D-I-TASSER P54750-D1

D-I-TASSER results for P54750-D1

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

Input Sequence in FASTA format

>P54750 (144 residues)
MGSSATEIEELENTTFKYLTGEQTEKMWQRLKGILRCLVKQLERGDVNVVDLKKNIEYAA
SVLEAVYIDETRRLLDTEDELSDIQTDSVPSEVRDWLASTFTRKMGMTKKKPEEKPKFRS
IVHAVQAGIFVERMYRKTYHMVGL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGSSATEIEELENTTFKYLTGEQTEKMWQRLKGILRCLVKQLERGDVNVVDLKKNIEYAASVLEAVYIDETRRLLDTEDELSDIQTDSVPSEVRDWLASTFTRKMGMTKKKPEEKPKFRSIVHAVQAGIFVERMYRKTYHMVGL
Prediction	CCCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Confidence	999877644567864222455578999999999999999999717889999999899999999999998621455430256545887799899999999710430121144334512789999999987777766522444579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGSSATEIEELENTTFKYLTGEQTEKMWQRLKGILRCLVKQLERGDVNVVDLKKNIEYAASVLEAVYIDETRRLLDTEDELSDIQTDSVPSEVRDWLASTFTRKMGMTKKKPEEKPKFRSIVHAVQAGIFVERMYRKTYHMVGL
Prediction	874574535527444264246462561054043204201431556514363045205100410542345534613746551462667413740450113021454555564556344031103013001202311443444456
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC
MGSSATEIEELENTTFKYLTGEQTEKMWQRLKGILRCLVKQLERGDVNVVDLKKNIEYAASVLEAVYIDETRRLLDTEDELSDIQTDSVPSEVRDWLASTFTRKMGMTKKKPEEKPKFRSIVHAVQAGIFVERMYRKTYHMVGL

1sumB

0.08

3.24

0.57

CEthreader

VLKAGWFIEKMFRNSISSLVERN-ESLAREVIADEEVVDQMEVEIQEKAELIENIADKCHDIAKNVLELMEEPPLKPLEDIPAM-ANQTSEMLKFALRMFADVNVEKSFEVCRMDSKVDDLYEKVREELLLYMMESPKYVKRAL

3mmiA

0.06

2.50

0.62

EigenThreader

TVVSSLVRNTVESIVMSLPKDETMLGGIFWLSNLSPAFAANQKTLYYLNDLENETLKVFDKIYSTWLVKFMKHASAHIENDLITKCPALNWKYGYEVDRNIERLVSWFEPRIEQIIQAVKILQLQAILLKEILNYLANVIKREN

2yruA

0.13

0.09

3.14

0.58

FFAS-3D

SETLIEDVLRPLEQALEDCHGHTKKQVCDDISRRLALLREQWAGGKLS-IPVKKRMALLVQELLHHQWDAADDI------HRSLMVDH-VTEVSQWMVG------------------VKRLIAEKKS-----------------

6egcA

0.16

0.14

4.65

0.63

SPARKS-K

----------TRTEIIRELERREQEELAKRLKELLRELERLQREGSSDVRELLREIKELVEEIEKLAREQKYLVEELKRQ-----GNEIIRELERSLREQEEERLQREGSSDEDVRELREIKELVEEIEKLAREQKYLVEELKR

4q25A

0.11

0.08

2.74

0.54

CNFpred

------------------------NAELEDVRSHLLAMGG----------LVEKQVNDAVNALIDADSGLAQQVREIDDQINQM-----ERNIDEECVRILARRQPAAS-------DLRLIISISKSVIDLERIGDEASKVARR

1sjjA2

0.07

0.06

2.59

1.00

DEthreader

AGPWIQTKMEEIGRI-SIETLEDQLNHLRQYEKSIVNYKPKIDQLEMIRVGWEQLLTTIARTINEVENQILTRDRASFNHFCISMGY--NMG--EAEFARMSI-D--R----MG-VV-FQAFIDFMSRTADTDTADQVMYMSFS

2i0mA

0.03

1.93

0.87

MapAlign

FLGLGQLVLETAS-KALLALASKDKEMAELIINKDHAINQGQSFVISIMSSCSDLERMGDHMAGIAKAVLQLKENQLAEEQLHQMGKLSKDEQIDQYYYALSKEIIGLMNGTQYLYIIGHLERFADYIANICERLVYLETGELV

5eqzA

0.10

0.09

3.38

0.56

MUSTER

HHHYVEEKKEIDSEDVLALVNDSSGGKFKDYKDKINELKENLK--DIGNAELKEKLLNLQNSFQDKLAAKLAALKAAKNTIENITDKDQDISKRKIWSEAKLVGVTVPLLGSNTSGNGDKMSKNAVEQIDKVIKFLEE------

3g45A

0.12

0.06

2.21

1.14

HHsearch

-------------------------------------------------------------------SNKFKRMLNELTHLSEMSR--SGNQVSEYISNTFLDTSISRFGVNTENDHLAKELVAGYSHCIMYAIFQERDLLKRI

1xwmA

0.04

2.12

0.52

CEthreader

LIEMGRLTEVALQQAIEAFLAMAVIDGDGSIDALEEEVNDFALWDLRRIVAAIKIASDIERIADFAVNIAKACIRIGGQPFVMDILVLMYRLATDMVSTAIAAYDREDASLAAQIADMDHRVDEQYGEMMASLLAVAKTDAATL

(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	0.4808

(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	5yfpC	0.55	4.26	0.081	0.840	model1_5yfpC.pdb.gz
2	5mpbZ	0.54	3.77	0.075	0.819	model1_5mpbZ.pdb.gz
3	4a01A	0.54	4.64	0.063	0.924	model1_4a01A.pdb.gz
4	4iu8A	0.54	4.62	0.074	0.903	model1_4iu8A.pdb.gz
5	3ihvA	0.54	4.43	0.073	0.882	model1_3ihvA.pdb.gz
6	6h7dA	0.53	4.88	0.043	0.938	model1_6h7dA.pdb.gz
7	1w99A	0.53	4.00	0.037	0.819	model1_1w99A.pdb.gz
8	5x0mA	0.53	4.10	0.040	0.792	model1_5x0mA.pdb.gz
9	5k7vA	0.53	4.87	0.051	0.882	model1_5k7vA.pdb.gz
10	4apsA	0.53	4.34	0.021	0.819	model1_4apsA.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:0003824	0.98	catalytic activity
GO:0004114	0.97	3',5'-cyclic-nucleotide phosphodiesterase activity
GO:0047555	0.92	3',5'-cyclic-GMP phosphodiesterase activity
GO:0048101	0.78	calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity
GO:0004115	0.66	3',5'-cyclic-AMP phosphodiesterase activity
GO:1901363	0.52	heterocyclic compound binding
GO:0097159	0.52	organic cyclic compound binding
GO:0036094	0.51	small molecule binding
GO:0000166	0.50	nucleotide 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	0.97	single-organism process
GO:0008152	0.85	metabolic process
GO:0009987	0.84	cellular process
GO:0044281	0.83	small molecule metabolic process
GO:0071704	0.80	organic substance metabolic process
GO:0044763	0.80	single-organism cellular process
GO:0044238	0.80	primary metabolic process
GO:0044237	0.80	cellular metabolic process
GO:0006139	0.79	nucleobase-containing compound metabolic process
GO:0055086	0.78	nucleobase-containing small molecule metabolic process
GO:0006753	0.75	nucleoside phosphate metabolic process
GO:1901564	0.74	organonitrogen compound metabolic process
GO:0009117	0.74	nucleotide metabolic process
GO:0009150	0.73	purine ribonucleotide metabolic process
GO:0046068	0.71	cGMP metabolic process
GO:0046058	0.69	cAMP metabolic process
GO:0065007	0.60	biological regulation
GO:0050789	0.58	regulation of biological process
GO:0050794	0.56	regulation of cellular process
GO:1901292	0.50	nucleoside phosphate catabolic 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:0044464	0.95	cell part
GO:0044424	0.81	intracellular part
GO:0044444	0.52	cytoplasmic part
GO:0043226	0.49	organelle
GO:0097458	0.44	neuron part
GO:0043025	0.43	neuronal cell body
GO:0043227	0.41	membrane-bounded organelle
GO:0043229	0.40	intracellular organelle
GO:0043231	0.39	intracellular membrane-bounded organelle
GO:0005829	0.38	cytosol
GO:0005634	0.36	nucleus
GO:0005737	0.33	cytoplasm
GO:0044421	0.32	extracellular region 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	2pfdB	0.431	4.40	0.094	0.694	2.1.2.5 4.3.1.4	NA
2	0.060	1y8pA	0.480	4.63	0.056	0.806	2.7.11.2	70
3	0.060	2v8tA	0.491	4.11	0.045	0.764	1.11.1.6	NA
4	0.060	2e1qA	0.504	4.75	0.050	0.812	1.17.3.2 1.17.1.4	NA
5	0.060	1jroB	0.485	4.78	0.087	0.799	1.1.1.204	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	1fo4A	0.498	4.71	0.043	0.812	0.48	FES	complex1.pdb.gz	38,40,41,42,53,55
2	0.01	2ckjC	0.487	4.89	0.035	0.819	0.43	FES	complex2.pdb.gz	42,43,45,47,48
3	0.01	2ckjD	0.469	4.92	0.031	0.806	0.55	FES	complex3.pdb.gz	5,38,39,43,44,45,47
4	0.01	2ckjA	0.487	4.94	0.050	0.819	0.42	FES	complex4.pdb.gz	128,129,131,135

	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.