D-I-TASSER Q96LT4-D1

D-I-TASSER results for Q96LT4-D1

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

Input Sequence in FASTA format

>Q96LT4 (140 residues)
MAGPNQLCIRRWTTKHVAVWLKDEGFFEYVDILCNKHRLDGITLLTLTEYDLRSPPLEIK
VLGDIKRLMLSVRKLQKIHIDVLEEMGYNSDSPMGSMTPFISALQSTDWLCNGELSHDCD
GPITDLNSDQYQYMNGKNKH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAGPNQLCIRRWTTKHVAVWLKDEGFFEYVDILCNKHRLDGITLLTLTEYDLRSPPLEIKVLGDIKRLMLSVRKLQKIHIDVLEEMGYNSDSPMGSMTPFISALQSTDWLCNGELSHDCDGPITDLNSDQYQYMNGKNKH
Prediction	CCCCCCCCHHHCCHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	99977677221999999999999198789999999928985998639999985047898630389999999999999988876521577777666778886666776655678865567998788886532223566689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAGPNQLCIRRWTTKHVAVWLKDEGFFEYVDILCNKHRLDGITLLTLTEYDLRSPPLEIKVLGDIKRLMLSVRKLQKIHIDVLEEMGYNSDSPMGSMTPFISALQSTDWLCNGELSHDCDGPITDLNSDQYQYMNGKNKH
Prediction	77567543166043730153057451460054016526031620140347204647161640241330141055035544542564544554444444444444444533455536551614354474742435435458
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCHHHCCHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MAGPNQLCIRRWTTKHVAVWLKDEGFFEYVDILCNKHRLDGITLLTLTEYDLRSPPLEIKVLGDIKRLMLSVRKLQKIHIDVLEEMGYNSDSPMGSMTPFISALQSTDWLCNGELSHDCDGPITDLNSDQYQYMNGKNKH

6zfxA3

0.17

0.16

5.19

1.62

SPARKS-K

----ILPSVPSWKEAEVQTWLQQIGFSKYCESFREQ-QVDGDLLLRLTEEELQTD-LGMKSGITRKRFFRELTELKTFAN--YSTCDRSNLADWLGSLDPRFRQYTYGLVSCGLDRSLLHRVSEQQLLEDCGIHLGVHRA

2d8cA

0.25

0.16

4.88

1.48

HHsearch

LSARTMKEVVYWSPKKVADWLLENAMPEYCEPL---EHFTGQDLINLTQEDFKKPPLYRVSSDNGQRLLDMIETLKMEHHMEAHKNSG-PSSG-----------------------------------------------

6qwvA1

0.29

0.15

4.57

1.15

FFAS-3D

---PILPSVPSWKEAEVQTWLQQIGFSKYCESF-REQQVDGDLLLRLTEEELQT-DLGMKSGITRKRFFRELTELKTF--------------------------------------------------------------

6zfxA

0.22

0.14

4.50

0.83

DEthreader

PRPILP-SVPSWKEAEVQTWLQQIGFSKYCESF-REQQVDGDLLLRLTEEELQT-DLGMKSGITRKRFFRELTELKTFA--NYS-RSNLTYLVSCG--------------------------------------------

6qwvA1

0.28

0.15

4.59

1.58

SPARKS-K

---PILPSVPSWKEAEVQTWLQQIGFSKYCESFREQ-QVDGDLLLRLTEEELQTD-LGMKSGITRKRFFRELTELKTFAN------------------------------------------------------------

6qwvA

0.18

0.16

5.37

0.79

MapAlign

----ILPSVPSWKEAEVQTWLQQIGFSKYCES-FREQQVDGDLLLRLTEEELQTDLG-MKSGITRKRFFRELTELKTANADWLGSDPRFRQYTYGLVSCGLDRSLLHRVSEQQLLEDCGIHLGVHRARILTAAREML---

6qwvA

0.17

0.16

5.39

0.61

CEthreader

---PILPSVPSWKEAEVQTWLQQIGFSKYCESFREQQ-VDGDLLLRLTEEELQT-DLGMKSGITRKRFFRELTELKTFA--NYSTCDRSNLADWLGSLDPRFRQYTYGLVSCGLDRSLLHRVSEQQLLEDCGIHLGVHRA

6qwvA

0.20

0.19

5.92

0.89

MUSTER

IL----PSVPSWKEAEVQTWLQQIGFSKYCESFREQQ-VDGDLLLRLTEEELQT-DLGMKSGITRKRFFRELTELKTFANYSTC-------DRSNLADWLGSLDPRFRQYTYGLVSCGLDRSLHRVSEQQLLEDCGIHLG

1uqvA

0.14

0.08

2.70

1.44

HHsearch

GSHMNNEDFSQWSVDDVITWCISTETDPLCQRL-RENDIVGDLLPELCLQDCQDLC--DGDLNKAIKFKILINKMRDSKLEWKD--------------------------------------------------------

7cm5A3

0.29

0.15

4.57

1.14

FFAS-3D

---PILPSVPSWKEAEVQTWLQQIGFSKYCESF-REQQVDGDLLLRLTEEELQT-DLGMKSGITRKRFFRELTELKTF--------------------------------------------------------------

(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	0.6739

(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	7anwA	0.66	3.43	0.179	0.843	model1_7anwA.pdb.gz
2	6wpkA	0.65	3.34	0.179	0.836	model1_6wpkA.pdb.gz
3	6qwvA	0.64	3.49	0.183	0.821	model1_6qwvA.pdb.gz
4	6lvfB	0.57	4.18	0.087	0.893	model1_6lvfB.pdb.gz
5	6krjA	0.55	3.51	0.051	0.757	model1_6krjA.pdb.gz
6	3imxA1	0.55	3.83	0.065	0.786	model1_3imxA1.pdb.gz
7	1dgkN	0.54	3.72	0.066	0.771	model1_1dgkN.pdb.gz
8	5zqtA1	0.54	3.65	0.058	0.764	model1_5zqtA1.pdb.gz
9	3o08B	0.54	3.80	0.067	0.771	model1_3o08B.pdb.gz
10	6vyfA	0.54	3.50	0.044	0.750	model1_6vyfA.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	0.69	catalytic activity
GO:0043167	0.54	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:0044763	1.00	single-organism cellular process
GO:0008152	0.98	metabolic process
GO:0071704	0.97	organic substance metabolic process
GO:0044710	0.97	single-organism metabolic process
GO:0044238	0.97	primary metabolic process
GO:0044237	0.97	cellular metabolic process
GO:0044255	0.93	cellular lipid metabolic process
GO:0006807	0.78	nitrogen compound metabolic process
GO:0065007	0.77	biological regulation
GO:1901564	0.76	organonitrogen compound metabolic process
GO:0050789	0.76	regulation of biological process
GO:0006796	0.76	phosphate-containing compound metabolic process
GO:0019637	0.75	organophosphate metabolic process
GO:0034641	0.74	cellular nitrogen compound metabolic process
GO:0050794	0.72	regulation of cellular process
GO:0006643	0.72	membrane lipid metabolic process
GO:0006665	0.71	sphingolipid metabolic process
GO:0006644	0.70	phospholipid metabolic process
GO:1901576	0.69	organic substance biosynthetic process
GO:0044249	0.69	cellular biosynthetic process
GO:0008610	0.68	lipid biosynthetic process
GO:1901566	0.67	organonitrogen compound biosynthetic process
GO:0044271	0.67	cellular nitrogen compound biosynthetic process
GO:0043603	0.67	cellular amide metabolic process
GO:0090407	0.66	organophosphate biosynthetic process
GO:0043604	0.66	amide biosynthetic process
GO:0030148	0.66	sphingolipid biosynthetic process
GO:0008654	0.65	phospholipid biosynthetic process
GO:0006686	0.64	sphingomyelin biosynthetic process
GO:0006672	0.61	ceramide metabolic process
GO:0046513	0.59	ceramide biosynthetic process
GO:0080090	0.58	regulation of primary metabolic process
GO:0060255	0.58	regulation of macromolecule metabolic process
GO:0031323	0.58	regulation of cellular metabolic process
GO:2000303	0.57	regulation of ceramide 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:0044464	0.98	cell part
GO:0044424	0.96	intracellular part
GO:0044444	0.92	cytoplasmic part
GO:0044446	0.80	intracellular organelle part
GO:0044425	0.79	membrane part
GO:0044432	0.68	endoplasmic reticulum part
GO:0016021	0.67	integral component of membrane
GO:0030176	0.58	integral component of endoplasmic reticulum membrane
GO:0016020	0.58	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	0.279	3bq7C	0.469	1.19	0.314	0.500	2.7.1.107	14,32,51,57
2	0.238	1b4fA	0.458	1.81	0.113	0.507	2.7.10.1	17,29,51
3	0.151	1b0xA	0.457	1.40	0.141	0.493	2.7.10.1	20
4	0.060	1syyA	0.474	4.45	0.053	0.771	1.17.4.1	NA
5	0.060	1vb3A	0.483	4.92	0.048	0.829	4.2.3.1	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	1dgkN	0.542	3.72	0.066	0.771	0.52	ADP	complex1.pdb.gz	10,11,41,43,46,96,97,100

	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.