D-I-TASSER P39086-D1

D-I-TASSER results for P39086-D1

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

Input Sequence in FASTA format

>P39086 (258 residues)
MEHGTLLAQPGLWTRDTSWALLYFLCYILPQTAPQVLRIGGIFETVENEPVNVEELAFKF
AVTSINRNRTLMPNTTLTYDIQRINLFDSFEASRRACDQLALGVAALFGPSHSSSVSAVQ
SICNALEVPHIQTRWKHPSVDNKDLFYINLYPDLLNIDNPHVSSIIEKWSMERLQAPPRP
ETGLLDGMMTTEAALMYDAVYMVAIASHRASQLTVSSLQCHRHKPWRLGPRFMNLIKEAR
WDGLTGHITFNKTNGLRK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MEHGTLLAQPGLWTRDTSWALLYFLCYILPQTAPQVLRIGGIFETVENEPVNVEELAFKFAVTSINRNRTLMPNTTLTYDIQRINLFDSFEASRRACDQLALGVAALFGPSHSSSVSAVQSICNALEVPHIQTRWKHPSVDNKDLFYINLYPDLLNIDNPHVSSIIEKWSMERLQAPPRPETGLLDGMMTTEAALMYDAVYMVAIASHRASQLTVSSLQCHRHKPWRLGPRFMNLIKEARWDGLTGHITFNKTNGLRK
Prediction	CCCCSSSSCCHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSSSCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCSSSSSSSSCCCCCHHHHHHHHHHHHCCCSSSSSSCCCCCHHHHHHHHHHHHCCCSSSSCCCCCCCCCCCCCSSSSCCCHHHHHHHHHHHHHHHHCCSSSSSSSCCCCCCHHHHHHHHHHHHCCSSSSSSSSCCCCCCCCSCCCCCCCCCCCCCCHHHHHHHHHCCSCCCSSSSSSCCCCCCCC
Confidence	974303314525552578999999999703589976899999607986431589999999999996296658981899999974899736666666775315808999289731699999999761897576124675446777762662687789999999999998197399999438963100456667664111499999613666543100146898853588517999998600126515589747888529
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MEHGTLLAQPGLWTRDTSWALLYFLCYILPQTAPQVLRIGGIFETVENEPVNVEELAFKFAVTSINRNRTLMPNTTLTYDIQRINLFDSFEASRRACDQLALGVAALFGPSHSSSVSAVQSICNALEVPHIQTRWKHPSVDNKDLFYINLYPDLLNIDNPHVSSIIEKWSMERLQAPPRPETGLLDGMMTTEAALMYDAVYMVAIASHRASQLTVSSLQCHRHKPWRLGPRFMNLIKEARWDGLTGHITFNKTNGLRK
Prediction	663122213023113300111112101011333453020000013456433412320032005401646631462303020440444222301332153245200000002232114001300532411101220434424544422130203323224300320053140530000044453234344434421332102012313443451315405154642064033014104514154111403055563548
	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                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCSSSSCCHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSSSCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCSSSSSSSSCCCCCHHHHHHHHHHHHCCCSSSSSSCCCCCHHHHHHHHHHHHCCCSSSSCCCCCCCCCCCCCSSSSCCCHHHHHHHHHHHHHHHHCCSSSSSSSCCCCCCHHHHHHHHHHHHCCSSSSSSSSCCCCCCCCSCCCCCCCCCCCCCCHHHHHHHHHCCSCCCSSSSSSCCCCCCCC
MEHGTLLAQPGLWTRDTSWALLYFLCYILPQTAPQVLRIGGIFETVENEPVNVEELAFKFAVTSINRNRTLMPNTTLTYDIQRINLFDSFEASRRACDQLALGVAALFGPSHSSSVSAVQSICNALEVPHIQTRWKHPSVDNKDLFYINLYPDLLNIDNPHVSSIIEKWSMERLQAPPRPETGLLDGMMTTEAALMYDAVYMVAIASHRASQLTVSSLQCHRHKPWRLGPRFMNLIKEARWDGLTGHITFNKTNGLRK

3h6gB

0.74

0.64

18.03

1.33

DEthreader

---------------------------------THVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKINLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVSLYPDILNTENTQVSSIIEKWSMERLQ-APPK-DSLLDGFMTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGLRD

3om0A1

0.28

0.23

7.11

1.64

SPARKS-K

---------------------------------LSSLRMAAILDD-QTVCGRGERLALALAREQINGIIEVPAKARVEVDIFELQRDSQYETTDTMCQILPKGVVSVLGPSSPASASTVSHICGEKEIPHIKVG---PEETPLRFASVSLYPM-FNTSHPFYPEFVRSLNMSWRENCEASTYPG----PALSAALMFDAVHVVVSAVRELNRIGVKPLACTSANIWPHGTSLMNYLRMVEYDGLTGRVEFNSK-GQRT

4uqqA

0.75

0.65

18.45

0.71

MapAlign

---------------------------------THVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKINLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVSLYPDILNTENTQVSSIIEKWSMERLQAPPKPDSGLLDGFMTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGLRT

4uqqA

0.74

0.65

18.35

0.49

CEthreader

---------------------------------THVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKINLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVSLYPDFSNTENTQVSSIIEKWSMERLQAPPKPDSGLLDGFMTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGLRT

3om0A1

0.28

0.23

7.11

1.44

MUSTER

---------------------------------LSSLRMAAILDDQTV-CGRGERLALALAREQINGIIEVPAKARVEVDIFELQRDSQYETTDTMCQILPKGVVSVLGPSSSASASTVSHICGEKEIPHIKVGPEET---PLRFASVSLYP-MFNTSHPFYPEFVRSLNMSWRENCEASTY----PGPALSAALMFDAVHVVVSAVRELNRIGVKPLACTSANIWPHGTSLMNYLRMVEYDGLTGRVEFNS-KGQRT

7ks0B

0.75

0.65

18.45

1.80

HHsearch

---------------------------------THVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKINLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVSLYPDILNTENTQVSSIIEKWSMERLQAPPKPDSGLLDGFMTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGLRT

4uqqA1

0.74

0.54

15.28

2.02

FFAS-3D

---------------------------------THVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKINLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVSLY-------------------------------------PTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGLRT

4uqqA

0.62

0.52

14.98

0.88

EigenThreader

---------------------------------THVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTL-LPNTTLTYDINLYD--SFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNAL-GVPHIQTRWKHQVSDNKDSFYVSLYPDLNTENTQVSSIIEKWSMERLQAPPKPDSGLLDGFMTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNG--L

4uqqA

0.75

0.65

18.45

1.44

CNFpred

----------------------------------HVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKINLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVSLYPD-LNTENTQVSSIIEKWSMERLQAPPKPDSGLLDGFMTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGLRT

4uqqA

0.74

0.64

18.03

1.33

DEthreader

---------------------------------THVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKINLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVSLYPDILNTENTQVSSIIEKWSMERLQ-APPK-DSLLDGFMTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGLRD

(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	0.7343

(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	4uqqA	0.85	1.32	0.742	0.872	model1_4uqqA.pdb.gz
2	3h6gB	0.85	1.32	0.742	0.872	model1_3h6gB.pdb.gz
3	7ks0A	0.78	2.17	0.274	0.849	model1_7ks0A.pdb.gz
4	3om0A	0.76	2.23	0.264	0.837	model1_3om0A.pdb.gz
5	4gpaA	0.76	2.20	0.258	0.826	model1_4gpaA.pdb.gz
6	5kcaA	0.74	2.64	0.206	0.833	model1_5kcaA.pdb.gz
7	3o21A	0.73	2.36	0.283	0.818	model1_3o21A.pdb.gz
8	4mqeA	0.73	2.64	0.175	0.822	model1_4mqeA.pdb.gz
9	3kg2A	0.72	2.17	0.277	0.795	model1_3kg2A.pdb.gz
10	3sajA	0.70	2.42	0.289	0.787	model1_3sajA.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:0099600	0.96	transmembrane receptor activity
GO:0038023	0.94	signaling receptor activity
GO:0004888	0.93	transmembrane signaling receptor activity
GO:0008066	0.92	glutamate receptor activity
GO:0005216	0.85	ion channel activity
GO:0022836	0.84	gated channel activity
GO:0005230	0.83	extracellular ligand-gated ion channel activity
GO:0004970	0.78	ionotropic glutamate receptor 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:0050794	0.89	regulation of cellular process
GO:0044699	0.71	single-organism process
GO:0023051	0.71	regulation of signaling
GO:0044763	0.70	single-organism cellular process
GO:0010646	0.70	regulation of cell communication
GO:0050804	0.69	modulation of synaptic transmission
GO:0007165	0.59	signal transduction
GO:0007166	0.53	cell surface receptor signaling pathway
GO:0044700	0.52	single organism signaling
GO:0007215	0.52	glutamate receptor signaling pathway

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:0044459	0.92	plasma membrane part
GO:0016020	0.82	membrane
GO:0005886	0.76	plasma membrane
GO:0044456	0.74	synapse part
GO:0016021	0.74	integral component of membrane
GO:0043234	0.69	protein complex
GO:0043235	0.67	receptor complex
GO:0098802	0.66	plasma membrane receptor complex
GO:0097458	0.63	neuron part
GO:0008328	0.63	ionotropic glutamate receptor complex
GO:0097060	0.62	synaptic membrane
GO:0042995	0.55	cell projection
GO:0044424	0.54	intracellular part
GO:0043005	0.52	neuron projection
GO:0045202	0.51	synapse

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	3bx1B	0.519	5.24	0.052	0.748	3.4.21.62	NA
2	0.060	1bjrE	0.498	5.00	0.050	0.713	3.4.21.64	NA
3	0.060	1tecE	0.511	4.87	0.046	0.713	3.4.21.66	NA
4	0.060	2w2mA	0.510	5.01	0.056	0.729	3.4.21.-	NA
5	0.060	1scaA	0.516	4.92	0.061	0.721	3.4.21.62	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	0.17	3kg2D	0.723	2.17	0.277	0.795	0.14	ZK1	complex1.pdb.gz	110,130,131,136,193
2	0.01	3h06P	0.324	6.10	0.044	0.539	0.15	VBP	complex2.pdb.gz	100,106,107,108,109,119
3	0.01	3pd9A	0.348	5.46	0.043	0.531	0.14	HA5	complex3.pdb.gz	42,83,84
4	0.01	3kfmA	0.320	6.09	0.021	0.543	0.21	KAI	complex4.pdb.gz	87,89,108,119
5	0.01	1ftlA	0.336	6.02	0.051	0.550	0.11	DNQ	complex5.pdb.gz	107,108,198,202
6	0.01	1ftjA	0.333	5.95	0.052	0.554	0.17	GLU	complex6.pdb.gz	104,105,106,130
7	0.01	1nnkA	0.348	5.46	0.071	0.535	0.17	CE2	complex7.pdb.gz	130,131,200
8	0.01	3b7dC	0.346	5.50	0.061	0.531	0.13	CNI	complex8.pdb.gz	106,107,108
9	0.01	3b7dB	0.345	5.59	0.067	0.535	0.18	CNI	complex9.pdb.gz	110,131,201
10	0.01	3keiA	0.331	5.63	0.030	0.535	0.24	GLU	complex10.pdb.gz	41,42,43,51,111,112

	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.