D-I-TASSER P42262-D2

D-I-TASSER results for P42262-D2

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

Input Sequence in FASTA format

>P42262 (271 residues)
LPSGNDTSGLENKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKY
KLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGI
SIMIKKPQVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSV
FVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSS
LRNAVNLAVLKLNEQGLLDKLKNKWWYDKGE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| LPSGNDTSGLENKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDKGE
Prediction	CCCCCCCCCCCCCSSSSSSCCCCCCSSSCCCCCCCCCCCCSSSSSHHHHHHHHHHHCCSSSSSSCCCCCCCCCCCCCCCCHHHHHHHHHCCCCSSSSCCSCCHHHHHCSSSCCHHHCCCSSSSSSCCCCCCCCCHHHCCCCSSSSSSSSCHHHHHHHHHHCCCHHHHHHHHHHHCCCCCSSSCCHHHHHHHHHHCCCCSSSSSCHHHHHHHHHHCCCCSSSSCCCCCCCCSSSSSSCCCHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCC
Confidence	9999875112698899996578996243377543178996898719999999999699499998678755554667876314789998568888986361488897311115124305749999879887877877739937999997443359986412243034668887633687336346289999999489868999368999999981999689927778874259999389789999999999999808799999965356899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| LPSGNDTSGLENKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDKGE
Prediction	4345455651562101000243311212344552356743010000100420074161514033164453444446434031003304534020000001025404411210323142100000215473434334234431002202311110242246442522542252146443312243334003203654200000002101300363574412202561566300000314460152035025403741415303723357578
	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                 260

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

SS
Seq

CCCCCCCCCCCCCSSSSSSCCCCCCSSSCCCCCCCCCCCCSSSSSHHHHHHHHHHHCCSSSSSSCCCCCCCCCCCCCCCCHHHHHHHHHCCCCSSSSCCSCCHHHHHCSSSCCHHHCCCSSSSSSCCCCCCCCCHHHCCCCSSSSSSSSCHHHHHHHHHHCCCHHHHHHHHHHHCCCCCSSSCCHHHHHHHHHHCCCCSSSSSCHHHHHHHHHHCCCCSSSSCCCCCCCCSSSSSSCCCHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCC
LPSGNDTSGLENKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDKGE

5dt6A

0.53

0.51

14.81

1.50

DEthreader

----GS--YDRNHTYIVSSLLEEPYLSLKQYTESLVGNDRFEGYCKDLADMLAAQLGIKYEIRLVQDGNYGAENQYAPGWDGMVGELIRKEADIAISAMTITAERERVIDFSKPFMTLGISIMIKKG-TPIKT-PEDLTMQTDVNYGTLLYGSTWEFFRRSQIGLHNKMWEYMNA-NQHHSVHTYDEGIRRVRQSKGKYALLVEPKNEYVNAR-PPCDTMKVGRNIDTKGFGVATPIGSPLRKRLNEAVLTLKENGELLRIRNKWWFDKTE

5dt6A

0.56

0.54

15.61

1.81

SPARKS-K

------GSYDRNHTYIVSSLLEEPYLSLKQYTESLVGNDRFEGYCKDLADMLAAQLGIKYEIRLVQDGNYGAENQYAPGWDGMVGELIRKEADIAISAMTITAERERVIDFSKPFMTLGISIMIKKG--TPIKTPEDLTMQTDVNYGTLLYGSTWEFFRRSQIGLHNKMWEYMNAN-QHHSVHTYDEGIRRVRQSKGKYALLVESPKNEYVNARPPCDTMKVGRNIDTKGFGVATPIGSPLRKRLNEAVLTLKENGELLRIRNKWWFDKTE

5dtbA

0.55

0.52

14.89

0.61

MapAlign

----------KNKTLVVTTILSNPYCMRKESAIPLSGNDQFEGYAVDLIHEISKSLGFNYKIQLVPDGSYGSLNKLTGEWNGMIRELLEQRADLAIADLTITFEREQAVDFTTPFMNLGVSILYRK--GTPIESAEDLAKQTRIKYGALKGGSTAAFFRDSKISTYQRMWSFMESARPSVFTASNGEGVERVAKGKGSYAFLMESTSIEYVTE-RNCELTQVGGMLDTKSYGIATPPNSPYRTAINSVILKLQEEGKLHILKTKWWKEK--

5dtbA

0.54

0.52

14.90

0.49

CEthreader

----------KNKTLVVTTILSNPYCMRKESAIPLSGNDQFEGYAVDLIHEISKSLGFNYKIQLVPDGSYGSLNKLTGEWNGMIRELLEQRADLAIADLTITFEREQAVDFTTPFMNLGVSILYRKGT--PIESAEDLAKQTRIKYGALKGGSTAAFFRDSKISTYQRMWSFMESARPSVFTASNGEGVERVAKGKGSYAFLMESTSIEYVTE-RNCELTQVGGMLDTKSYGIATPPNSPYRTAINSVILKLQEEGKLHILKTKWWKEKRG

5dtbA

0.54

0.51

14.80

1.48

MUSTER

----------KNKTLVVTTILSNPYCMRKESAIPLSGNDQFEGYAVDLIHEISKSLGFNYKIQLVPDGSYGSLNKLTGEWNGMIRELLEQRADLAIADLTITFEREQAVDFTTPFMNLGVSILYRKGTP--IESAEDLAKQTRIKYGALKGGSTAAFFRDSKISTYQRMWSFMESARPSVFTASNGEGVERVAKGKGSYAFLMESTSIEYVTERNC-ELTQVGGMLDTKSYGIATPPNSPYRTAINSVILKLQEEGKLHILKTKWWKEKRG

5l2eA

0.34

0.32

9.51

1.31

HHsearch

NPVTGLN-GSLGVVLRVVTVLEEPFVMVSENV--LGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQE-DGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRR----SIQSLQDLSKQTDIPYGTVLDSAVYQHVRMKGLSMYSQMWRMIN-----NNVLESQAGIQKVKYGN--YAFVWDAAVLEYVAIDPDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQSGDMDILKHKWWPKNGQ

1yaeA

0.49

0.47

13.61

2.61

FFAS-3D

-PAN-ITDSLSNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKIDS-----ADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSD---YAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNG-

5dt6A

0.55

0.53

15.21

0.95

EigenThreader

------GSYDRNHTYIVSSLLEEPYLSLKQYTYGESLVDRFEGYCKDLADMLAAQLGIKYEIRLVQDGNYGAENQYAPGWDGMVGELIRKEADIAISAMTITAERERVIDFSKPFMTLGISIMIKK--GTPIKTPEDLTMQTDVNYGTLLYGSTWEFFRRSQIGLHNKMWEYMNAN-QHHSVHTYDEGIRRVRQSKGKYALLVESPKNEYVNARPPCDTMKVGRNIDTKGFGVATPIGSPLRKRLNEAVLTLKENGELLRIRNKWWFDKTE

5ybfA

0.99

0.94

26.46

2.85

CNFpred

-----------NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKG--TPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDKGE

5dtbA

0.52

0.49

14.20

1.50

DEthreader

----------KNKTLVVTTILSNPYCMRKESAIPLSGNDQFEGYAVDLIHEISKSLGFNYKIQLVPDGSYGSLNKLTGEWNGMIRELLEQRADLAIADLTITFEREQAVDFTTPFMNLGVSILYRKG-TPIES-AEDLAKQTRIKYGALKGGSTAAFFRDSKISTYQRMWSFMESARPSVFTASNGEGVERVAKGKGSYAFLMETSIEYVTER-N-CELTQVGGMLDTKSYGIATPPNSPYRTAINSVILKLQEEGKLHILKTKWWKEGGK

(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	0.8801

(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	5dt6A	0.94	1.19	0.557	0.967	model1_5dt6A.pdb.gz
2	5dtbA	0.94	0.85	0.550	0.952	model1_5dtbA.pdb.gz
3	4wxjA	0.90	1.21	0.397	0.930	model1_4wxjA.pdb.gz
4	4uqqA	0.90	1.76	0.511	0.945	model1_4uqqA.pdb.gz
5	5ikbA	0.90	0.96	0.566	0.919	model1_5ikbA.pdb.gz
6	1yaeA	0.90	1.91	0.521	0.959	model1_1yaeA.pdb.gz
7	4pe5A	0.86	2.19	0.298	0.934	model1_4pe5A.pdb.gz
8	1y20A	0.85	1.90	0.319	0.915	model1_1y20A.pdb.gz
9	4ykiA	0.85	1.81	0.239	0.911	model1_4ykiA.pdb.gz
10	4zdmA	0.85	1.78	0.227	0.911	model1_4zdmA.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:0005230	1.00	extracellular ligand-gated ion channel activity
GO:0004970	0.99	ionotropic glutamate receptor activity
GO:0004971	0.95	AMPA glutamate receptor activity
GO:0005234	0.90	extracellular-glutamate-gated ion channel activity
GO:0030165	0.86	PDZ domain binding
GO:0015277	0.83	kainate selective glutamate receptor activity
GO:0042802	0.81	identical protein binding
GO:0019899	0.81	enzyme binding
GO:0019901	0.80	protein kinase binding
GO:0005246	0.80	calcium channel regulator 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	0.97	regulation of cellular process
GO:0044763	0.97	single-organism cellular process
GO:0007215	0.94	glutamate receptor signaling pathway
GO:0006810	0.94	transport
GO:0050896	0.93	response to stimulus
GO:0035235	0.93	ionotropic glutamate receptor signaling pathway
GO:0060992	0.92	response to fungicide
GO:0023051	0.92	regulation of signaling
GO:0006811	0.92	ion transport
GO:0034220	0.91	ion transmembrane transport
GO:0060255	0.89	regulation of macromolecule metabolic process
GO:0031323	0.89	regulation of cellular metabolic process
GO:0010038	0.88	response to metal ion
GO:0010226	0.87	response to lithium ion
GO:0001919	0.87	regulation of receptor recycling
GO:0044710	0.83	single-organism metabolic process
GO:0044260	0.83	cellular macromolecule metabolic process
GO:0016043	0.83	cellular component organization
GO:0051262	0.82	protein tetramerization
GO:0045184	0.82	establishment of protein localization
GO:0031623	0.82	receptor internalization
GO:0010646	0.62	regulation of cell communication
GO:0050804	0.60	modulation of synaptic transmission
GO:0065008	0.57	regulation of biological quality

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:0016020	1.00	membrane
GO:0044425	0.95	membrane part
GO:0044459	0.94	plasma membrane part
GO:1902495	0.90	transmembrane transporter complex
GO:0098797	0.90	plasma membrane protein complex
GO:0043235	0.90	receptor complex
GO:0008328	0.89	ionotropic glutamate receptor complex
GO:0005886	0.62	plasma membrane
GO:0016021	0.61	integral component of membrane
GO:0044456	0.58	synapse part
GO:0098590	0.55	plasma membrane region
GO:0097060	0.54	synaptic membrane
GO:0045202	0.54	synapse
GO:0045211	0.53	postsynaptic membrane
GO:0032281	0.50	AMPA glutamate receptor complex

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	0.067	2vd2A	0.541	3.65	0.053	0.683	2.4.2.17	69,103,155,205,212
2	0.067	1ve4A	0.503	3.71	0.067	0.649	2.4.2.17	69
3	0.066	1z7mH	0.500	3.86	0.056	0.653	2.4.2.17	88,109
4	0.060	2dkfA	0.438	5.82	0.057	0.727	3.1.-.-	NA
5	0.060	2o7qA	0.441	5.82	0.072	0.727	4.2.1.10 1.1.1.25	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	0.92	3pd9A	0.930	1.03	0.984	0.948	1.78	HA5	complex1.pdb.gz	70,98,99,100,105,152,153,154,204,207
2	0.89	2cmoA	0.834	2.34	0.961	0.941	1.50	M1L	complex2.pdb.gz	22,25,70,71,72,98,100,105,153,204,207,231
3	0.81	1n0tB	0.834	2.34	0.957	0.941	1.10	AT1	complex3.pdb.gz	22,70,98,99,100,105,231
4	0.78	3h06B	0.806	2.77	0.871	0.941	0.92	VBP	complex4.pdb.gz	149,154,185,203,204,207
5	0.65	1yaeB	0.900	1.78	0.523	0.959	1.67	DOQ	complex5.pdb.gz	22,69,70,71,98,100,105,149,150,151,152,153,154,185,204
6	0.55	3rnnC	0.935	0.82	0.984	0.948	1.66	RNN	complex6.pdb.gz	101,113,114,117,229,230,250,253
7	0.49	3h6wA	0.940	1.06	0.977	0.959	1.73	NS7	complex7.pdb.gz	113,114,116,117,250,258,259,262
8	0.49	3lslA	0.933	0.86	0.984	0.948	1.56	PZI	complex8.pdb.gz	44,115,116,253,258,259,262
9	0.49	1ftl0	0.859	2.05	0.984	0.945	1.76	III	complex9.pdb.gz	102,103,106,111,112,113,114,228,246,247,250,251,253,254
10	0.42	1pb8A	0.860	1.85	0.317	0.919	0.83	DSN	complex10.pdb.gz	70,98,100,105,153

	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.