D-I-TASSER P51864-D1

D-I-TASSER results for P51864-D1

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

Input Sequence in FASTA format

>P51864 (188 residues)
MDCRKMVRFSYSVIWIMAISKAFELGLVAGLGHQEFARPSRGDLAFRDDSIWPQEEPAIR
PRSSQRVLPMGIQHSKELNRTCCLNGGTCMLESFCACPPSFYGRNCEHDVRKENCGSVPH
DTWLPKKCSLCKCWHGQLRCFPQAFLPGCDGLVMDEHLVASRTPELPPSARTTTFMLAGI
CLSIQSYY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MDCRKMVRFSYSVIWIMAISKAFELGLVAGLGHQEFARPSRGDLAFRDDSIWPQEEPAIRPRSSQRVLPMGIQHSKELNRTCCLNGGTCMLESFCACPPSFYGRNCEHDVRKENCGSVPHDTWLPKKCSLCKCWHGQLRCFPQAFLPGCDGLVMDEHLVASRTPELPPSARTTTFMLAGICLSIQSYY
Prediction	CCCHHHHHHHHHHHHHHHHHHHSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCSSSSCCCCCSCSSCCCCCCCCCCCCCCCCCSCCCCCCCCCCCHHHHHHHHHHHHSSSSCC
Confidence	97301234678999999986531212323666421246766654313565566666543556644456656567664679987889684379672189997568864445568888789983761795774379996211336788887654235762036788877531034545776764134229
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MDCRKMVRFSYSVIWIMAISKAFELGLVAGLGHQEFARPSRGDLAFRDDSIWPQEEPAIRPRSSQRVLPMGIQHSKELNRTCCLNGGTCMLESFCACPPSFYGRNCEHDVRKENCGSVPHDTWLPKKCSLCKCWHGQLRCFPQAFLPGCDGLVMDEHLVASRTPELPPSARTTTFMLAGICLSIQSYY
Prediction	85454242000100101211311313314625454445355442314356245574454463456413423145365046410311030344220301451415301333456614512444103741320302412220124424753443354551320324613411302011111111223337
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHHHHHHSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCSSSSCCCCCSCSSCCCCCCCCCCCCCCCCCSCCCCCCCCCCCHHHHHHHHHHHHSSSSCC
MDCRKMVRFSYSVIWIMAISKAFELGLVAGLGHQEFARPSRGDLAFRDDSIWPQEEPAIRPRSSQRVLPMGIQHSKELNRTCCLNGGTCMLESFCACPPSFYGRNCEHDVRKENCGSVPHDTWLPKKCSLCKCWHGQLRCFPQAFLPGCDGLVMDEHLVASRTPELPPSARTTTFMLAGICLSIQSYY

3s8vA2

0.06

0.05

2.30

0.44

CEthreader

------------------------TTFLLFSQKSAINRMVIDEQPDIILPIHSLRNVRSRQNMIRKAQEDGSQGFTVVVSIQPYDLSIDIYSRYIYWTCEATNVINVTRLDGRSVGVVLKGE--QDRPRAIVVNPEKGYMYFTNLQERSPKIERAALDGTEREVQLSDIHAVKELNLQEYRQHPCAQD

5m45A

0.03

1.82

0.55

EigenThreader

EEGIEAYWKFAYEAVEHGRLGLQARIKAMTIPWGWHTYNAHPKGTWMNPDDRRVAFSYSYLEEVNAGNANTSNWLSFECAANGTGAGLSHAAAIKGGSGKYRGGCGG--------NGHISSDWGLMGGYPAASGYYMRGGPGFGDPLDREPQAVADDINGGYVLERFAGEVYGTATAAARAQIRKDRL

2j5hA

0.79

0.16

4.66

0.52

FFAS-3D

---------------------------------------------------------------------------------------------------------------KEHCGSILHGTWLPKKCSLCRCWHGQLHCLPQTFLPGCD--------------------------------------

5aftV

0.13

0.10

3.51

0.74

SPARKS-K

--------------------SGNKVSRQSVLCGSQNIVLNGKTIIMNDCIIRGDLANVVKSRSVIRPPFKKFSKGVAFFPL--------HIGDHVFIEEDCVVNAAQIGSY----VHVGKNCVIGRRCVLKDCCK---------ILDNTPETVVPPFTVFSGCPGLELPECTQELMIDVTKSYYQKFL

2j5hA

0.79

0.16

4.66

0.72

CNFpred

---------------------------------------------------------------------------------------------------------------KEHCGSILHGTWLPKKCSLCRCWHGQLHCLPQTFLPGCD--------------------------------------

5doqB

0.06

0.04

1.92

0.83

DEthreader

ILHRIIQRYLSPVWEVTNVFLVFFFVGIVGFFP-KTAYGSILL-V-P------A--SIVLALTGLFIPA-LSVLTVVSVTSVL---YISA---VFLTYYAAR--LRRYALLWSLVIVWLGRQRFGWAFIALL-----FQYAFAF------------YA--I---P-IVAFIAGLLLLIPSLYLLMLFL

1vt4I3

0.07

2.85

0.68

MapAlign

FYKPYICDNDPKYERLVNAIFEEAHKQVQGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG---GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-

4xbmB3

0.16

0.13

4.41

0.95

MUSTER

QQCNCQEGWGGLF--------------QDLNYCTHHKPCKNGATNTGQGSYTCSCRPGYTGATCE-------LGIDECDPSPCKNGGSCTDLYSCTCPPGFYGKICELSAMTCADGPCFNGGRCSDGGYSCRCPVGYSGFNCEKKIDYCSSSPCSNGAKCVDLGDA------------YLCRCHCDD-

2j5hA

0.79

0.16

4.66

3.13

HHsearch

---------------------------------------------------------------------------------------------------------------KEHCGSILHGTWLPKKCSLCRCWHGQLHCLPQTFLPGCD--------------------------------------

5mwbA

0.15

0.09

3.05

0.44

CEthreader

---------DVDECAMANSNPCEHAGKCVNTDGAFHCECLKGYAGPRCEMDINE-----------------------CHSDPCQNDATCLDKFTCLCMPGFKGVHCELEINECQSN-------PCVNNGQCVDKVNRFQCLCPPGFTGPVCQID----------------------------------

(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	0.5078

(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	6r3qA1	0.49	5.27	0.045	0.856	model1_6r3qA1.pdb.gz
2	6hraA	0.47	5.26	0.049	0.771	model1_6hraA.pdb.gz
3	5xamA	0.47	4.52	0.061	0.692	model1_5xamA.pdb.gz
4	6ajfA	0.46	4.40	0.068	0.697	model1_6ajfA.pdb.gz
5	3pjzA	0.46	5.38	0.050	0.782	model1_3pjzA.pdb.gz
6	1mb8A	0.46	4.86	0.047	0.713	model1_1mb8A.pdb.gz
7	4zohA	0.46	5.21	0.042	0.793	model1_4zohA.pdb.gz
8	7kgdA	0.46	4.51	0.025	0.692	model1_7kgdA.pdb.gz
9	1jqnA	0.46	4.94	0.025	0.729	model1_1jqnA.pdb.gz
10	1t3qB	0.46	5.19	0.048	0.777	model1_1t3qB.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:0004980	0.98	melanocyte-stimulating hormone receptor activity
GO:0005102	0.81	receptor binding
GO:0008083	0.76	growth factor 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	0.95	biological regulation
GO:0050789	0.95	regulation of biological process
GO:0044699	0.89	single-organism process
GO:0044767	0.84	single-organism developmental process
GO:0009653	0.84	anatomical structure morphogenesis
GO:0050794	0.83	regulation of cellular process
GO:0007165	0.81	signal transduction
GO:0048729	0.70	tissue morphogenesis
GO:0007166	0.67	cell surface receptor signaling pathway
GO:0016477	0.66	cell migration
GO:0007389	0.66	pattern specification process
GO:0048583	0.64	regulation of response to stimulus
GO:0048513	0.62	animal organ development
GO:0048518	0.60	positive regulation of biological process
GO:0055009	0.58	atrial cardiac muscle tissue morphogenesis
GO:0048584	0.58	positive regulation of response to stimulus
GO:0040017	0.58	positive regulation of locomotion
GO:0007507	0.58	heart development
GO:0016055	0.50	Wnt signaling pathway

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	0.93	cell part
GO:0044421	0.80	extracellular region part
GO:0016020	0.74	membrane
GO:0005578	0.66	proteinaceous extracellular matrix
GO:0044459	0.63	plasma membrane part
GO:0005886	0.59	plasma membrane

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	1rm6A	0.432	5.29	0.068	0.750	1.3.99.20	NA
2	0.060	1zkxB	0.421	5.61	0.020	0.723	3.4.24.69	NA
3	0.060	1g6tA	0.446	5.48	0.063	0.761	2.5.1.19	110
4	0.060	1epsA	0.428	5.27	0.070	0.713	2.5.1.19 2.5.1.9	NA
5	0.060	2nvrA	0.412	5.39	0.051	0.723	3.5.1.98	150

	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	3sqgE	0.452	5.28	0.076	0.761	0.42	TP7	complex1.pdb.gz	86,87,102
2	0.01	2vqoB	0.444	5.33	0.030	0.734	0.45	TFG	complex2.pdb.gz	79,80,104
3	0.01	2vqoA	0.443	5.34	0.030	0.734	0.49	TFG	complex3.pdb.gz	86,88,102,105
4	0.01	3sqgB	0.451	5.63	0.023	0.798	0.42	TP7	complex4.pdb.gz	86,104,105

	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.