D-I-TASSER A8MXD5-D1

D-I-TASSER results for A8MXD5-D1

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

Input Sequence in FASTA format

>A8MXD5 (128 residues)
MLKREMKPESDRPRKVRFRIASSHSGRVLKEVYEDGQPSGSLDSECASICGIDGLGDSDG
QQNGHIESEGDENENDQDSLLVLARAASEKGFGTRRVNILSKNGTVRGVKYKVSAGQALF
NNLTKVLQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLKREMKPESDRPRKVRFRIASSHSGRVLKEVYEDGQPSGSLDSECASICGIDGLGDSDGQQNGHIESEGDENENDQDSLLVLARAASEKGFGTRRVNILSKNGTVRGVKYKVSAGQALFNNLTKVLQ
Prediction	CCCCCCCCCCCCCCSSSSSSSCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCSSSSSSSCCCCSSCSSSSSCCHHHHHHHHHHHHC
Confidence	98656788888873589998227763489999832898877421256755567888887432466667656688875541110455786776530589971588331234442113578877888749
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLKREMKPESDRPRKVRFRIASSHSGRVLKEVYEDGQPSGSLDSECASICGIDGLGDSDGQQNGHIESEGDENENDQDSLLVLARAASEKGFGTRRVNILSKNGTVRGVKYKVSAGQALFNNLTKVLQ
Prediction	74457455577434403130344342400440175553474447615536526435747454444345435756754431132243347441444313003652414324341431331154145338
	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 AttentionPotential. 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

CCCCCCCCCCCCCCSSSSSSSCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCSSSSSSSCCCCSSCSSSSSCCHHHHHHHHHHHHC
MLKREMKPESDRPRKVRFRIASSHSGRVLKEVYEDGQPSGSLDSECASICGIDGLGDSDGQQNGHIESEGDENENDQDSLLVLARAASEKGFGTRRVNILSKNGTVRGVKYKVSAGQALFNNLTKVLQ

6jnfA

0.06

2.69

0.56

CEthreader

ALPKYAFSALFANDNLFAQGNIDNDLSVSGRLNYGWKNISKVNLQISDGQPTMCQLEQDYQASDFSVNVKTLNPGEFTGVAVASFLQSVTPQLALGLETLYSRTDGSAPGDAGVSYLTRYVSKKQDWI

7cyzA

0.05

2.23

0.53

EigenThreader

EYSELLDKAAQIKGFQFFSEQVHHPPISACHAESRNFIHNIRWIEHFIKAKYWSTNAHLFGKWHESIYGNPMPKGYEQYYFALELNP----TDTRFRPDQRFLEEGNLEEAEIQKQRIEQLQRERRRV

1kl7A1

0.12

0.10

3.58

0.32

FFAS-3D

-------PEGEKKQITVVGATSGDTGSAAIYGLRGKKPTGRISPIQEEQTTVPDEN-----------VQTLSVTGTFDNCQDIVKAIFGDKEFNHNVGAVNKKKLKFIERADVELVKNAIEELAK---

6n7pY

0.11

0.09

3.40

0.77

SPARKS-K

PNGLQELRESMKSSTIYVGLSFYTSEEQIYELFSKCGTIKRIIMGLDRFKFT-------PCGFCFIIYS------CPDEALNALKYLSDTKLDEKTITIDLDPGFEDGRQ----FGRGKSGGQVSDEL

3zgbA

0.10

0.08

2.87

0.46

CNFpred

-------------VKLDIRQESDRHTDVLDAITQHL-----EIGSYREWSEEKRQEWAELSGKRPLFGSDLPKTEEVKDVLDTFNVLAELP-----------SDCFGAYI--ISMATSPSDVLAVELL

5u47A

0.05

0.04

1.85

0.83

DEthreader

---------RNGLSAQLEQMFMTKGINASATVV-----EILT--LTQVQMLAFIAETRNY-----MISVDPFGTLKSGTSVV-A-MVPSDPEYIMYVT--VQEPKTWNNNF-FAVVNPVLEEAMSMGA

2pffB

0.09

3.23

0.66

MapAlign

-----------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGYKTSKAAQDVWNRADNHFKDTYGFSILDKRTGWLVEIVNYNVENQQYVAAGDLRALDT-

5bq9A1

0.12

4.14

0.59

MUSTER

VTKIIWVSNNGKP-NLKIEFVSEEE-KEVKKKASELGLNFPLVQGSGNSLLIEASNYPINPCGCYISPGGKLAINFGK-VELSHFILPKVGVKTEHAEIFKDHNTIFFHKHKLPGVNSELTFIPTGTP

1wryA

0.08

0.05

2.20

0.90

HHsearch

------GSSGSSGMV--IRVYIASSTQDVLGFLEANKNRKWMRENVPENSATGYPLPPQIFNESQYRYDAFFEARE-------NNAVYAFLGLTAPPGSAEVSGPSSG--------------------

7ck6A

0.13

4.59

0.56

CEthreader

VTYVGTKQLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSAVTLGNPDVLVGSGILVAHYLQSITPCLALGGELVYHRRPGEEGTVMSLAGKYTLNNWLATVT

(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	0.5055

(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 AttentionPotential, 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	5twvB	0.49	4.46	0.040	0.781	model1_5twvB.pdb.gz
2	2uwxA	0.48	4.41	0.041	0.805	model1_2uwxA.pdb.gz
3	4p9kA	0.48	4.76	0.042	0.805	model1_4p9kA.pdb.gz
4	3eqvA	0.47	4.73	0.050	0.805	model1_3eqvA.pdb.gz
5	4pddA	0.47	4.98	0.075	0.844	model1_4pddA.pdb.gz
6	5khnB	0.47	4.22	0.070	0.734	model1_5khnB.pdb.gz
7	1pyyA	0.47	4.82	0.034	0.797	model1_1pyyA.pdb.gz
8	3e2tA	0.47	4.48	0.098	0.781	model1_3e2tA.pdb.gz
9	3udfA	0.46	4.59	0.078	0.805	model1_3udfA.pdb.gz
10	3dwkC2	0.46	4.95	0.033	0.820	model1_3dwkC2.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:0022857	0.20	transmembrane transporter activity
GO:0003824	0.20	catalytic activity
GO:0046872	0.17	metal ion binding
GO:0015075	0.17	ion transmembrane transporter activity
GO:0016787	0.16	hydrolase activity
GO:0015267	0.12	channel activity
GO:1901363	0.11	heterocyclic compound binding
GO:0097159	0.11	organic cyclic compound 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:0007605	1.00	sensory perception of sound
GO:0044699	0.91	single-organism process
GO:0009987	0.91	cellular process
GO:0065007	0.89	biological regulation
GO:0044763	0.89	single-organism cellular process
GO:0050794	0.87	regulation of cellular process
GO:0032502	0.87	developmental process
GO:0048856	0.86	anatomical structure development
GO:0044767	0.86	single-organism developmental process
GO:0016043	0.86	cellular component organization
GO:0060122	0.85	inner ear receptor stereocilium organization
GO:0060118	0.85	vestibular receptor cell development
GO:0010923	0.85	negative regulation of phosphatase 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 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:0098858	1.00	actin-based cell projection
GO:0044422	0.88	organelle part
GO:0097458	0.87	neuron part
GO:0043226	0.86	organelle
GO:0060091	0.85	kinocilium
GO:0032420	0.85	stereocilium

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	2nz6A	0.444	4.58	0.035	0.781	3.1.3.48	85
2	0.060	1h2aL	0.440	5.08	0.040	0.812	1.12.2.1	NA
3	0.060	1cc1L	0.444	4.86	0.025	0.797	1.12.99.6	NA
4	0.060	1ofdA	0.451	4.95	0.051	0.875	1.4.7.1	33
5	0.060	3fwmA	0.465	4.89	0.066	0.812	2.4.1.129	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	2y2iA	0.403	4.88	0.077	0.750	0.20	ZA3	complex1.pdb.gz	23,100,101
2	0.01	1cc1L	0.444	4.86	0.025	0.797	0.30	FCO	complex2.pdb.gz	22,23,26,105
3	0.01	2fffB	0.391	5.23	0.065	0.766	0.25	III	complex3.pdb.gz	27,28,30,31,32,33,35,37
4	0.01	1ofdA	0.451	4.95	0.051	0.875	0.21	F3S	complex4.pdb.gz	27,28,29
5	0.01	1kw0A	0.471	4.48	0.071	0.766	0.16	TIH	complex5.pdb.gz	34,37,38,96
6	0.01	3hf8A	0.433	4.45	0.064	0.742	0.21	ML0	complex6.pdb.gz	76,80,84,87,88,112,114
7	0.01	2z2mE	0.471	4.75	0.026	0.789	0.12	CDS	complex7.pdb.gz	27,29,30,95,96
8	0.01	2zc3B	0.351	5.27	0.043	0.664	0.20	BMG	complex8.pdb.gz	29,78,101
9	0.01	2y2pA	0.480	4.58	0.041	0.820	0.24	Z10	complex9.pdb.gz	46,47,50,86,88
10	0.01	1llwA	0.455	5.14	0.051	0.906	0.12	FMN	complex10.pdb.gz	77,112,113,114

	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.