D-I-TASSER P20800-D1

D-I-TASSER results for P20800-D1

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

Input Sequence in FASTA format

>P20800 (178 residues)
MVSVPTTWCSVALALLVALHEGKGQAAATLEQPASSSHAQGTHLRLRRCSCSSWLDKECV
YFCHLDIIWVNTPEQTAPYGLGNPPRRRRRSLPRRCQCSSARDPACATFCLRRPWTEAGA
VPSRKSPADVFQTGKTGATTGELLQRLRDISTVKSLFAKRQQEAMREPRSTHSRWRKR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVSVPTTWCSVALALLVALHEGKGQAAATLEQPASSSHAQGTHLRLRRCSCSSWLDKECVYFCHLDIIWVNTPEQTAPYGLGNPPRRRRRSLPRRCQCSSARDPACATFCLRRPWTEAGAVPSRKSPADVFQTGKTGATTGELLQRLRDISTVKSLFAKRQQEAMREPRSTHSRWRKR
Prediction	CCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCSSSSCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCCCC
Confidence	9763147999999999874069887666656667788898876556544467667862368874027997278732404779975456667777631368997488988611534212235688874245531530101225899999999863115665566641367897611269
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVSVPTTWCSVALALLVALHEGKGQAAATLEQPASSSHAQGTHLRLRRCSCSSWLDKECVYFCHLDIIWVNTPEQTAPYGLGNPPRRRRRSLPRRCQCSSARDPACATFCLRRPWTEAGAVPSRKSPADVFQTGKTGATTGELLQRLRDISTVKSLFAKRQQEAMREPRSTHSRWRKR
Prediction	7242422303102101111353444444547545545755455434430306525444001102010011334642132223444455556465304134572540241044445455543556545541363455234545214314503535442353455346655354555468
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCSSSSCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCCCC
MVSVPTTWCSVALALLVALHEGKGQAAATLEQPASSSHAQGTHLRLRRCSCSSWLDKECVYFCHLDIIWVNTPEQTAPYGLGNPPRRRRRSLPRRCQCSSARDPACATFCLRRPWTEAGAVPSRKSPADVFQTGKTGATTGELLQRLRDISTVKSLFAKRQQEAMREPRSTHSRWRKR

1vt4I3

0.04

2.21

0.48

CEthreader

DLLRIALMAEDEAIFEEAHKQVQRGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

6sriq

0.04

0.03

1.75

0.50

EigenThreader

LEIALKNTQELLIRDLEILGWNNAKYPTEPDSLIDIHNQFLAALGKTWVLEPECATSRRIAIGNNVSVNIEVDPRECYFLGAAVNPLRTKLNNNNLKDLLEIDF------PSDQVCNEPRCGQPFHQACLYEWLQGLPSSR----------------------QSFNVIFGECPYCNK

5xtbB

0.14

0.11

3.62

0.42

FFAS-3D

---------ELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEEERCACKL-----CEAIC---------PAQAITIEAEPRADGSRRTTRTKCICG-----FCQEACPVDAIVEGPNFEFSTETHEEL-----LYNKEKLLNNGDKWEAEIAANIQADYLYR-------------

5cqcA1

0.11

3.84

0.87

SPARKS-K

NKGMNSSRLHKLYSLFFAFYLGDDVSVLTGAYGFQSKKNDQQRPDSDYVAGYHVDAKEISEFCTFILPFVEMPTDTISYDPKSSIGRDTYSESYRTTC----DEILTQSIEKAIKSTDFTLGKF----TRAAYNTEGNCGSYTFRTIKEVISSSAQHVQDIESCIKYRNLGVVDIESA

2h3pA

0.14

0.07

2.30

0.64

CNFpred

EKLSPDAFIQVALQLAYYRIYG----------------------------------QACATYESASLRMFHLG---------------------RTDTIRSASIDSLAFVKGMGDSTVPE--------------------QQKVELLRKAVQAHRAYTDR------------------

6l7eA

0.07

0.05

2.08

0.83

DEthreader

QFWRKTILKRAFNIYGKLLAIHLNTLHTQKGD-N-LG-E----VEQLADLDA-------NLL-----LQA-------SIQAQNPVTPASTILQWVNQ-----------------------SLALQRKFSNQALYNWLRGRLAAIYFQFYDLAVARCLMAEQAYRWELNDKAL--IRYA

5oqlO

0.05

0.04

2.13

0.71

MapAlign

QGAIRKKARKWESVVTAHKDDPYARTWFWGRRRAGRWAFKTGDGEPVSTVAISSCGTFALVGSTGGSIDMFNLQRHRQRFPSRFAPGTGRHTNAVTGIVVDLNRHVVSCSLQAWMTVFLRLHFDLIMENEELLQALGEWREHQARERDRLSELVGYCGGVVSFL--------------

6etxG

0.12

0.11

3.96

0.65

MUSTER

LARWLALFLSLKASYRLHQLRSWGAPEGYLRNKDFLLGVNFPLSFPNLCSCPLLKSL------------VFSSHCKAVSGYSDQVVHQRRSATSSLRRCLLTELP-SFLCVASPRVTAVPLDSYCNDRSAEYERRVLKEGGSLAAKQCLLNGAPELAADWLNRRSQFFPEPAGGLWSI

2pffB

0.14

0.13

4.39

0.80

HHsearch

LLSIPISCPLIGVIQYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVA-IAETDSWESFFVSVLFFIGVRCYEAYPNTSL--PPSILEDSLENNEGVEQVQDNKTNSHLPAGKQVE----ISLVNGAKNLVV-------SGPPQSL---YGLNLTLRKAKAPSGLDQSIPQIPVYDT

3keoA

0.09

0.08

2.99

0.46

CEthreader

LGIDSATVRRDFSYFGELGRRGFGYDVKKLMNFFAEILNDHSTTNVMLVGCGNIQISMAFDLDSNDLVGKTTEDGIPVYGISTINDHLDSDIETAILTVPSEAQEVADILVKAGIKGILSFSPVHLTLPKDIIVQYVDLTSELQTLLYFMNQQR------------------------

(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	0.4256

(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	4ro1A	0.43	4.75	0.057	0.685	model1_4ro1A.pdb.gz
2	6fszJJ	0.43	4.93	0.042	0.702	model1_6fszJJ.pdb.gz
3	6rc9A	0.43	5.13	0.037	0.736	model1_6rc9A.pdb.gz
4	7dcyA	0.43	4.76	0.067	0.697	model1_7dcyA.pdb.gz
5	4pmwA	0.43	4.92	0.050	0.685	model1_4pmwA.pdb.gz
6	4k2bA	0.43	5.07	0.076	0.702	model1_4k2bA.pdb.gz
7	6d6qK	0.43	4.99	0.036	0.702	model1_6d6qK.pdb.gz
8	1mdoA	0.40	5.48	0.047	0.685	model1_1mdoA.pdb.gz
9	1bw0B	0.37	5.77	0.064	0.685	model1_1bw0B.pdb.gz
10	2id0A	0.37	5.11	0.034	0.624	model1_2id0A.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	0.92	endothelin B receptor binding
GO:0005179	0.82	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	0.96	biological regulation
GO:0032501	0.96	multicellular organismal process
GO:0050789	0.95	regulation of biological process
GO:0044699	0.91	single-organism process
GO:0050794	0.90	regulation of cellular process
GO:0065008	0.87	regulation of biological quality
GO:0003008	0.87	system process
GO:0050880	0.86	regulation of blood vessel size
GO:0044057	0.86	regulation of system process
GO:0032879	0.84	regulation of localization
GO:0048522	0.80	positive regulation of cellular process
GO:0009987	0.80	cellular process
GO:0007165	0.80	signal transduction
GO:0044763	0.78	single-organism cellular process
GO:0051240	0.74	positive regulation of multicellular organismal process
GO:0042310	0.74	vasoconstriction
GO:0019222	0.68	regulation of metabolic process
GO:0008217	0.68	regulation of blood pressure
GO:1903522	0.66	regulation of blood circulation
GO:0048583	0.64	regulation of response to stimulus
GO:0048584	0.62	positive regulation of response to stimulus
GO:0035556	0.62	intracellular signal transduction
GO:0009893	0.62	positive regulation of metabolic process
GO:0030335	0.61	positive regulation of cell migration
GO:0014829	0.61	vascular smooth muscle contraction
GO:0008284	0.61	positive regulation of cell proliferation
GO:0008152	0.56	metabolic process
GO:0006874	0.56	cellular calcium ion homeostasis
GO:0032101	0.55	regulation of response to external stimulus
GO:0014824	0.55	artery smooth muscle contraction
GO:0007166	0.55	cell surface receptor signaling pathway
GO:0048016	0.54	inositol phosphate-mediated signaling
GO:0044237	0.54	cellular metabolic process
GO:0043085	0.54	positive regulation of catalytic activity
GO:0014826	0.54	vein smooth muscle contraction
GO:0010460	0.54	positive regulation of heart rate
GO:0003100	0.54	regulation of systemic arterial blood pressure by endothelin
GO:1903530	0.52	regulation of secretion by cell
GO:0007204	0.51	positive regulation of cytosolic calcium ion concentration
GO:0050921	0.50	positive regulation of chemotaxis
GO:0023051	0.50	regulation of signaling
GO:0010646	0.50	regulation of cell communication
GO:0002682	0.50	regulation of immune system 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	0.80	cell part
GO:0005576	0.50	extracellular region

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	1c7gA	0.396	5.78	0.055	0.736	4.1.99.2	NA
2	0.060	1galA	0.398	5.26	0.033	0.680	1.1.3.4	NA
3	0.060	3cskA	0.393	5.29	0.007	0.674	3.4.14.4	NA
4	0.060	2vdcF	0.388	6.08	0.047	0.758	1.4.1.13	NA
5	0.060	1j38A	0.411	5.28	0.044	0.702	3.4.15.1	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	1q4gA	0.365	5.64	0.057	0.657	0.49	UUU	complex1.pdb.gz	53,79,80
2	0.01	1q4gA	0.365	5.64	0.057	0.657	0.43	UUU	complex2.pdb.gz	59,71,79,83
3	0.01	3n8yA	0.362	5.76	0.050	0.680	0.41	UUU	complex3.pdb.gz	69,79,83,88

	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.