D-I-TASSER P43246-D1

D-I-TASSER results for P43246-D1

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

Input Sequence in FASTA format

>P43246 (137 residues)
MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKT
QGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLA
YKASPGNLSQFEDILFG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDILFG
Prediction	CCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCSSSSSSCCCCSSSSCCHHHHHHHHHHHCCHHHSSCCCCCCCCCCSSSSCHHHHHHHHHHHHHHHCCSSSSSSCCCCCCCCCCCCSSSSSSSCCCCHHHHHHHHCC
Confidence	99876433477613444699999967989998699996598189967169999999973214211116789887537996177899999999997198899995589987666664799999689976899999639
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDILFG
Prediction	74544555152646535302410571474364101002354201001420320053214231002413566655143233444304400330034461301012455554545454040234032231541354258
	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

CCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCSSSSSSCCCCSSSSCCHHHHHHHHHHHCCHHHSSCCCCCCCCCCSSSSCHHHHHHHHHHHHHHHCCSSSSSSCCCCCCCCCCCCSSSSSSSCCCCHHHHHHHHCC
MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDILFG

2o8cB

0.13

0.12

4.04

1.17

DEthreader

DSTLYVPELNSC---TP-GMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMK-G--------NWAHSGFPEIAFGRYSDSLVQ-KGYKVARVEQTEMECIDRVVRREICRIITKGTQTY-SVLEKK

2o8fA1

1.00

0.98

27.39

3.26

SPARKS-K

MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAG---SKENDWYLAYKASPGNLSQFEDILFG

3thwB1

0.18

0.15

4.75

1.21

MapAlign

---------------YTPLELQYIEMKQQHKDAVLCVECGYKYRFFGEDAEIAARELNIYC--HLDHN------FMTASIPTHRLFVHVRRLVA-KGYKVGVVKQTEKAIGDNRFSRKLTALYTKSTLIGEDVNP--

1nneA1

0.17

0.16

5.28

1.28

CEthreader

---MEGMLKGEGPGPLPPLLQQYVELRDQYPDYLLLFQVGDFYECFGEDAERLARALGLVLTHKTS----KDFTTPMAGIPLRAFEAYAERLLKM-GFRLAVADQVEPAEEAGLVRREVTQLLTPGTLLQESLLPRE

2o8fA1

1.00

0.98

27.39

2.75

MUSTER

MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAG---SKENDWYLAYKASPGNLSQFEDILFG

2o8fA1

1.00

0.98

27.39

3.44

HHsearch

MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAG---SKENDWYLAYKASPGNLSQFEDILFG

2o8fA1

0.97

0.95

26.60

2.52

FFAS-3D

MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGSKEND---WYLAYKASPGNLSQFEDILFG

2o8fA1

0.95

0.90

25.19

1.28

EigenThreader

PKETLQ----LESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGS---KENDWYLAYKASPGNLSQFEDILFG

2o8eA

0.99

0.97

27.19

2.23

CNFpred

MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDAYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAG---SKENDWYLAYKASPGNLSQFEDILFG

1e3mA

0.12

0.10

3.63

1.17

DEthreader

------ENFDAH---TP---QQYLRLKAQHPEILLFYR-GDFYELFYDDAKRASQLLDISLTKR-GAS--AGEPIP-AGIPYHAVENYLAKLVN-QGESVAICEQIGDPTSKGPVERKVVRIVTPGTISDEARTARP

(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	0.7832

(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	2o8fA	0.93	0.99	0.955	0.971	model1_2o8fA.pdb.gz
2	3thwB	0.70	2.64	0.188	0.839	model1_3thwB.pdb.gz
3	1nneA	0.69	2.54	0.189	0.839	model1_1nneA.pdb.gz
4	1e3mA	0.68	2.46	0.117	0.818	model1_1e3mA.pdb.gz
5	2o8cB1	0.67	2.49	0.127	0.810	model1_2o8cB1.pdb.gz
6	2d5bA	0.39	4.62	0.056	0.671	model1_2d5bA.pdb.gz
7	2pjzA	0.38	4.75	0.052	0.664	model1_2pjzA.pdb.gz
8	2q0hB	0.37	4.64	0.033	0.635	model1_2q0hB.pdb.gz
9	2ad5B	0.36	5.30	0.043	0.686	model1_2ad5B.pdb.gz
10	1iy8A	0.35	4.79	0.058	0.635	model1_1iy8A.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:0030983	1.00	mismatched DNA binding
GO:0032137	0.99	guanine/thymine mispair binding
GO:0003684	0.92	damaged DNA binding
GO:0032138	0.91	single base insertion or deletion binding
GO:0000406	0.91	double-strand/single-strand DNA junction binding
GO:0000404	0.91	heteroduplex DNA loop binding
GO:0000403	0.91	Y-form DNA binding
GO:0000400	0.91	four-way junction DNA 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:0006298	1.00	mismatch repair
GO:0043570	0.99	maintenance of DNA repeat elements
GO:0050794	0.93	regulation of cellular process
GO:0080090	0.92	regulation of primary metabolic process
GO:0060255	0.92	regulation of macromolecule metabolic process
GO:0031323	0.92	regulation of cellular metabolic process
GO:0006310	0.92	DNA recombination
GO:0000710	0.92	meiotic mismatch repair
GO:0045128	0.91	negative regulation of reciprocal meiotic recombination
GO:0006311	0.91	meiotic gene conversion
GO:0006301	0.91	postreplication repair
GO:0007131	0.90	reciprocal meiotic recombination
GO:0007165	0.61	signal transduction
GO:0044699	0.60	single-organism process
GO:0007093	0.60	mitotic cell cycle checkpoint
GO:0042771	0.59	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:0031573	0.59	intra-S DNA damage checkpoint
GO:0010224	0.59	response to UV-B
GO:0010165	0.59	response to X-ray
GO:0006302	0.59	double-strand break repair
GO:0044763	0.54	single-organism cellular process
GO:0044710	0.51	single-organism metabolic 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:0044428	1.00	nuclear part
GO:0032300	1.00	mismatch repair complex
GO:0032301	0.99	MutSalpha complex
GO:0032302	0.95	MutSbeta complex
GO:0043229	0.94	intracellular organelle
GO:0000228	0.92	nuclear chromosome

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	1tufA	0.528	3.73	0.043	0.788	4.1.1.20	NA
2	0.060	1p91A	0.459	4.87	0.061	0.810	2.1.1.51	NA
3	0.060	2p8uA	0.464	4.86	0.060	0.832	2.3.3.10	NA
4	0.060	1l1eA	0.408	5.25	0.053	0.745	2.1.1.79	NA
5	0.060	2opbB	0.449	5.02	0.068	0.803	2.1.1.28	53

	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	0.15	1fw6A	0.691	2.54	0.189	0.839	0.84	QNA	complex1.pdb.gz	19,41,70,105,114,115,117
2	0.11	1e3mA	0.706	2.43	0.121	0.847	0.84	QNA	complex2.pdb.gz	18,19,39,40,41,42,44,66,105,115,117
3	0.06	1ewqA	0.684	2.54	0.181	0.839	0.93	QNA	complex3.pdb.gz	19,41,71,72,105,114,115,117

	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.