D-I-TASSER Q13002-D2

D-I-TASSER results for Q13002-D2

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

Input Sequence in FASTA format

>Q13002 (261 residues)
NRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYG
AQDDANGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKPNGSP
IDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQR
VLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQE
EGKLHMMKEKWWRGNGCPEEE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| NRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDANGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKPNGSPIDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCPEEE
Prediction	CCSSSSSSCCCCCCCCSSCCCCCCCCCCCSSSSHHHHHHHHHHHHCCSSSSSSCCCCCCCCCCCCCCCHHHHHHHHHHCCCCSSSSCCSCCHHHHHHCCSCHHHHCCCSSSSSSCCCCCCCCHHHHCCCCCCSSSSSSCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCSSSSSCHHHHHHHHHCCCCSSSSCCCCCCCSSSSSSSCCCHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCCCCCC
Confidence	957999973669975511378766789938987399999999996993999984787655445678871456777753457879874430798985200015464057089998587777773554046420699980443468887651464102355544432134431255889999852774999345889999970996799487677723799982892899999999999998083999999755899998779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| NRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDANGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKPNGSPIDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCPEEE
Prediction	832010001334112013455651535430100002004200741605140322644532444445440310032043340200000100143034102102211300000002143543252443444432221003222102211334525334322422443344212432442233033121000013210311265555132026514462000003244601530150055037524153036210776615688
	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 AttentionPotential. 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

CCSSSSSSCCCCCCCCSSCCCCCCCCCCCSSSSHHHHHHHHHHHHCCSSSSSSCCCCCCCCCCCCCCCHHHHHHHHHHCCCCSSSSCCSCCHHHHHHCCSCHHHHCCCSSSSSSCCCCCCCCHHHHCCCCCCSSSSSSCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCSSSSSCHHHHHHHHHCCCCSSSSCCCCCCCSSSSSSSCCCHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCCCCCC
NRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDANGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKPNGSPIDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCPEEE

5dtbA

0.57

0.56

16.19

1.50

DEthreader

NKTLVVTTILSNPYCMRKESAIPLSGNDQFEGYAVDLIHEISKSLGFNYKIQLVPDGSYGSLNKLTGEWNGMIRELLEQRADLAIADLTITFEREQAVDFTTPFMNLGVSILYRKG-TPIES-AEDLAKQTRIKYGALKGGSTAAFFRDSKISTYQRMWSFMESARPSVFTASNGEGVERVAKGSYAFLMESTSIEYVTERNCELTQVGGMLDTKSYGIATPPNSPYRTAINSVILKLQEEGKLHILKTKWWKEGGKCR--

5dtbA

0.58

0.57

16.51

1.91

SPARKS-K

NKTLVVTTILSNPYCMRKESAIPLSGNDQFEGYAVDLIHEISKSLGFNYKIQLVPDGSYGSLNKLTGEWNGMIRELLEQRADLAIADLTITFEREQAVDFTTPFMNLGVSILYRK--GTPIESAEDLAKQTRIKYGALKGGSTAAFFRDSKISTYQRMWSFMESARPSVFTASNGEGVERVAKGSYAFLMESTSIEYVTERNCELTQVGGMLDTKSYGIATPPNSPYRTAINSVILKLQEEGKLHILKTKWWKEKRGGGKC

5dtbA

0.60

0.58

16.70

0.66

MapAlign

NKTLVVTTILSNPYCMRKESAIPLSGNDQFEGYAVDLIHEISKSLGFNYKIQLVPDGSYGSLNKLTGEWNGMIRELLEQRADLAIADLTITFEREQAVDFTTPFMNLGVSILYRK--GTPIESAEDLAKQTRIKYGALKGGSTAAFFRDSKISTYQRMWSFMESARPSVFTASNGEGVERVAKGSYAFLMESTSIEYVTERNCELTQVGGMLDTKSYGIATPPNSPYRTAINSVILKLQEEGKLHILKTKWWKGGKC----

4uqqA2

0.97

27.28

0.49

CEthreader

NRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKGVERPIDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCPEQN

1yaeA

0.99

0.95

26.72

1.76

MUSTER

NRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKID-----SADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGC----

5l2eA

0.38

0.36

10.66

1.44

HHsearch

GVVLRVVTVLEEPFVMVSEN--VLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQ-EDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRR----SIQSLQDLSKQTDIPYGTVLDSAVYQHVRMKGLSMYSQMWRMIN-----NNVLESQAGIQKVKYGNYAFVWDAAVLEYVADPDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQSGDMDILKHKWWPKNQC----

1yaeA

0.98

0.95

26.62

2.78

FFAS-3D

NRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKIDS-----ADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGC----

4uqqA2

0.98

27.38

0.97

EigenThreader

NRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKGVFSPIDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCPEQN

3g3iA

0.97

0.95

26.74

3.03

CNFpred

NRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTHLGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREEVIDFSKPFMTLGISILYRKG--TPIDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITLAILKLQEEGKLHMMKEKWWRGNGCP---

4wxjA

0.38

0.36

10.79

1.50

DEthreader

-IRYTVATRVGKPYFSWREEPY--EGNERFEGYAVDLIYMLAQECKFDFNFEPVRDNKYGSYDANTDEWDGIIRQLIDNNAQIGICDLTITQARRSVVDFTVPFMQLGISILSYKG-TDIGS-LHDLVDQNKVQFGTIRGGATSVYFSESNDTDNRMAWNKMLSFKPDAFTKNNEEGVDRVKLKTYAFLMETTNLQYYVQRNCELTQIGESFGEKHYGIAVPLNADFRSNLSVGILRLSERGELFKLRNKWFN-S-C----

(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	0.9105

(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 AttentionPotential, 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	5dtbA	0.97	0.64	0.594	0.981	model1_5dtbA.pdb.gz
2	4uqqA2	0.95	1.05	0.973	0.977	model1_4uqqA2.pdb.gz
3	5dt6A	0.94	1.38	0.480	0.973	model1_5dt6A.pdb.gz
4	5ikbA	0.93	0.94	0.631	0.954	model1_5ikbA.pdb.gz
5	4wxjA	0.93	1.11	0.392	0.958	model1_4wxjA.pdb.gz
6	1yaeA	0.92	1.49	0.996	0.966	model1_1yaeA.pdb.gz
7	4pe5A	0.90	1.96	0.325	0.966	model1_4pe5A.pdb.gz
8	1y20A	0.89	1.91	0.343	0.950	model1_1y20A.pdb.gz
9	4ykiA	0.88	1.68	0.286	0.939	model1_4ykiA.pdb.gz
10	2rcaA	0.87	1.72	0.290	0.923	model1_2rcaA.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:0005234	1.00	extracellular-glutamate-gated ion channel activity
GO:0004888	1.00	transmembrane signaling receptor activity
GO:0004970	0.99	ionotropic glutamate receptor activity
GO:0015277	0.93	kainate selective glutamate receptor activity
GO:0042802	0.83	identical protein binding
GO:0030165	0.83	PDZ domain binding
GO:0042803	0.82	protein homodimerization activity
GO:0031625	0.82	ubiquitin protein ligase binding
GO:0031624	0.82	ubiquitin conjugating enzyme 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:0035235	1.00	ionotropic glutamate receptor signaling pathway
GO:0034220	1.00	ion transmembrane transport
GO:0050804	0.95	modulation of synaptic transmission
GO:0048519	0.93	negative regulation of biological process
GO:0051967	0.92	negative regulation of synaptic transmission, glutamatergic
GO:0065008	0.88	regulation of biological quality
GO:0007610	0.88	behavior
GO:0044708	0.87	single-organism behavior
GO:0044707	0.87	single-multicellular organism process
GO:0042391	0.87	regulation of membrane potential
GO:0050896	0.86	response to stimulus
GO:0048583	0.85	regulation of response to stimulus
GO:0048522	0.85	positive regulation of cellular process
GO:0080090	0.84	regulation of primary metabolic process
GO:0060255	0.84	regulation of macromolecule metabolic process
GO:0055074	0.84	calcium ion homeostasis
GO:0050806	0.84	positive regulation of synaptic transmission
GO:0048167	0.84	regulation of synaptic plasticity
GO:0031323	0.84	regulation of cellular metabolic process
GO:0016043	0.84	cellular component organization
GO:0009966	0.84	regulation of signal transduction
GO:1902531	0.83	regulation of intracellular signal transduction
GO:0071702	0.83	organic substance transport
GO:0060079	0.83	excitatory postsynaptic potential
GO:0051649	0.83	establishment of localization in cell
GO:0051246	0.83	regulation of protein metabolic process
GO:0048172	0.83	regulation of short-term neuronal synaptic plasticity
GO:0048169	0.83	regulation of long-term neuronal synaptic plasticity
GO:0045184	0.83	establishment of protein localization
GO:0043523	0.83	regulation of neuron apoptotic process
GO:0043065	0.83	positive regulation of apoptotic process
GO:0034613	0.83	cellular protein localization
GO:0006950	0.83	response to stress
GO:0001508	0.83	action potential
GO:0060080	0.82	inhibitory postsynaptic potential
GO:0046328	0.82	regulation of JNK cascade
GO:0043525	0.82	positive regulation of neuron apoptotic process
GO:0043524	0.82	negative regulation of neuron apoptotic process
GO:0043113	0.82	receptor clustering
GO:0019228	0.82	neuronal action potential
GO:0006886	0.82	intracellular protein transport
GO:0006874	0.82	cellular calcium ion homeostasis
GO:0001662	0.82	behavioral fear response
GO:0032502	0.59	developmental process
GO:0048856	0.56	anatomical structure development
GO:0048731	0.54	system development

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	0.95	plasma membrane part
GO:0008328	0.88	ionotropic glutamate receptor complex
GO:0044456	0.68	synapse part
GO:0016021	0.66	integral component of membrane
GO:0005886	0.66	plasma membrane
GO:0097060	0.64	synaptic membrane
GO:0045202	0.64	synapse
GO:0045211	0.63	postsynaptic membrane
GO:0030054	0.59	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	0.308	3kbrA	0.725	2.31	0.141	0.816	4.2.1.91 4.2.1.51	6,8
2	0.067	2vd2A	0.555	3.52	0.082	0.701	2.4.2.17	58,195
3	0.067	1o64A	0.533	3.37	0.073	0.674	2.4.2.17	224
4	0.066	1ve4A	0.516	3.59	0.069	0.667	2.4.2.17	NA
5	0.060	1z7mH	0.513	3.82	0.068	0.674	2.4.2.17	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	0.89	1yaeA	0.917	1.49	0.996	0.966	1.86	DOQ	complex1.pdb.gz	11,58,59,87,89,94,138,139,141,142,143,191
2	0.88	3g3fA	0.941	1.03	0.992	0.962	1.44	GLU	complex2.pdb.gz	59,87,88,89,94,141,142,143,217
3	0.54	1n0tC	0.874	2.11	0.530	0.969	0.84	AT1	complex3.pdb.gz	89,138,142,143,191,194,217
4	0.54	2cmoA	0.845	2.45	0.494	0.962	1.30	M1L	complex4.pdb.gz	11,14,59,60,87,89,94,137,142,171,191,194,217
5	0.50	3r7xA	0.796	3.22	0.456	0.966	1.33	QSN	complex5.pdb.gz	11,14,59,87,88,89,94
6	0.48	3h06J	0.805	3.05	0.468	0.966	0.81	VBP	complex6.pdb.gz	138,143,190,191,194
7	0.42	3o28A	0.955	1.10	0.527	0.981	1.51	O28	complex7.pdb.gz	90,103,106,214,215,216,236,239
8	0.41	1pb8A	0.893	1.87	0.340	0.954	0.83	DSN	complex8.pdb.gz	59,87,89,94,142
9	0.32	1lbcA	0.950	1.12	0.529	0.977	1.44	CYZ	complex9.pdb.gz	102,103,105,236,239,244,245,248
10	0.32	3lslA	0.949	1.05	0.528	0.973	1.34	PZI	complex10.pdb.gz	33,104,105,239,244,245,248

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.