D-I-TASSER A6NEF3-D1

D-I-TASSER results for A6NEF3-D1

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

Input Sequence in FASTA format

>A6NEF3 (153 residues)
MWPQPRFPPHPAMSEKTQQGKLAAAKKKLKAYWQRKSPGIPAGANRKKKINGSSPDTATS
GGYHSPGDSATGIYGEGRASSTTLEDLESQYQELAVALDSSSAIISQLTENINSLVRTSK
EEKKHEIHLVQKLGRSLFKLKNQTAEPLAPEPP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MWPQPRFPPHPAMSEKTQQGKLAAAKKKLKAYWQRKSPGIPAGANRKKKINGSSPDTATSGGYHSPGDSATGIYGEGRASSTTLEDLESQYQELAVALDSSSAIISQLTENINSLVRTSKEEKKHEIHLVQKLGRSLFKLKNQTAEPLAPEPP
Prediction	CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Confidence	999999999962356778889999999999987622688884122224446898655434577772466776511343203454212331124566641137899999999999988889999989999999999999998740578899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MWPQPRFPPHPAMSEKTQQGKLAAAKKKLKAYWQRKSPGIPAGANRKKKINGSSPDTATSGGYHSPGDSATGIYGEGRASSTTLEDLESQYQELAVALDSSSAIISQLTENINSLVRTSKEEKKHEIHLVQKLGRSLFKLKNQTAEPLAPEPP
Prediction	834653325432147514653145036405624555545345545546565554463345442543653454145534534441754625444242314344332541475165345544644444354155145534514455275346768
	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

CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
MWPQPRFPPHPAMSEKTQQGKLAAAKKKLKAYWQRKSPGIPAGANRKKKINGSSPDTATSGGYHSPGDSATGIYGEGRASSTTLEDLESQYQELAVALDSSSAIISQLTENINSLVRTSKEEKKHEIHLVQKLGRSLFKLKNQTAEPLAPEPP

3tnfB

0.07

2.76

0.62

CEthreader

EKLTQLMEKHKGDEKTVQSLQREHHDIKAKLANLQVLHDAHTGKKSYVNEKGNPVSSLKDAHLAINKDQEVVEHEGQFYLLQKGQWDAIKNNPAALEKAQKDYSQSKHDLATIKMEALIHKLSLEMEKQLETINNLIMSTDPKENEEATKLLH

7ko4P

0.08

3.12

0.58

EigenThreader

GTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNL

3l4qC

0.13

0.10

3.42

0.73

FFAS-3D

-----------RTSQELQMKRTAAFNETIKIFEEQ-----------GQTQEKSSKEYLERFRREGNEKEMQRILLNSERLKSRIAEIHESRTKLEQELRAQASDNREIDKRMNSLKPDLMQLRKIRDQYLVWLQKKINEW-------------

4oydB

0.14

0.09

3.14

0.88

SPARKS-K

----ADPKKVLDKAKDQAENRVRELKQKLEELYKEAR--------------------------------------KLDLTQEMRRKLELRYGDIYNAIRQAKQEADKLKKQLDELKRRLEELKEEASRKARDYGREFQLKLEYG---------

5y05A

0.13

0.10

3.65

0.62

CNFpred

-----------------VNDRLAALGIALEDLDAQVAKYESEIDSVRQREDRDRA----------GAKQVTEIQHELETLQRRQASLEEQLLEVMERREELMAERSEELRRVDELQTELTEAQQARDAALVELDQARHQCATRRDALVNAIDD

5yfpD

0.06

2.51

1.00

DEthreader

--------DVVNEHSQVFNTNVASYGKAVSSIMQAQEQLNNC-EAEKITTD-KGSLQELNDNNLKYKMIDVLV--NIEELLQIPEKIENHEEHLLFNNLIEEIDMYSEIILDEELLVRYNIFMSFLPINREKISYCILLKDETIDGFKLKSIG

5bv9A

0.09

3.47

0.76

MapAlign

ALSSDKGGLKPSSATGASDWEKTLKRQLEFYVWLQSKEGAIAGGATNSWNGDYSAYPAGRSTFYDMAYEDAPVYHDPPSNNWFGMQAWPMERVAELYYIFVKGDKTENVQMAKSCITKWVNYTGVLGSLVKAFTFFAAATKLETGNYTALGVR

2otoB

0.14

0.12

4.25

0.74

MUSTER

------AANNPAIQNIRLRHENKDLKARLENAEVAGRDFKRAEELEKAKQALEDQRKDLETKL---KELQQDYDLAKESTSWDRQRLEKELEEKKEALELAIDQASRDYHRATALEKELEEKKKALELAIDQASQDYNRANVLEKE-------

6f1tX2

0.10

0.05

1.95

0.81

HHsearch

-------------------------------------------------------------------QH---II-RLESLQAEIKMLSDRKRELEHRLSATLEENDLLQGTVEELQDRLERQGHDKDLQLHQSQLELQEVRLSYRQLQGGGGG

3q0xA

0.09

0.08

3.26

0.56

CEthreader

ILTGVAKQNHNLRILRIHISTLEVSEEDFQSLKNDQGILVDFASFPGKIIEKCILAQPGDSPRFQAVLTIRGGESVFKTLAFRPGNDSVVKQFLAFRLSEVKGTCHDLSDDLSRTRDDRDSMVAQLAQCRQQLAQLREQYDKHLLEVQ-----

(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	0.4102

(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	3qweA	0.64	4.01	0.063	0.941	model1_3qweA.pdb.gz
2	4avmA	0.62	3.66	0.113	0.863	model1_4avmA.pdb.gz
3	6sihA	0.62	4.01	0.067	0.889	model1_6sihA.pdb.gz
4	6ewyA	0.61	3.73	0.034	0.882	model1_6ewyA.pdb.gz
5	2efkA	0.61	4.09	0.049	0.908	model1_2efkA.pdb.gz
6	4wpcA	0.60	4.07	0.057	0.889	model1_4wpcA.pdb.gz
7	7jw1E	0.60	3.60	0.076	0.837	model1_7jw1E.pdb.gz
8	6q0xA	0.59	4.15	0.095	0.882	model1_6q0xA.pdb.gz
9	6iknA	0.59	3.58	0.064	0.830	model1_6iknA.pdb.gz
10	4dylA	0.59	4.06	0.057	0.856	model1_4dylA.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:0019899	0.50	enzyme binding
GO:0019901	0.49	protein kinase binding
GO:0061676	0.48	importin-alpha family protein binding
GO:0008017	0.48	microtubule binding
GO:0000149	0.39	SNARE binding
GO:0019905	0.38	syntaxin binding
GO:0030234	0.31	enzyme regulator 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:0044699	1.00	single-organism process
GO:0009987	0.90	cellular process
GO:0044763	0.86	single-organism cellular process
GO:0071704	0.81	organic substance metabolic process
GO:0065007	0.81	biological regulation
GO:0044238	0.80	primary metabolic process
GO:0044237	0.79	cellular metabolic process
GO:0043170	0.79	macromolecule metabolic process
GO:0006810	0.79	transport
GO:0050789	0.78	regulation of biological process
GO:0044260	0.78	cellular macromolecule metabolic process
GO:0016043	0.78	cellular component organization
GO:0050794	0.77	regulation of cellular process
GO:0044710	0.77	single-organism metabolic process
GO:0006464	0.77	cellular protein modification process
GO:0071822	0.76	protein complex subunit organization
GO:0048193	0.76	Golgi vesicle transport
GO:0046907	0.76	intracellular transport
GO:0044723	0.76	single-organism carbohydrate metabolic process
GO:0022411	0.76	cellular component disassembly
GO:0006996	0.76	organelle organization
GO:0090307	0.75	mitotic spindle assembly
GO:0090306	0.75	spindle assembly involved in meiosis
GO:0090166	0.75	Golgi disassembly
GO:0090161	0.75	Golgi ribbon formation
GO:0051297	0.75	centrosome organization
GO:0051289	0.75	protein homotetramerization
GO:0008356	0.75	asymmetric cell division
GO:0007020	0.75	microtubule nucleation
GO:0006888	0.75	ER to Golgi vesicle-mediated transport
GO:0006486	0.75	protein glycosylation
GO:0065009	0.74	regulation of molecular function
GO:0060255	0.61	regulation of macromolecule metabolic process
GO:2000112	0.60	regulation of cellular macromolecule biosynthetic process
GO:0080090	0.60	regulation of primary metabolic process
GO:0048518	0.60	positive regulation of biological process
GO:0060050	0.59	positive regulation of protein glycosylation
GO:0032091	0.59	negative regulation of protein binding
GO:0010507	0.59	negative regulation of autophagy

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:0043231	1.00	intracellular membrane-bounded organelle
GO:0044444	0.92	cytoplasmic part
GO:0005801	0.85	cis-Golgi network
GO:0016020	0.74	membrane
GO:0044422	0.64	organelle part
GO:0005737	0.63	cytoplasm
GO:0044446	0.60	intracellular organelle part
GO:0005886	0.52	plasma membrane
GO:0044425	0.50	membrane 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	1c3cA	0.430	4.29	0.062	0.627	4.3.2.2	NA
2	0.060	2zy2A	0.420	4.19	0.044	0.634	4.1.1.12	NA
3	0.060	1p49A	0.452	4.81	0.028	0.732	3.1.6.2	NA
4	0.060	3gehA	0.437	3.89	0.053	0.621	3.6.-.-	NA
5	0.060	1dcnB	0.441	4.56	0.068	0.647	4.3.2.1	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	2w6dB	0.516	4.23	0.088	0.804	0.56	CPL	complex1.pdb.gz	52,57,58,61
2	0.01	2jizG	0.480	4.29	0.053	0.726	0.77	STL	complex2.pdb.gz	52,57,58,61,62
3	0.01	1i4d1	0.511	3.77	0.051	0.719	0.66	III	complex3.pdb.gz	37,40,43,44,47,50,51,52,54,55,81,84,88,91,92
4	0.01	2w6iG	0.504	4.14	0.063	0.739	0.50	III	complex4.pdb.gz	48,49,52,53,58

	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.