D-I-TASSER Q16478-D2

D-I-TASSER results for Q16478-D2

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

Input Sequence in FASTA format

>Q16478 (269 residues)
DINLSQTLANKTLVVTTILENPYVMRRPNFQALSGNERFEGFCVDMLRELAELLRFRYRL
RLVEDGLYGAPEPNGSWTGMVGELINRKADLAVAAFTITAEREKVIDFSKPFMTLGISIL
YRVHMGRMEVPVESADDLADQTNIEYGTIHAGSTMTFFQNSRYQTYQRMWNYMQSKQPSV
FVKSTEEGIARVLNSRYAFLLESTMNEYHRRLNCNLTQIGGLLDTKGYGIGMPLGSPFRD
EITLAILQLQENNRLEILKRKWWEGGRCP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| DINLSQTLANKTLVVTTILENPYVMRRPNFQALSGNERFEGFCVDMLRELAELLRFRYRLRLVEDGLYGAPEPNGSWTGMVGELINRKADLAVAAFTITAEREKVIDFSKPFMTLGISILYRVHMGRMEVPVESADDLADQTNIEYGTIHAGSTMTFFQNSRYQTYQRMWNYMQSKQPSVFVKSTEEGIARVLNSRYAFLLESTMNEYHRRLNCNLTQIGGLLDTKGYGIGMPLGSPFRDEITLAILQLQENNRLEILKRKWWEGGRCP
Prediction	CCCHHHHCCCCSSSSSSCCCCCCSSSCCCCCCCCCCCCSSSSHHHHHHHHHHHHCCSSSSSSCCCCCCCCCCCCCCHHHHHHHHHHCCCCSSSSCCCCCHHHHHSSSSSHHHHHCCSSSSSSCCCCCCCCCHHHHCCCCCCSSSSSSSSSHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHCHHHHHHHHHCCCCSSSSCHHHHHHHHHHCCCSSSSCCCCCCCCSSSSSCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCCCC
Confidence	98754411597899998267871342589763379995898719999999999799089998678766655778876699999980998789746868978964133104465246599998587666652022022124031478775146688887751762555566542124631344237999999966982899612678999973997698377567775069962991899999999999998092999999745899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| DINLSQTLANKTLVVTTILENPYVMRRPNFQALSGNERFEGFCVDMLRELAELLRFRYRLRLVEDGLYGAPEPNGSWTGMVGELINRKADLAVAAFTITAEREKVIDFSKPFMTLGISILYRVHMGRMEVPVESADDLADQTNIEYGTIHAGSTMTFFQNSRYQTYQRMWNYMQSKQPSVFVKSTEEGIARVLNSRYAFLLESTMNEYHRRLNCNLTQIGGLLDTKGYGIGMPLGSPFRDEITLAILQLQENNRLEILKRKWWEGGRCP
Prediction	84545541562201000133311103345253357754010000100420074170514033264553344445330320032045440100002331364044313102011321000002154443443342152344333320111213203321333424234323423444424212422540142035431000001030421265546133135415664200004244601530150044037524154036211765618
	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

CCCHHHHCCCCSSSSSSCCCCCCSSSCCCCCCCCCCCCSSSSHHHHHHHHHHHHCCSSSSSSCCCCCCCCCCCCCCHHHHHHHHHHCCCCSSSSCCCCCHHHHHSSSSSHHHHHCCSSSSSSCCCCCCCCCHHHHCCCCCCSSSSSSSSSHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHCHHHHHHHHHCCCCSSSSCHHHHHHHHHHCCCSSSSCCCCCCCCSSSSSCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCCCC
DINLSQTLANKTLVVTTILENPYVMRRPNFQALSGNERFEGFCVDMLRELAELLRFRYRLRLVEDGLYGAPEPNGSWTGMVGELINRKADLAVAAFTITAEREKVIDFSKPFMTLGISILYRVHMGRMEVPVESADDLADQTNIEYGTIHAGSTMTFFQNSRYQTYQRMWNYMQSKQPSVFVKSTEEGIARVLNSRYAFLLESTMNEYHRRLNCNLTQIGGLLDTKGYGIGMPLGSPFRDEITLAILQLQENNRLEILKRKWWEGGRCP

5dt6A

0.43

0.42

12.20

1.50

DEthreader

---GSYDR-NHTYIVSSLLEEPYLSLKQYTY-SLVGDRFEGYCKDLADMLAAQLGIKYEIRLVQDGNYGAENQYAPWDGMVGELIRKEADIAISAMTITAERERVIDFSKPFMTLGISIMIKK-G-TP-IKT--PEDLTMQTDVNYGTLLYGSTWEFFRRSQIGLHNKMWEYMNA-NQHHSVHTYDEGIRRVRQKKYALLVESPKNEYVNARPCDTMKVGRNIDTKGFGVATPIGSPLRKRLNEAVLTLKENGELLRIRNKWWFDKTEC

1yaeA

0.62

0.60

17.13

1.79

SPARKS-K

PANITDSLSNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKI--------DSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGC-

5dtbA

0.55

0.52

15.10

0.63

MapAlign

--------KNKTLVVTTILSNPYCMRKESAIPLSGNDQFEGYAVDLIHEISKSLGFNYKIQLVPDGSYGSLNLTGEWNGMIRELLEQRADLAIADLTITFEREQAVDFTTPFMNLGVSILYRK-----GTPIESAEDLAKQTRIKYGALKGGSTAAFFRDSKISTYQRMWSFMESARPSVFTASNGEGVERVAKGSYAFLMESTSIEYVTERNCELTQVGGMLDTKSYGIATPPNSPYRTAINSVILKLQEEGKLHILKTKWWKGGKCR

5dt6A

0.45

0.43

12.61

0.49

CEthreader

----GSYDRNHTYIVSSLLEEPYLSLKQYTYGESLVDRFEGYCKDLADMLAAQLGIKYEIRLVQDGNYGAENQPGGWDGMVGELIRKEADIAISAMTITAERERVIDFSKPFMTLGISIMIKKG-----TPIKTPEDLTMQTDVNYGTLLYGSTWEFFRRSQIGLHNKMWEYMNANQHH-SVHTYDEGIRRVRQSKYALLVESPKNEYVNARPCDTMKVGRNIDTKGFGVATPIGSPLRKRLNEAVLTLKENGELLRIRNKWWFDKTEC

1yaeA

0.62

0.60

17.13

1.74

MUSTER

PANITDSLSNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRK--------IDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGC-

5l2eA

0.35

0.33

9.77

1.45

HHsearch

VTGLNG-SLGVVLRVVTVLEEPFVMVSENV--LGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRR-------SIQSLQDLSKQTDIPYGTVLDSAVYQHVRMKGLSMYSQMWRMIN-----NNVLESQAGIQKVKYGNYAFVWDAAVLEYVADPDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQSGDMDILKHKWWPKGQC-

1yaeA

0.62

0.59

17.03

2.61

FFAS-3D

PANITDSLSNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGADDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKIDS--------ADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGC-

1yaeA

0.62

0.60

17.13

0.97

EigenThreader

PANITDSLSNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRK--------IDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGC-

5ikbA

0.84

0.78

21.90

2.76

CNFpred

-----------TLVVTTILENPYLMLKGNHQDMEGNDRYEGFCVDMLKELAEILRFNYKIRLVGDGVYGVPEANGTWTGMVGELIARKADLAVAGLTITAEREKVIDFSKPFMTLGISILYRKG-----TPIESVDDLADQTAIEYGTIHGGSSMTFFQNSRYQTYQRMWNYMYSKQPSVFVKSTEEGIARVLNSNYAFLLESTMNEYYRQRNCNLTQIGGLLDTKGYGIGMPVGSVFRDEFDLAILQLQENNRLEILKRKWWEG----

1yaeA

0.62

0.59

16.91

1.33

DEthreader

---ITDSLSNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRK--------IDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWR-GNGC

(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	0.903

(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	1.16	0.452	0.963	model1_5dt6A.pdb.gz
2	1yaeA	0.93	1.23	0.615	0.967	model1_1yaeA.pdb.gz
3	5dtbA	0.93	1.04	0.543	0.952	model1_5dtbA.pdb.gz
4	4uqqA	0.91	1.50	0.599	0.948	model1_4uqqA.pdb.gz
5	5ikbA	0.91	1.02	0.839	0.926	model1_5ikbA.pdb.gz
6	4wxjA	0.90	1.09	0.390	0.926	model1_4wxjA.pdb.gz
7	4pe5A	0.86	2.23	0.300	0.937	model1_4pe5A.pdb.gz
8	4zdmA	0.86	1.76	0.223	0.918	model1_4zdmA.pdb.gz
9	1y20A	0.86	1.91	0.316	0.918	model1_1y20A.pdb.gz
10	4ykiA	0.85	1.78	0.240	0.914	model1_4ykiA.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:0015276	1.00	ligand-gated ion channel activity
GO:0005230	0.99	extracellular ligand-gated ion channel activity
GO:0008066	0.98	glutamate receptor activity
GO:0004970	0.97	ionotropic glutamate receptor activity
GO:0005234	0.91	extracellular-glutamate-gated ion channel activity
GO:0004971	0.75	AMPA glutamate receptor activity
GO:0015277	0.68	kainate selective glutamate receptor activity
GO:0030165	0.62	PDZ domain 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	0.98	biological regulation
GO:0050789	0.98	regulation of biological process
GO:0050794	0.97	regulation of cellular process
GO:0044699	0.97	single-organism process
GO:0009987	0.97	cellular process
GO:0044763	0.96	single-organism cellular process
GO:0051234	0.94	establishment of localization
GO:0007215	0.94	glutamate receptor signaling pathway
GO:0006810	0.93	transport
GO:0035235	0.92	ionotropic glutamate receptor signaling pathway
GO:0006811	0.92	ion transport
GO:0034220	0.90	ion transmembrane transport
GO:0023051	0.76	regulation of signaling
GO:0010646	0.75	regulation of cell communication
GO:0050804	0.74	modulation of synaptic transmission
GO:0065008	0.72	regulation of biological quality
GO:0050896	0.71	response to stimulus
GO:0042391	0.69	regulation of membrane potential
GO:0042221	0.67	response to chemical
GO:0060255	0.65	regulation of macromolecule metabolic process
GO:0031323	0.65	regulation of cellular metabolic process
GO:0051966	0.64	regulation of synaptic transmission, glutamatergic
GO:0048519	0.64	negative regulation of biological process
GO:0060992	0.63	response to fungicide
GO:0050805	0.63	negative regulation of synaptic transmission
GO:0010035	0.63	response to inorganic substance
GO:0051967	0.62	negative regulation of synaptic transmission, glutamatergic
GO:0010226	0.62	response to lithium ion
GO:0001919	0.62	regulation of receptor recycling
GO:0032502	0.50	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:0044464	1.00	cell part
GO:0016020	1.00	membrane
GO:0044459	0.94	plasma membrane part
GO:0008328	0.88	ionotropic glutamate receptor complex
GO:0044456	0.67	synapse part
GO:0016021	0.66	integral component of membrane
GO:0005886	0.66	plasma membrane
GO:0097060	0.64	synaptic membrane
GO:0045211	0.63	postsynaptic membrane
GO:0045202	0.63	synapse
GO:0030054	0.58	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	0.265	3kbrA	0.714	2.70	0.157	0.818	4.2.1.91 4.2.1.51	15,17,42,44
2	0.067	2vd2A	0.541	3.60	0.107	0.684	2.4.2.17	NA
3	0.066	1ve4A	0.504	3.64	0.079	0.651	2.4.2.17	157
4	0.060	5acnA	0.343	6.32	0.036	0.602	4.2.1.3	NA
5	0.060	1ah5A	0.546	4.31	0.101	0.732	2.5.1.61 4.3.1.8	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	0.77	2xxtA	0.904	0.78	0.636	0.918	1.64	KAI	complex1.pdb.gz	20,68,95,97,102,149,152,153,154,185,202
2	0.72	2p2aB	0.905	1.15	0.538	0.933	1.73	MP9	complex2.pdb.gz	21,22,23,68,95,96,97,102,152,153,154,202,204,205,228
3	0.71	3g3fA	0.905	1.03	0.632	0.929	0.91	GLU	complex3.pdb.gz	68,100,152,153,154,202,228
4	0.70	2qs2A	0.789	2.68	0.590	0.926	1.28	UBF	complex4.pdb.gz	20,23,68,95,96,97,102,202,228
5	0.54	1p1uB	0.875	1.90	0.535	0.944	0.83	AMQ	complex5.pdb.gz	68,95,96,97,102
6	0.48	3h06B	0.806	2.76	0.468	0.937	0.84	VBP	complex6.pdb.gz	149,154,185,201,202,205,228
7	0.46	2xhdB	0.910	1.07	0.546	0.933	1.82	7T9	complex7.pdb.gz	111,114,225,226,227
8	0.39	1pb7A	0.862	1.85	0.323	0.922	0.86	GLY	complex8.pdb.gz	95,96,97,102,152,153,201,202
9	0.32	3m3lG	0.916	1.18	0.531	0.944	1.63	P99	complex9.pdb.gz	98,111,113,114,226,227,250
10	0.32	3o29A	0.926	1.35	0.533	0.955	1.44	O29	complex10.pdb.gz	98,111,112,113,114,225,226,227,247,250,255,256

	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.