
RFLMWDIGGQESLRSSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGL
LIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRLKIR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGILFTRIWRLFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGGQESLRSSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRLKIR
Prediction	CCCHHHHHHHHCCCCSSSSSSSCCCCCCCHHHSHHHHCCCCSSSSCCCCCCSSSSSSCCSSSSSSSCCCCHHHHHHHHHHHCCCCSSSSSSSCCCHHHHHHHHHHHHHHHHCHHHCCCSSSSSSCCCCCCCCCCHHHHHHHHCCCCCCCCCSSSSSSSCCCCCCHHHHHHHHHHHHHHC
Confidence	97478999986288722899986899982400016409972136157586179999899999999789980277899998436977999996776568999999999997525434871999933678755899999999958300269965999987558959999999999999719
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGILFTRIWRLFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGGQESLRSSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRLKIR
Prediction	72222230141265440200000033011100022246652321211311314305376030200000225402420441044031100000122441053035003301534514300000001233276314273036306166057250201000034444044004130640578
	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                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHCCCCSSSSSSSCCCCCCCHHHSHHHHCCCCSSSSCCCCCCSSSSSSCCSSSSSSSCCCCHHHHHHHHHHHCCCCSSSSSSSCCCHHHHHHHHHHHHHHHHCHHHCCCSSSSSSCCCCCCCCCCHHHHHHHHCCCCCCCCCSSSSSSSCCCCCCHHHHHHHHHHHHHHC
MGILFTRIWRLFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGGQESLRSSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRLKIR

1r4aA

0.50

0.46

13.29

1.50

DEthreader

--------------REMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTPSEMANALGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKSR

6a8dA

0.44

12.91

1.65

SPARKS-K

MGQAFTKLFDRWGNREMRVVMLGLDAAGKTTILYKLHIGEVLTTVPTIGFNVEKVQYKNVVFTVWDVGGQEKLRPLWRHYFNNTDGLIFVVDSQDRDRIGKAAQEFQAILQDPLMLHSAILVFANKQDMKGCLTPAEVCTALGLSDMRTRKWHVQSSVATRGEGLYEGLDWLATTLKN-

6bbpA2

0.42

0.41

11.98

0.55

MapAlign

---KGKVLSKIFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGLDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY---

6bbpA

0.41

12.00

0.41

CEthreader

ANKKGKVLSKIFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGLDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYN--

6a8dA

0.44

12.91

1.75

MUSTER

MGQAFTKLFDRWFGREMRVVMLGLDAAGKTTILYKLHIGEVLTTVPTIGFNVEKVQYKNVVFTVWDVGGQEKLRPLWRHYFNNTDGLIFVVDSQDRDRIGKAAQEFQAILQDPLMLHSAILVFANKQDMKGCLTPAEVCTALGLSDMRTRKWHVQSSVATRGEGLYEGLDWLATTLKN-

6a8dA

0.44

12.91

0.89

HHsearch

MGQAFTKLFDRWGNREMRVVMLGLDAAGKTTILYKLHIGEVLTTVPTIGFNVEKVQYKNVVFTVWDVGGQEKLRPLWRHYFNNTDGLIFVVDSQDRDRIGKAAQEFQAILQDPLMLHSAILVFANKQDMKGCLTPAEVCTALGLSDMRTRKWHVQSSVATRGEGLYEGLDWLATTLKN-

1r4aA

0.50

0.46

13.29

2.65

FFAS-3D

--------------REMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTPSEMANALGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKSR

3dofA

0.41

12.01

0.63

EigenThreader

-GLLTILKKMKQKERELRLLMLGLDNAGKTTILKKFNGEDIDTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGALSSNAIREVLELDSIRSHHWCIQGCSAVTGENLLPGIDWLLDDISSR

1zj6A

1.00

0.97

27.06

1.81

CNFpred

-GILFTRIWRLFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGG----RSSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRLKI-

3dofA

0.42

0.39

11.49

1.50

DEthreader

------------KERELRLLMLGLDNAGKTTILKKFNGEDIDTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGALSSNAIREVLELDSIRSHHWCIQGCSAVTGENLLPGIDWLLDDISSI

(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	0.8946

(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	1r4aA	0.90	0.84	0.497	0.922	model1_1r4aA.pdb.gz
2	6bbpA2	0.90	0.99	0.407	0.922	model1_6bbpA2.pdb.gz
3	3lvqE2	0.90	0.75	0.445	0.916	model1_3lvqE2.pdb.gz
4	3dofA	0.89	1.23	0.399	0.927	model1_3dofA.pdb.gz
5	8d9rC	0.89	1.73	0.464	0.944	model1_8d9rC.pdb.gz
6	5di3A	0.88	1.16	0.427	0.916	model1_5di3A.pdb.gz
7	4m9qA	0.88	1.35	0.279	0.922	model1_4m9qA.pdb.gz
8	2h57B	0.86	1.30	0.387	0.911	model1_2h57B.pdb.gz
9	4basA	0.86	1.36	0.393	0.911	model1_4basA.pdb.gz
10	2qtvB	0.85	1.42	0.275	0.894	model1_2qtvB.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	0.74	heterocyclic compound binding
GO:0097159	0.74	organic cyclic compound binding
GO:0097367	0.71	carbohydrate derivative binding
GO:0000166	0.71	nucleotide binding
GO:0032555	0.70	purine ribonucleotide binding
GO:0032550	0.70	purine ribonucleoside binding
GO:0035639	0.68	purine ribonucleoside triphosphate binding
GO:0003824	0.68	catalytic activity
GO:0016787	0.64	hydrolase activity
GO:0003924	0.62	GTPase activity
GO:0032561	0.61	guanyl ribonucleotide binding
GO:0005525	0.59	GTP 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:0065007	0.90	biological regulation
GO:0050794	0.88	regulation of cellular process
GO:0009987	0.83	cellular process
GO:0051179	0.82	localization
GO:0006810	0.81	transport
GO:0007165	0.79	signal transduction
GO:0035556	0.77	intracellular signal transduction
GO:0007264	0.76	small GTPase mediated signal transduction
GO:0044699	0.75	single-organism process
GO:0016192	0.68	vesicle-mediated transport
GO:0044763	0.66	single-organism cellular process
GO:0051641	0.65	cellular localization
GO:0051649	0.60	establishment of localization in cell
GO:0016043	0.59	cellular component organization
GO:0048193	0.57	Golgi vesicle transport
GO:0046907	0.57	intracellular transport
GO:0006996	0.51	organelle 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:0044444	0.94	cytoplasmic part
GO:0043226	0.89	organelle
GO:0043227	0.87	membrane-bounded organelle
GO:0043229	0.86	intracellular organelle
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0016020	0.70	membrane
GO:0044446	0.67	intracellular organelle part
GO:0031982	0.53	vesicle
GO:0031988	0.51	membrane-bounded vesicle

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	0.468	2atxA	0.790	2.16	0.168	0.899	3.6.5.2	70
2	0.355	2f9mA	0.798	2.02	0.198	0.899	3.6.5.2	70
3	0.067	1cb7A	0.568	3.35	0.082	0.743	5.4.99.1	23
4	0.067	1rflA	0.595	3.92	0.162	0.804	3.6.-.-	NA
5	0.067	1bdjA	0.523	3.33	0.118	0.704	2.7.13.3	118

	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	0.91	1z6yA	0.800	2.04	0.749	0.888	2.01	GDP	complex1.pdb.gz	26,27,28,29,30,31,125,126,128,158,159,160
2	0.54	1u81A	0.687	3.22	0.408	0.866	1.79	GDP	complex2.pdb.gz	26,27,29,30,31,125,126
3	0.27	1mr3F	0.820	2.42	0.398	0.922	0.89	PDO	complex3.pdb.gz	50,67,68,69
4	0.09	1ksh0	0.883	1.09	0.439	0.916	1.50	III	complex4.pdb.gz	37,38,48,49,50,51,52,53,54,63,65,76,79,80
5	0.06	1m2o2	0.846	1.45	0.275	0.894	1.40	III	complex5.pdb.gz	25,26,30,34,41,42,43,44,45,46,47,48,49,50,51,52,53,54,65,72,75,76,80,83,160
6	0.05	1cul1	0.822	1.96	0.218	0.922	0.88	III	complex6.pdb.gz	50,74,75,78,82,106,109,112,113,114
7	0.04	2heiB	0.778	2.36	0.188	0.894	0.96	D1D	complex7.pdb.gz	23,67,74,76,77,80,105

	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.