D-I-TASSER P14138-D2

D-I-TASSER results for P14138-D2

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

Input Sequence in FASTA format

>P14138 (122 residues)
LQGPSPGSPGQEQAAEGAPEHHRSRRCTCFTYKDKECVYYCHLDIIWINTPEQTVPYGLS
NYRGSFRGKRSAGPLPGNLQLSHRPHLRCACVGRYDKACLHFCTQTLDVSSNSRTAEKTD
KE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| LQGPSPGSPGQEQAAEGAPEHHRSRRCTCFTYKDKECVYYCHLDIIWINTPEQTVPYGLSNYRGSFRGKRSAGPLPGNLQLSHRPHLRCACVGRYDKACLHFCTQTLDVSSNSRTAEKTDKE
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSSSSSCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCC
Confidence	98888999887778889876555665445655787357997520898548982553347999888643445555677765556898752226999827999862442123454333474449
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| LQGPSPGSPGQEQAAEGAPEHHRSRRCTCFTYKDKECVYYCHLDIIWINTPEQTVPYGLSNYRGSFRGKRSAGPLPGNLQLSHRPHLRCACVGRYDKACLHFCTQTLDVSSNSRTAEKTDKE
Prediction	87434575546654675445544443141652444400110202001243554110110133545444445466355554467545420403567154024004435624556544654688
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSSSSSCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCC
LQGPSPGSPGQEQAAEGAPEHHRSRRCTCFTYKDKECVYYCHLDIIWINTPEQTVPYGLSNYRGSFRGKRSAGPLPGNLQLSHRPHLRCACVGRYDKACLHFCTQTLDVSSNSRTAEKTDKE

3bh3D

0.11

4.10

0.52

CEthreader

VRQRAFAMPLTSPAFPPGPYRFVNREYMIITYRPVVRYEFIRMSESGQVIPSYTLAMFLDDQPPLAGGRELWGFAGKPRLEVHQDTLVGSLDFGPVRIATGTMGYKYEALDRSALLASLAEP

3j20F

0.03

1.87

0.50

EigenThreader

DEWEPKTKLGMMVKEGQITDPEVNARENQVLDIALVLAAVGNGYVGLGIGHGKAKLNKRGCGSWPHSVPGPRGLGLVIGLRLAGVQDVWSTGETRTTVNFAKAVFNALYNTNRVAISPEM--

6lntD

0.17

0.16

5.11

0.33

FFAS-3D

-RGSAYYDRNDAGEAISFPTTLGMNKCYCDATMSYECPMLC-----WCNTTSTWVVYGTHKKGEARRSRRAVTLPSHSTRKLQTRSQTWLESREYTKHLIRVENWIFRNPGFALAA------

7jjvA

0.14

0.13

4.45

0.90

SPARKS-K

LDGADGTSNGQASGLAGGPNCNGGKGGKGAPGVGTAGG----AGGVGGNTNGGAGGSG-GNSDVAAGGAGAAGGAAGGAGTGGTGGNGGAG-KPGGAPG-----AGGAGTPAGSAGSPGQTT

2x2zA

0.08

0.02

0.66

0.41

CNFpred

--------------------------GKCALSDVPDCLVSDSAAVSYTAAGS----------------------------------------------------------------------

6vdeA

0.04

0.03

1.61

0.83

DEthreader

--LDGSLFRFDEADIALAQAQEALAYLVLARI----DSLLLQTATG------TVLGRRRY-L-P-E--------L---DSSNVRAAEAA------L-NAIQGSAADIIKVAMINVDQAIKDA

3bh3D

0.05

0.04

1.97

0.68

MapAlign

--RAFAMPLTSPAFPPGPYRFVNREYMIITYAEPVVRYEFIRMSESGQVIPSYTLAMFLD---------DQPPLAGGRELWGFPKKAGKPRLEVHQDTLVGSLDFGPVRIATGTMG------

2wdqB2

0.18

0.16

5.33

0.64

MUSTER

NNGQNPPAREHLQMPEQREKLDGLYECICAC-----CSTSCPSF--WWNPDKFIGPAGLAAYRFLIDSRDTETDSRLDGLSDAFSVFRCSI-----MNCVSVCPKGLNPTRAIGHIKSMLLQ

6tgbA1

0.14

0.13

4.50

0.69

HHsearch

PEIIMPGDVRNDIYNKTTQRNVEVIMCVCAELPNAICVGAGDKPMNEYRS---VVYYQVKQPRWMETVKVAVPIEDQRIHL-RFMRHR-SSLESKDKGEKNFAMSYVKLMKEDTTLHDGFHD

2zb6A1

0.07

2.70

0.46

CEthreader

RNPGLGAPVFHMTNYLEQPVSNLSSNLVILPGQDLQYVLATYAVVYYVYSPSRSFSYFYPFRLPIKGVPIELQVECFTWDQKLWCRHFCVLADSESGGHITHSGMVGMGVSCT---------

(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	0.4302

(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	1r6vA	0.48	4.31	0.076	0.844	model1_1r6vA.pdb.gz
2	3afgA	0.48	4.67	0.061	0.893	model1_3afgA.pdb.gz
3	1qo9A	0.48	4.46	0.026	0.795	model1_1qo9A.pdb.gz
4	6g4qB	0.48	4.75	0.044	0.861	model1_6g4qB.pdb.gz
5	4owdA	0.48	3.96	0.032	0.770	model1_4owdA.pdb.gz
6	4k90A	0.48	4.58	0.045	0.836	model1_4k90A.pdb.gz
7	1mx9D	0.46	4.55	0.066	0.828	model1_1mx9D.pdb.gz
8	1thgA	0.44	5.44	0.059	0.902	model1_1thgA.pdb.gz
9	1ukcA	0.44	4.97	0.050	0.828	model1_1ukcA.pdb.gz
10	1y9zB2	0.42	4.76	0.051	0.746	model1_1y9zB2.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:0031705	1.00	bombesin receptor binding
GO:0031708	0.84	endothelin B receptor binding
GO:0005179	0.76	hormone 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:0065007	0.94	biological regulation
GO:0032501	0.94	multicellular organismal process
GO:0050789	0.93	regulation of biological process
GO:0050794	0.89	regulation of cellular process
GO:0044699	0.87	single-organism process
GO:0065008	0.83	regulation of biological quality
GO:0051239	0.82	regulation of multicellular organismal process
GO:0050880	0.82	regulation of blood vessel size
GO:0032879	0.82	regulation of localization
GO:0044057	0.81	regulation of system process
GO:0009987	0.81	cellular process
GO:0044763	0.80	single-organism cellular process
GO:0048518	0.74	positive regulation of biological process
GO:0048522	0.73	positive regulation of cellular process
GO:0007165	0.72	signal transduction
GO:1903530	0.71	regulation of secretion by cell
GO:1903522	0.69	regulation of blood circulation
GO:0023051	0.67	regulation of signaling
GO:0019222	0.67	regulation of metabolic process
GO:0010646	0.67	regulation of cell communication
GO:0010817	0.66	regulation of hormone levels
GO:0051240	0.65	positive regulation of multicellular organismal process
GO:0046883	0.65	regulation of hormone secretion
GO:0042310	0.64	vasoconstriction
GO:0008217	0.64	regulation of blood pressure
GO:0048583	0.61	regulation of response to stimulus
GO:0051047	0.60	positive regulation of secretion
GO:0048584	0.60	positive regulation of response to stimulus
GO:0035556	0.60	intracellular signal transduction
GO:0009893	0.60	positive regulation of metabolic process
GO:0080090	0.58	regulation of primary metabolic process
GO:0060255	0.58	regulation of macromolecule metabolic process
GO:0032502	0.58	developmental process
GO:0031323	0.58	regulation of cellular metabolic process
GO:0030335	0.58	positive regulation of cell migration
GO:0014829	0.58	vascular smooth muscle contraction
GO:0008284	0.58	positive regulation of cell proliferation
GO:0048856	0.57	anatomical structure development
GO:0044767	0.57	single-organism developmental process
GO:1903532	0.54	positive regulation of secretion by cell
GO:0007166	0.53	cell surface receptor signaling pathway
GO:0048016	0.52	inositol phosphate-mediated signaling
GO:0043085	0.52	positive regulation of catalytic activity
GO:0014826	0.52	vein smooth muscle contraction
GO:0010460	0.52	positive regulation of heart rate
GO:0003100	0.52	regulation of systemic arterial blood pressure by endothelin
GO:0044707	0.51	single-multicellular organism process
GO:0032101	0.51	regulation of response to external stimulus
GO:0031325	0.51	positive regulation of cellular metabolic process
GO:0010604	0.51	positive regulation of macromolecule metabolic process
GO:0051179	0.50	localization
GO:0032268	0.50	regulation of cellular protein metabolic 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:0005615	1.00	extracellular space
GO:0044464	0.78	cell part
GO:0005576	0.55	extracellular region
GO:0044424	0.51	intracellular part

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	1xnyA	0.452	4.65	0.036	0.795	6.4.1.3	NA
2	0.060	2fj0A	0.469	4.66	0.052	0.820	3.1.1.1	NA
3	0.060	1jkjB	0.335	5.76	0.049	0.738	6.2.1.5	NA
4	0.060	3edyA	0.472	4.24	0.056	0.828	3.4.14.9	NA
5	0.060	3nwoA	0.455	3.92	0.060	0.713	3.4.11.5	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	0.01	2h7cA	0.461	4.55	0.057	0.828	0.20	COA	complex1.pdb.gz	28,38,57,58,97,98,99,106
2	0.01	2h7cF	0.467	4.49	0.057	0.828	0.13	COA	complex2.pdb.gz	39,58,101,102
3	0.01	2dr0B	0.441	4.76	0.042	0.853	0.12	TCH	complex3.pdb.gz	42,58,64,87,88

	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.