D-I-TASSER Q96AX1-D2

D-I-TASSER results for Q96AX1-D2

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

Input Sequence in FASTA format

>Q96AX1 (235 residues)
DLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQV
ANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPLATQYPTIRKTLRLWMDDVNEQN
PTDISYVYSGYAPLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPLPTGLQKKRQPGE
NRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| DLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPLATQYPTIRKTLRLWMDDVNEQNPTDISYVYSGYAPLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPLPTGLQKKRQPGENRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF
Prediction	CCCCCCCCSSSSCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCSSSSCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHSSSCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHCCCCCCSSSCCCCCCCCCCCCCCCCCSSSSSSSCCCCHHHHHHHHHHHHHHCCCCSSSSSSCCCCCHHHHHHHHHHCCC
Confidence	9444568724424852378863169954799999999999999688863167452389999999999986244545665411131120212465542122489999974687654444687750120367455299999999504987489999738998501320367665556678998579999987956999999999998517993599993784237899999852489
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| DLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPLATQYPTIRKTLRLWMDDVNEQNPTDISYVYSGYAPLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPLPTGLQKKRQPGENRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF
Prediction	8313126100002144003301044032103300400230043212133020214203301400440475355545544440420130354242344334303302530513365255644522312330101001200310255615414400640524413444435454545557654300000001121300010022016447351300000031132440043027538
	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                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCSSSSCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCSSSSCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHSSSCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHCCCCCCSSSCCCCCCCCCCCCCCCCCSSSSSSSCCCCHHHHHHHHHHHHHHCCCCSSSSSSCCCCCHHHHHHHHHHCCC
DLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPLATQYPTIRKTLRLWMDDVNEQNPTDISYVYSGYAPLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPLPTGLQKKRQPGENRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF

4bx8A

0.97

0.92

25.88

1.33

DEthreader

DLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTLVCNNYPTIRKTLRLWMDDVNEQNPTDISYVYSGYAPLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPL---P--------NRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKP-

4bx8A4

0.99

0.82

22.88

2.44

SPARKS-K

DLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPLATQ-------------------------------PLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPLPN-----------RVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF

4bx8A

0.99

0.92

25.86

1.79

MapAlign

DLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPLATNYPTIRKTLRLWMDDVNEQNPTDISYVYSGYAPLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPL-----------PNRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEAL-----

4bx8A

1.00

0.95

26.57

1.46

CEthreader

DLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPLATQYPTIRKTLRLWMDDVNEQNPTDISYVYSGYAPLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPL-----------PNRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF

4bx8A4

0.99

0.82

22.88

1.93

MUSTER

DLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPLATQ-------------------------------PLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPL-----------PNRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF

4jc8A2

0.41

0.37

11.03

4.28

HHsearch

YFFPLERDVLSLELNDSFRDLYLAKDPTPVFLLSRAL-GIQKKHGLFPRIIGKGENAKRVADLLSR-RQELLA-GLSPSTTIESVIIIDREVDFVTPLLTQLTYLRKQLRLIVDEVNEQDPNDIAYVYSGYAPLSIRLVQCVLQQGWKGFEEIVKHARGPTFDEIQ------------KDKKTVFVVFVGGITFTEIAALRFIAKQEEARRNIVICTTSIINGNRNAAIETA---

4bx8A4

0.97

0.80

22.31

2.35

FFAS-3D

DLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPLATQPLSV-------------------------------RLAQLLSRPGWRSIEEVLRILPGPHFEERQP-----------LPNRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF

4bx8A

0.95

0.90

25.18

1.55

EigenThreader

DLDGD---LLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLLEKAGNYPTIRKTLRLWMDDVNEQNPTDISYVYSGYAPLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQ-----------PLPNRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF

4bx8A

0.99

0.94

26.46

1.72

CNFpred

DLIPFDGDLLSMESEGAFKECYLEGDQTSLYHAAKGLMTLQALYGTIPQIFGKGECARQVANMMIRMKREFTGSQNSIFPVFDNLLLLDRNVDLLTPLATQLTTIRKTLRLWMDDVNEQNPTDISYVYSGYAPLSVRLAQLLSRPGWRSIEEVLRILPGPHFEERQPLP-----------NRVTLIFFLGGVTFAEIAALRFLSQLEDGGTEYVIATTKLMNGTSWIEALMEKPF

4jc8A

0.40

0.37

10.80

1.33

DEthreader

YFFPLERDVLSLELNDSFRDLYLAKDPTPVFLLSRAL-GIQKKHGLFPRIIGKGENAKRVADLLSR-RQELLA-GLSPSTTIESVIIIDREVDFVTLCISNYTYLRKQLRLIVDEVNEQDPNDIAYVYSGYAPLSIRLVQCVLGAQWKGFEEIVKHARGPTFDEIQK-----------D-KKTVFVVFVGGITFTEIAALRFIAKQEEARRNIVICTTSIINGN-RN-AAIETA-

(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	0.927

(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	4bx8A	0.93	1.03	1.000	0.953	model1_4bx8A.pdb.gz
2	8ditA	0.90	2.34	0.400	1.000	model1_8ditA.pdb.gz
3	3c98A	0.72	3.39	0.171	0.868	model1_3c98A.pdb.gz
4	4ccaA2	0.72	3.47	0.184	0.877	model1_4ccaA2.pdb.gz
5	2pjxA2	0.72	3.41	0.160	0.877	model1_2pjxA2.pdb.gz
6	1epuA2	0.71	3.25	0.162	0.860	model1_1epuA2.pdb.gz
7	2xheA	0.70	3.40	0.167	0.851	model1_2xheA.pdb.gz
8	1mqsA3	0.65	3.14	0.155	0.770	model1_1mqsA3.pdb.gz
9	2ehhA	0.35	6.03	0.070	0.625	model1_2ehhA.pdb.gz
10	2d33A	0.33	6.41	0.044	0.630	model1_2d33A.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:0000149	0.28	SNARE binding
GO:0019905	0.27	syntaxin binding
GO:0032403	0.22	protein complex binding
GO:0003824	0.18	catalytic activity
GO:0016874	0.17	ligase activity
GO:0030348	0.11	syntaxin-3 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:0009987	0.91	cellular process
GO:0006810	0.88	transport
GO:0016043	0.87	cellular component organization
GO:0044699	0.86	single-organism process
GO:0006996	0.85	organelle organization
GO:0044763	0.83	single-organism cellular process
GO:0007033	0.81	vacuole organization
GO:0051641	0.74	cellular localization
GO:0016192	0.71	vesicle-mediated transport
GO:1902589	0.67	single-organism organelle organization
GO:0097576	0.65	vacuole fusion
GO:0046907	0.65	intracellular transport
GO:0007034	0.65	vacuolar transport
GO:0065007	0.62	biological regulation
GO:0050789	0.62	regulation of biological process
GO:0051875	0.60	pigment granule localization
GO:0016197	0.59	endosomal transport
GO:0044767	0.58	single-organism developmental process
GO:0007041	0.58	lysosomal transport
GO:0048869	0.52	cellular developmental 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:0044424	1.00	intracellular part
GO:0044444	0.92	cytoplasmic part
GO:0016020	0.82	membrane
GO:0044446	0.72	intracellular organelle part
GO:0043227	0.72	membrane-bounded organelle
GO:0043234	0.68	protein complex
GO:0043231	0.66	intracellular membrane-bounded organelle
GO:0044437	0.64	vacuolar part
GO:0098588	0.63	bounding membrane of organelle
GO:0044425	0.61	membrane part
GO:0098805	0.60	whole membrane
GO:0005774	0.58	vacuolar membrane
GO:0098796	0.55	membrane protein complex
GO:0031410	0.53	cytoplasmic 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	0.060	2w00B	0.420	5.36	0.061	0.651	3.1.21.3	NA
2	0.060	2gzmA	0.419	4.91	0.069	0.630	5.1.1.3	NA
3	0.060	1i5eA	0.443	3.71	0.060	0.570	2.4.2.9	NA
4	0.060	2hs4A	0.408	5.50	0.062	0.677	6.3.5.3	NA
5	0.060	1o5oA	0.451	3.93	0.086	0.587	2.4.2.9	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	1xtuE	0.442	4.57	0.023	0.617	0.48	CTP	complex1.pdb.gz	191,223,225

	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.