D-I-TASSER P07510-D2

D-I-TASSER results for P07510-D2

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

Input Sequence in FASTA format

>P07510 (175 residues)
PLFYVINIIAPCVLISSVAILIHFLPAKAGGQKCTVAINVLLAQTVFLFLVAKKVPETSQ
AVPLISKYLTFLLVVTILIVVNAVVVLNVSLRSPHTHSMARGVRKVFLRLLPQLLRMHVN
EEWFLVGRVLDRVCFLAMLSLFICGTAGIFLMAHYNRVPALPFPGDPRPYLPSPD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| PLFYVINIIAPCVLISSVAILIHFLPAKAGGQKCTVAINVLLAQTVFLFLVAKKVPETSQAVPLISKYLTFLLVVTILIVVNAVVVLNVSLRSPHTHSMARGVRKVFLRLLPQLLRMHVNEEWFLVGRVLDRVCFLAMLSLFICGTAGIFLMAHYNRVPALPFPGDPRPYLPSPD
Prediction	CCSSSSHHHHHHHHHHHHHHHHHSCCCCCCCCSSSSSSHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHSSSSSCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9146543799999999999999505788888615663159999999999999862333577853898899999999999998752256653799999866899999999869997356776544444445551204444444247520136665789988899999877899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| PLFYVINIIAPCVLISSVAILIHFLPAKAGGQKCTVAINVLLAQTVFLFLVAKKVPETSQAVPLISKYLTFLLVVTILIVVNAVVVLNVSLRSPHTHSMARGVRKVFLRLLPQLLRMHVNEEWFLVGRVLDRVCFLAMLSLFICGTAGIFLMAHYNRVPALPFPGDPRPYLPSPD
Prediction	6431331033113312321320010224344430101011131312323312430443352022022113211110021123000000012434544401400120004300310123244645444422432122223333212222222343354247423545346246658
	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

CCSSSSHHHHHHHHHHHHHHHHHSCCCCCCCCSSSSSSHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHSSSSSCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
PLFYVINIIAPCVLISSVAILIHFLPAKAGGQKCTVAINVLLAQTVFLFLVAKKVPETSQAVPLISKYLTFLLVVTILIVVNAVVVLNVSLRSPHTHSMARGVRKVFLRLLPQLLRMHVNEEWFLVGRVLDRVCFLAMLSLFICGTAGIFLMAHYNRVPALPFPGDPRPYLPSPD

6pv7A

0.42

0.37

10.75

1.33

DEthreader

PLFYTINLIIPCLLISFLTVLVFYLPSDCG-EKVTLCISVLLSLTVFLLVITETIPSTSLVIPLIGEYLLFTMIFVTLSIVITVFVLNVHYRTPTTHTMPSWVKTVFLNLLPRVFMTREIDDWKYVAMVIDRIFLWVFTLVCILGTAGLLQPLM---------------------

5kxiA2

0.45

0.39

11.52

1.88

SPARKS-K

PLFYTINLIIPCLLISCLTVLVFYLPS-ECGEKITLCISVLLSLTVFLLLITEIIPSTSLVIPLIGEYLLFTMIFVTLSIVITVFVLNVHHRSPRTHTMPTWVRRVFLDIVPRLLLERVKEDWKYVAMVIDRIFLWMFIIVCLLGTVGLFLPPW---------------------

7kooA2

0.37

0.34

10.02

0.84

MapAlign

TLYYGLNLLIPCVLISALALLVFLLPA-DSGEKISLGITVLLSLTVFMLLVAEIMPATSDSVPLIAQYFASTMIIVGLSVVVTVIVLQYHHHDPDGGKMPKWTRVILLNWCAWFLSEAVCSEWKFAACVVDRLCLMAFSVFTIICTIGILMSAFVEAVSKDF-------------

7kooA2

0.36

0.34

10.03

0.66

CEthreader

TLYYGLNLLIPCVLISALALLVFLLPAD-SGEKISLGITVLLSLTVFMLLVAEIMPATSDSVPLIAQYFASTMIIVGLSVVVTVIVLQYHHHDPDGGKMPKWTRVILLNWCAWFLRPAVCSEWKFAACVVDRLCLMAFSVFTIICTIGILMSAPNFVEAVSKDF-----------

5kxiB2

0.51

0.43

12.58

2.06

MUSTER

PLFYTINLIIPCVLITSLAILVFYLPSDC-GEKMTLCISVLLALTVFLLLISKIVPPTSLDVPLVGKYLMFTMVLVTFSIVTSVCVLNVHHRSPTTHTMAPWVKVVFLEKLPALL---FSEDWKYVAMVIDRLFLWIFVFVCVFGTIGMFLQPL---------------------

7kooA2

0.36

0.34

10.03

2.43

HHsearch

TLYYGLNLLIPCVLISALALLVFLLPAD-SGEKISLGITVLLSLTVFMLLVAEIMPATSDSVPLIAQYFASTMIIVGLSVVVTVIVLQYHHHDPDGGKMPKWTRVILLNWCAWFLRPDVCSEWKFAACVVDRLCLMAFSVFTIICTIGILMSAPNFVEAVSKDF-----------

5kxiB2

0.52

0.43

12.57

2.17

FFAS-3D

PLFYTINLIIPCVLITSLAILVFYLPSDC-GEKMTLCISVLLALTVFLLLISKIVPPTSLDVPLVGKYLMFTMVLVTFSIVTSVCVLNVHHRSPTTHTMAPWVKVVFLEKLPALLFS---EDWKYVAMVIDRLFLWIFVFVCVFGTIGMFL------------------------

7kooA2

0.36

0.34

10.03

1.15

EigenThreader

TLYYGLNLLIPCVLISALALLVFLLPAD-SGEKISLGITVLLSLTVFMLLVAEIMPATSDSVPLIAQYFASTMIIVGLSVVVTVIVLQYHHHDPDGGKMPKWTRVILLNWCAWFLREAVCSEWKFAACVVDRLCLMAFSVFTIICTIGILM-----SAPNFVEAVSKDF------

5kxiB

0.51

0.43

12.57

1.05

CNFpred

PLFYTINLIIPCVLITSLAILVFYLPSD-CGEKMTLCISVLLALTVFLLLISKIVPPTSLDVPLVGKYLMFTMVLVTFSIVTSVCVLNVHHRSPTTHTMAPWVKVVFLEKLPALLF---SEDWKYVAMVIDRLFLWIFVFVCVFGTIGMFLQ-----------------------

7kooA

0.37

0.33

9.83

1.33

DEthreader

TLYYGLNLLIPCVLISALALLVFLLPADS-GEKISLGITVLLSLTVFMLLVAEIMPATSDSVPLIAQYFASTMIIVGLSVVVTVIVLQYHHHDPDGGKMPKWTRVILLNWCAWFLR--AVSEWKFAACVVDRLCLMAFSVFTIICTIGILMSAPNFVE-----------------

(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	0.7749

(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	7kooA	0.82	1.82	0.374	0.886	model1_7kooA.pdb.gz
2	6pv7A	0.80	1.76	0.386	0.874	model1_6pv7A.pdb.gz
3	5kxiB	0.78	1.76	0.450	0.851	model1_5kxiB.pdb.gz
4	5kxiA	0.78	2.02	0.368	0.857	model1_5kxiA.pdb.gz
5	4pirA	0.72	2.31	0.188	0.834	model1_4pirA.pdb.gz
6	6plpA	0.67	2.15	0.143	0.760	model1_6plpA.pdb.gz
7	3rhwA	0.65	1.83	0.141	0.731	model1_3rhwA.pdb.gz
8	3eamA	0.64	1.65	0.164	0.697	model1_3eamA.pdb.gz
9	4cofA	0.64	1.76	0.154	0.703	model1_4cofA.pdb.gz
10	4yeuA2	0.61	2.04	0.164	0.697	model1_4yeuA2.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	1.00	transmembrane receptor activity
GO:0005231	0.98	excitatory extracellular ligand-gated ion channel activity
GO:0015464	0.97	acetylcholine receptor activity
GO:0004889	0.97	acetylcholine-activated cation-selective channel activity
GO:0042166	0.92	acetylcholine 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:0044699	0.99	single-organism process
GO:0044763	0.98	single-organism cellular process
GO:0007271	0.97	synaptic transmission, cholinergic
GO:0006810	0.70	transport
GO:0006811	0.69	ion transport
GO:0006812	0.68	cation transport
GO:0050896	0.66	response to stimulus
GO:0042221	0.64	response to chemical
GO:0034220	0.63	ion transmembrane transport
GO:0098655	0.62	cation transmembrane transport
GO:0035094	0.62	response to nicotine
GO:0007274	0.62	neuromuscular synaptic transmission

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:0016021	1.00	integral component of membrane
GO:0016020	1.00	membrane
GO:0044459	0.96	plasma membrane part
GO:0034702	0.93	ion channel complex
GO:0005892	0.92	acetylcholine-gated channel complex
GO:0005886	0.76	plasma membrane
GO:0045211	0.57	postsynaptic membrane
GO:0045202	0.57	synapse
GO:0030054	0.56	cell junction

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	1tj7A	0.494	4.04	0.046	0.714	4.3.2.1	NA
2	0.060	1r5zA	0.486	3.64	0.052	0.640	3.6.3.14	NA
3	0.060	1yrqI	0.498	4.49	0.063	0.743	1.12.2.1	NA
4	0.060	1k62B	0.482	4.01	0.040	0.703	4.3.2.1	NA
5	0.060	1h2rL	0.501	4.58	0.069	0.749	1.12.2.1	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:

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	0.11	3riaE	0.654	1.83	0.141	0.731	0.80	IVM	complex1.pdb.gz	34,37,79,80,83,84,87
	2	0.01	1rke1	0.475	4.07	0.052	0.703	0.47	III	complex2.pdb.gz	30,31,34,81,82,84,91,129,130,134,137,138,141,145

	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.