D-I-TASSER P42261-D1

D-I-TASSER results for P42261-D1

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

Input Sequence in FASTA format

>P42261 (234 residues)
MQHIFAFFCTGFLGAVVGANFPNNIQIGGLFPNQQSQEHAAFRFALSQLTEPPKLLPQID
IVNISDSFEMTYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQ
FVLQLQLVNYTDTIPAKIMQQWKNSDARDHTRVDWKRPKYTSALTYDGVKVMAEAFQSLR
RQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MQHIFAFFCTGFLGAVVGANFPNNIQIGGLFPNQQSQEHAAFRFALSQLTEPPKLLPQIDIVNISDSFEMTYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQFVLQLQLVNYTDTIPAKIMQQWKNSDARDHTRVDWKRPKYTSALTYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRT
Prediction	CCHHHHHHHHHHHHHHHCCCCCCSSSSSSSSCCCCHHHHHHHHHHHHHHHCCCCSCCCSSSSCCCCHHHHHHHHHHHHHCCCSSSSCCCCHHHHHHHHHHHHHCCCCSSSSCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCSSSSSCCCCCCC
Confidence	921899999999999705578864688998479986999999999999814981023047706787799999999987229089985897479999999975117851331112344456544434577314789999999998431023577655311035789999999999999998617543345677774557888765469999999972655751315757999859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MQHIFAFFCTGFLGAVVGANFPNNIQIGGLFPNQQSQEHAAFRFALSQLTEPPKLLPQIDIVNISDSFEMTYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQFVLQLQLVNYTDTIPAKIMQQWKNSDARDHTRVDWKRPKYTSALTYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRT
Prediction	433131232131101022362354030000036646423400430054116645023305404452023002200432442010010033431241033103433112023323244443423333224244421440243044233342441534334243312220031004003404755452445354250445454317304401510450525412240404763528
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHCCCCCCSSSSSSSSCCCCHHHHHHHHHHHHHHHCCCCSCCCSSSSCCCCHHHHHHHHHHHHHCCCSSSSCCCCHHHHHHHHHHHHHCCCCSSSSCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCSSSSSCCCCCCC
MQHIFAFFCTGFLGAVVGANFPNNIQIGGLFPNQQSQEHAAFRFALSQLTEPPKLLPQIDIVNISDSFEMTYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQFVLQLQLVNYTDTIPAKIMQQWKNSDARDHTRVDWKRPKYTSALTYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRT

7ks0A

0.22

0.19

5.94

1.33

DEthreader

--------------------L-SSLRMAAILDDQGRGERLALALAREQIGIKARVEVDIFELQRDSQYETTDTMCQILPKGVVSVLGPSSPASASTVSHICGEKEIPHIKVGPEERLQLRASVSLYPSMFNTSHYPEFVRSLNMSWR-ENCEATYPGPALSAALMFDAVHVVVSAVRELNRSQE-I--------GVKPLANIWPHGTSLMNYLRMVEYDGLTGRVEFNSKGQRT

3sajA1

0.96

0.86

24.21

1.82

SPARKS-K

------------------GAMPNNIQIGGLFPNQQSQEHAAFRFALSQLTEPPKLLPQIDIVNISDSFEMTYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQFVLQLRLVNYTDTIPARIMQQWRTSDSRD------KRPKYTSALTYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRT

4nv3A2

0.14

0.12

3.93

0.63

MapAlign

----------------------NTIPIGIALAQTGQEQVAGAKIAEKYFVNGTPIKLIFQDTAGD-EAGTINAFQTLINDKVVGIVGPTLSQQAFSANPIAERAKVPVVGPNTAIPEIGDYVARVSAYSPEYEINKAFRQAYVDQ--------YKKEPPQFSAQAFAAVQVYVESLKALDT------------KNKVSKIQLPELRTELNKQLLTGKYNTPLGEISFTPIGEVV

4n0qA1

0.13

0.10

3.54

0.46

CEthreader

-----------------------DITIGVIAPLTGDQVKKGAETAVEVINKGEKVVLKFADDAG-EPKQGVSAANQIVGDGIKFVVGLVTTGVAVPVSDVLSENGVLMVTPTALTARGLENVFRTCGAATKNPAAKDAIQALKAK---------NIPAEAFTMNAYAAVEVIKAGIERAG---------------------STDDSAAVAKALHGKPIETAIGTLTYSETGDLS

3sajA1

0.96

0.86

24.21

1.65

MUSTER

------------------GAMPNNIQIGGLFPNQQSQEHAAFRFALSQLTEPPKLLPQIDIVNISDSFEMTYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQFVLQLRLVNYTDTIPARIMQQWRTSDSRD------KRPKYTSALTYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRT

3kg2A1

0.56

0.50

14.52

1.71

HHsearch

----------------------NSIQIGGLFPRGADQEYSAFRVGMVQFSSEFRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRIVDYDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRI

3sajA1

0.95

0.85

23.97

2.52

FFAS-3D

------------------GAMPNNIQIGGLFPNQQSQEHAAFRFALSQLTEPPKLLPQIDIVNISDSFEMTYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQFVLQLRPLNYTDTIPARIMQQWRTSDSRD------KRPKYTSALTYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRT

3sajA1

0.95

0.84

23.62

0.93

EigenThreader

--------------------GAMPNNIGGLFPNQQSQEHAAFRFALSQLTEPPKLLPQIDIVNISDSFEMTYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQFVLQLRLVNYTDTIPARIMQQWRTSDSRD------KRPKYTSALTYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRT

5fwyB

0.33

0.32

9.50

1.28

CNFpred

MRPALKGAILSLLSYYK------WEKFVYLYDTRGFSVLQAIMEAAVQN--NWQVTARSVG-NIKDVQEFRRIIEEMDRRQEKRYLIDCEVERINTILEQVVILGYHYMLANLGFTD-GANITGFQIVNNENPMVQQFIQRWVRLDEREFPEAKNAPLKYTSALTHDAILVIAEAFRYLRRQRVDVSRRGSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRT

4gpaA

0.53

0.47

13.45

1.33

DEthreader

--------------------FPSSVQIGGLFIRNTDQEYTAFRLAIFLHSAPFNLVPHVDNIETANSFAVTNAFCSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSFPTEGESQFVLQLRPLVDFNTMVTKLMDRWKKLDQREY-PGSETPPKYTSALTYDGVLVMAETFRSLRRQKI-DI-------SRRGNAAPWGQGIDMERTLKQVRIQGLTGNVQFDHYGRRV

(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	0.755

(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	3kg2A	0.86	1.36	0.542	0.906	model1_3kg2A.pdb.gz
2	4gpaA	0.86	1.50	0.577	0.910	model1_4gpaA.pdb.gz
3	3sajA	0.84	1.60	0.938	0.897	model1_3sajA.pdb.gz
4	3o21A2	0.83	1.80	0.541	0.893	model1_3o21A2.pdb.gz
5	3h6gB	0.79	2.08	0.286	0.868	model1_3h6gB.pdb.gz
6	3om0A	0.78	2.45	0.223	0.880	model1_3om0A.pdb.gz
7	4mqeA	0.74	2.38	0.149	0.833	model1_4mqeA.pdb.gz
8	4uqqA1	0.70	1.62	0.316	0.744	model1_4uqqA1.pdb.gz
9	3q41A	0.67	2.46	0.184	0.756	model1_3q41A.pdb.gz
10	4pe5A1	0.65	2.25	0.225	0.722	model1_4pe5A1.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:0004970	0.99	ionotropic glutamate receptor activity
GO:0004971	0.92	AMPA glutamate receptor activity
GO:0005231	0.65	excitatory extracellular ligand-gated ion channel activity
GO:0005234	0.63	extracellular-glutamate-gated ion channel activity
GO:0030165	0.55	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:0044699	0.91	single-organism process
GO:0009987	0.90	cellular process
GO:0050794	0.89	regulation of cellular process
GO:0044763	0.89	single-organism cellular process
GO:0007165	0.77	signal transduction
GO:0051179	0.76	localization
GO:0006810	0.75	transport
GO:0007215	0.74	glutamate receptor signaling pathway
GO:0023051	0.72	regulation of signaling
GO:0050896	0.71	response to stimulus
GO:0042221	0.69	response to chemical
GO:0035235	0.69	ionotropic glutamate receptor signaling pathway
GO:1902578	0.68	single-organism localization
GO:0009636	0.68	response to toxic substance
GO:0060992	0.67	response to fungicide
GO:0044765	0.67	single-organism transport
GO:0006811	0.66	ion transport
GO:0034220	0.63	ion transmembrane transport
GO:0060255	0.58	regulation of macromolecule metabolic process
GO:0031323	0.58	regulation of cellular metabolic process
GO:0010646	0.56	regulation of cell communication
GO:0010226	0.56	response to lithium ion
GO:0001919	0.56	regulation of receptor recycling
GO:0050804	0.55	modulation of synaptic transmission
GO:0007268	0.50	chemical 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:0044459	1.00	plasma membrane part
GO:0044456	1.00	synapse part
GO:0016021	1.00	integral component of membrane
GO:0005886	1.00	plasma membrane
GO:0008328	0.91	ionotropic glutamate receptor complex
GO:0032281	0.80	AMPA glutamate receptor complex
GO:0097060	0.74	synaptic membrane
GO:0045202	0.74	synapse
GO:0045211	0.73	postsynaptic membrane
GO:0030054	0.71	cell junction
GO:0097458	0.57	neuron part
GO:0044424	0.55	intracellular part
GO:0043005	0.54	neuron projection
GO:0043226	0.50	organelle

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	0.066	2c4wA	0.471	2.76	0.080	0.556	4.2.1.10	NA
2	0.060	1lw6E	0.566	4.59	0.094	0.795	3.4.21.62	39
3	0.060	1tecE	0.560	4.64	0.095	0.791	3.4.21.66	NA
4	0.060	3edyA	0.565	4.88	0.106	0.829	3.4.14.9	NA
5	0.060	1up7A	0.450	4.42	0.033	0.624	3.2.1.86	108

	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	0.01	3pmvA	0.351	5.34	0.050	0.547	0.45	557	complex1.pdb.gz	85,102,103,104,105
2	0.01	3lslA	0.336	5.55	0.017	0.556	0.44	PZI	complex2.pdb.gz	86,169,170,173
3	0.01	3kgcA	0.350	4.89	0.083	0.517	0.40	LY7	complex3.pdb.gz	58,82,85
4	0.01	3iluH	0.336	5.72	0.023	0.564	0.61	HFZ	complex4.pdb.gz	85,169,173
5	0.01	2xx7B	0.349	5.55	0.037	0.556	0.51	1ND	complex5.pdb.gz	77,169,172
6	0.01	3lswA	0.335	5.78	0.023	0.573	0.63	4MP	complex6.pdb.gz	104,105,206,207
7	0.01	2xx8C	0.352	4.98	0.071	0.534	0.44	1NE	complex7.pdb.gz	84,85,86,87,168
8	0.01	3ijoH	0.350	5.51	0.083	0.560	0.60	B4D	complex8.pdb.gz	109,169,172,173,213
9	0.01	3iltB	0.352	5.50	0.071	0.560	0.46	TRU	complex9.pdb.gz	80,82,83,84,85,206,207,210

	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.