D-I-TASSER A0A087X1G2-D1

D-I-TASSER results for A0A087X1G2-D1

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

Input Sequence in FASTA format

>A0A087X1G2 (107 residues)
MDVVEVAGSWWAQEREDIIMKYEKGHRAGLPEDKGPKPFRSYNNNVDHLGIVHETELPPL
TAREAKQIRREISRKSKWVDMLGDWEKYKSSRKLIDRAYKGMPMNIR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MDVVEVAGSWWAQEREDIIMKYEKGHRAGLPEDKGPKPFRSYNNNVDHLGIVHETELPPLTAREAKQIRREISRKSKWVDMLGDWEKYKSSRKLIDRAYKGMPMNIR
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCC
Confidence	96035478888889999999998333347888998787655566668776435665788642568899999999999999997076667618899981627980029
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MDVVEVAGSWWAQEREDIIMKYEKGHRAGLPEDKGPKPFRSYNNNVDHLGIVHETELPPLTAREAKQIRREISRKSKWVDMLGDWEKYKSSRKLIDRAYKGMPMNIR
Prediction	86466455334454255025305514767473444644454344443432124755355465544543533352252125005517644637303510253227648
	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

                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCC
MDVVEVAGSWWAQEREDIIMKYEKGHRAGLPEDKGPKPFRSYNNNVDHLGIVHETELPPLTAREAKQIRREISRKSKWVDMLGDWEKYKSSRKLIDRAYKGMPMNIR

154lA

0.13

4.53

0.48

CEthreader

KTIIKKVGEKLCVEPAVIAGIISRESHAGKVLKNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVR

2es4D2

0.04

1.99

0.57

EigenThreader

TLSQKAARLAALDAQLTPDERAQQAALHAQQDAVTKIADLQKAGATPD--QMRAQIAQTLGPEAAARAAAWQTRYQAYAAERDRIAAQGLDARIAQLRQQTFAASLD

4p17A

0.16

0.08

2.79

0.83

FFAS-3D

---------------------------------------------HDLYGFPIQ------EDERRSCDVNAEREVPLWQHYIEKDKLPSNETKLKEMIRKGVPPTLR

2fueA1

0.13

0.12

4.21

0.79

SPARKS-K

QTIQNHLGE---ELLQDLINFCLSYALLRLPKKRGT-FIEFRNGL---NISPIGRSCTLEERIEFSELDKKEKIREKFVEALKTEFAGKGLRFSRGGISFDVFPEGW

4p17A

0.16

0.08

2.79

0.60

CNFpred

---------------------------------------------HDLYGFPI-------EDERRSCDVNAEREVPLWQHYIEKDKLPSNETKLKEMIRKGVPPTLR

6vrbA

0.06

2.42

1.00

DEthreader

TSLN-H-RF---EINYKLKTLLFINLEIGEQKINHKNIVQRILQEGK---ASYEIETVSLQ-KIKIEEAFALKFINACLFASNNLRNMVSWGLRGAIAPIEIIHDS-

6whgA

0.05

2.23

0.61

MapAlign

--AKLYETRNLASQQLCKLLIEREVIGSSGFQRCLKWIWRGWIVQNGLDPTTFIKDGYAHLSFWNLFNDTTYLIITFAMGFRAMSVTPYSSEDWDKISY-RVLSCAA

1l8dA

0.09

0.08

3.20

0.62

MUSTER

KKLLEELETKKTTIEEERNEITQRIGELKNKIGDLKTAIEELKKAKGK-GRELTDE--HREELLSKYHLDLNNSKNTLAKLIDRKSELERELRRIDMEIKRL-----

4p17A

0.16

0.08

2.80

2.47

HHsearch

--------------------------------------------VHDLYGFPIQE------DERRSCDVNAEREVPLWQHYIEKDKLPSNETKLKEMIRKGVPPTLR

5yf0A

0.09

3.52

0.39

CEthreader

KQFVRDWSETGKAERDACYQPIIKEILKNFPKERWDPSKVNILVPGAGLGRLYACQGNEWSFFMLFSSNFVLNRCSEINKYKLYPWIHQFSNNRRSADQIRPIFFPD

(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	0.773

(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	7z8bC	0.57	3.99	0.075	0.897	model1_7z8bC.pdb.gz
2	6r9tA	0.54	3.66	0.029	0.822	model1_6r9tA.pdb.gz
3	6ohmA	0.54	3.80	0.040	0.860	model1_6ohmA.pdb.gz
4	7r03A	0.52	4.48	0.047	0.935	model1_7r03A.pdb.gz
5	3iukA	0.52	4.08	0.093	0.897	model1_3iukA.pdb.gz
6	7y3eA	0.51	4.32	0.028	0.888	model1_7y3eA.pdb.gz
7	1riqA	0.51	4.52	0.089	0.906	model1_1riqA.pdb.gz
8	5fkzE	0.51	4.15	0.039	0.869	model1_5fkzE.pdb.gz
9	5w1hA4	0.50	4.31	0.079	0.832	model1_5w1hA4.pdb.gz
10	3hxxA	0.50	4.73	0.066	0.888	model1_3hxxA.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:0005096	0.97	GTPase activator activity
GO:0031267	0.93	small GTPase binding
GO:0017137	0.92	Rab GTPase binding
GO:0097159	0.54	organic cyclic compound binding
GO:1901363	0.53	heterocyclic compound 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	1.00	biological regulation
GO:0050794	0.97	regulation of cellular process
GO:0043087	0.94	regulation of GTPase activity
GO:0033043	0.93	regulation of organelle organization
GO:0060627	0.92	regulation of vesicle-mediated transport
GO:0071702	0.90	organic substance transport
GO:0045184	0.90	establishment of protein localization
GO:0008104	0.90	protein localization
GO:0090630	0.89	activation of GTPase activity
GO:0031338	0.89	regulation of vesicle fusion
GO:0006886	0.89	intracellular protein transport

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	0.99	cell part
GO:0012505	0.92	endomembrane system
GO:0005622	0.86	intracellular
GO:0044424	0.68	intracellular 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	2i2xA	0.469	3.70	0.097	0.701	2.1.1.90	NA
2	0.060	3g4dA	0.454	4.42	0.067	0.832	4.2.3.13	78
3	0.060	3cp8A	0.462	4.05	0.038	0.757	1.-.-.-	NA
4	0.060	1qxpB	0.479	5.00	0.047	0.944	3.4.22.53 3.4.22.52	NA
5	0.060	1ejiA	0.503	4.42	0.080	0.860	2.1.2.1	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:

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	2a2cA	0.504	4.39	0.067	0.860	0.17	NG1	complex1.pdb.gz	67,69,73,101,102,104
2	0.01	2xvqA	0.467	4.47	0.029	0.841	0.16	9DS	complex2.pdb.gz	69,70,73,74
3	0.01	1e7bA	0.449	4.44	0.061	0.804	0.17	HLT	complex3.pdb.gz	48,102,103,104
4	0.01	2vufA	0.424	4.76	0.029	0.832	0.16	FUA	complex4.pdb.gz	67,68,72
5	0.01	2xw0A	0.465	4.48	0.029	0.841	0.15	9NF	complex5.pdb.gz	49,67,98
6	0.01	2bxcA	0.329	5.75	0.069	0.776	0.12	P1Z	complex6.pdb.gz	49,69,101,102,103
7	0.01	2bxpA	0.312	4.46	0.050	0.533	0.14	MYR	complex7.pdb.gz	49,68,69
8	0.01	2bx8A	0.439	4.63	0.029	0.822	0.21	AZQ	complex8.pdb.gz	98,101,102
9	0.01	2bxkA	0.347	4.96	0.038	0.664	0.13	AZQ	complex9.pdb.gz	49,72,105
10	0.01	3cx9A	0.315	4.66	0.029	0.542	0.20	LPX	complex10.pdb.gz	77,78,81

	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.