D-I-TASSER P46736-D1

D-I-TASSER results for P46736-D1

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

Input Sequence in FASTA format

>P46736 (222 residues)
MAVQVVQAVQAVHLESDAFLVCLNHALSTEKEEVMGLCIGELNDDTRSDSKFAYTGTEMR
TVAEKVDAVRIVHIHSVIILRRSDKRKDRVEISPEQLSAASTEAERLAELTGRPMRVVGW
YHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQK
SSESLHGPRDFWSSSQHISIEGQKEEERYERIEIPIHIVPHV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MAVQVVQAVQAVHLESDAFLVCLNHALSTEKEEVMGLCIGELNDDTRSDSKFAYTGTEMRTVAEKVDAVRIVHIHSVIILRRSDKRKDRVEISPEQLSAASTEAERLAELTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQKSSESLHGPRDFWSSSQHISIEGQKEEERYERIEIPIHIVPHV
Prediction	CCCCCCCCCCSSSSCHHHHHHHHHHHHCCCCCSSSSSSSSSSSCCSSSSSCCCCCCCCCCCCCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCSSSSSCCCCCCCCCCHHHHHHHHHHHHHCCCSSSSSSCCCCCCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSSSSCCCC
Confidence	998888753189983899999999985299834677866899178156310014553442112345654226787531244568877643579999999999999999985977553028972899997379999999999985288639999647778775557828999999349866775545776566665533576655555279998527845799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MAVQVVQAVQAVHLESDAFLVCLNHALSTEKEEVMGLCIGELNDDTRSDSKFAYTGTEMRTVAEKVDAVRIVHIHSVIILRRSDKRKDRVEISPEQLSAASTEAERLAELTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQKSSESLHGPRDFWSSSQHISIEGQKEEERYERIEIPIHIVPHV
Prediction	773732630440403130001013003443433000000021344343343332433433232443433421312213225446456333424443024024413412433635341200010023331222332041033124234200000002234645344340201001024474444445434534344541446435435312406031412357
	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                 140                 160                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCSSSSCHHHHHHHHHHHHCCCCCSSSSSSSSSSSCCSSSSSCCCCCCCCCCCCCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCSSSSSCCCCCCCCCCHHHHHHHHHHHHHCCCSSSSSSCCCCCCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSSSSCCCC
MAVQVVQAVQAVHLESDAFLVCLNHALSTEKEEVMGLCIGELNDDTRSDSKFAYTGTEMRTVAEKVDAVRIVHIHSVIILRRSDKRKDRVEISPEQLSAASTEAERLAELTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQKSSESLHGPRDFWSSSQHISIEGQKEEERYERIEIPIHIVPHV

5l4kV

0.22

0.18

5.67

1.00

DEthreader

P-APAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVD--------------------D--YTVRVIDVFAMPQSG--TG---VSVEAVDPVFQAKMLDMLKQTGRP-EMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQS---V-KGKVVIDAFRLINANMMLGHEPRQTT--LLIHGLN--------RHYYSITINYRKNLE

5cw3A2

0.54

0.42

12.09

1.87

SPARKS-K

-----DSSLQKVELQTDVYMVCLQHALSTENFEVMGLLIGNFACG-------------------------IAKISAVIILRRLDKKKDRVEISSEQLLKAAAEAERLTVELNRPMRVLGWYHSHPHITVCPSHVDVRTQATYQTMDHSFVGLIFSVFSEGKESKEHEIFLNCFQSDNGEA------------TEIPLEIVHTPDISDRCLRTMT--------

5cw3A2

0.58

0.41

11.91

1.08

MapAlign

------SSLQKVELQTDVYMVCLQHALSTENFEVMGLLIGNFA------------------------CGIAKISAVI-ILRRLDKKKDRVEISSEQLLKAAAEAERLTVELNRPMRVLGWYHSHPHITVCPSHVDVRTQATYQTMDHSFVGLIFSVFSEGKESKEHEIFLNCFQSDNGE-------------------------------ATEIPLEIVHT-

5cw3A2

0.61

0.44

12.64

0.85

CEthreader

-----DSSLQKVELQTDVYMVCLQHALSTENFEVMGLLIGNF-------------------------ACGIAKISAVIILRRLDKKKDRVEISSEQLLKAAAEAERLTVELNRPMRVLGWYHSHPHITVCPSHVDVRTQATYQTMDHSFVGLIFSVFSEGKESKEHEIFLNCFQSDNG-------------------------------EATEIPLEIVHTP

5cw3A2

0.60

0.43

12.40

1.48

MUSTER

-----DSSLQKVELQTDVYMVCLQHALSTENFEVMGLLIGNFACG-------------------------IAKISAVIILRRLDKKKDRVEISSEQLLKAAAEAERLTVELNRPMRVLGWYHSHPHITVCPSHVDVRTQATYQTMDHSFVGLIFSVFSEGKESKEHEIFLNCFQSDNGE-------------------------------ATEIPLEIVHTP

5cw3A

0.60

0.43

12.40

2.64

HHsearch

-----DSSLQKVELQTDVYMVCLQHALSTENFEVMGLLIGNFACG-------------------------IAKISAVIILRRLDKKKDRVEISSEQLLKAAAEAERLTVELNRPMRVLGWYHSHPHITVCPSHVDVRTQATYQTMDHSFVGLIFSVFSEGKESKEHEIFLNCFQSDNGE-------------------------------ATEIPLEIVHTP

5cw3A2

0.60

0.43

12.39

2.39

FFAS-3D

------SSLQKVELQTDVYMVCLQHALSTENFEVMGLLIGNFACG-------------------------IAKISAVIILRRLDKKKDRVEISSEQLLKAAAEAERLTVELNRPMRVLGWYHSHPHITVCPSHVDVRTQATYQTMDHSFVGLIFSVFSEGKESKEHEIFLNCFQSDNGE-------------------------------ATEIPLEIVHT-

5cw3A

0.56

0.41

11.80

1.17

EigenThreader

-----DSSLQKVELQTDVYMVCLQHALSTENFEVMGLLIGNFACG-------------------------IAKISAVIILRRLDKKKDRVEISSEQLLKAAAEAERLTVELNRPMRVLGWYHSHPHITVCPSHVDVRTQATYQTMDHSFVGLIFSVFSEGKESKEHEIFLNCFQSD------------------------------NGEATEIPLEIVHTPD

6gvwB

0.96

0.73

20.34

2.15

CNFpred

-------AVQAVHLESDAFLVCLNHALSTEKEEVMGLCIGELNDDI----------------------IRIVHIHSVIILRRSDKRKDRVEISPEQLSAASTEAERLAELTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQ-------------------------KSSEYERIEIPIHIVPHI

4d10E

0.20

0.15

4.91

1.00

DEthreader

--TKDHHYFKYCKISALALLKMVMHARSGGNLEVMGLMLGKV-D-----------------G-----ETMIIMDSFALPVEG---T-ETRNAQAAAYEYMAAYIENAKQVGRL-ENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTIS-A-G-KVNLGAFRTYPKGYK---P---PDE-GPS---------V-CKQYYA-LEVSYFKSD

(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	0.7143

(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	5cw3A	0.70	1.24	0.602	0.725	model1_5cw3A.pdb.gz
2	5l4kV	0.67	3.43	0.253	0.824	model1_5l4kV.pdb.gz
3	5mpbV	0.66	3.52	0.220	0.820	model1_5mpbV.pdb.gz
4	4d10E	0.66	3.47	0.202	0.806	model1_4d10E.pdb.gz
5	6r8fA	0.66	1.00	1.000	0.680	model1_6r8fA.pdb.gz
6	6cddA	0.64	3.43	0.114	0.788	model1_6cddA.pdb.gz
7	6oa9G	0.63	3.55	0.099	0.793	model1_6oa9G.pdb.gz
8	5cw6A	0.61	2.16	0.772	0.671	model1_5cw6A.pdb.gz
9	3rzuA	0.58	3.05	0.180	0.694	model1_3rzuA.pdb.gz
10	4f7oA	0.58	3.34	0.196	0.707	model1_4f7oA.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	0.92	catalytic activity
GO:0070011	0.90	peptidase activity, acting on L-amino acid peptides
GO:0019783	0.83	ubiquitin-like protein-specific protease activity
GO:0008237	0.81	metallopeptidase activity
GO:0004843	0.81	thiol-dependent ubiquitin-specific protease activity
GO:0031593	0.68	polyubiquitin 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:0009987	0.93	cellular process
GO:0008152	0.88	metabolic process
GO:0044238	0.87	primary metabolic process
GO:0043170	0.87	macromolecule metabolic process
GO:0044237	0.86	cellular metabolic process
GO:0044260	0.85	cellular macromolecule metabolic process
GO:0019538	0.81	protein metabolic process
GO:0006508	0.78	proteolysis
GO:0065007	0.76	biological regulation
GO:0050794	0.75	regulation of cellular process
GO:0044267	0.75	cellular protein metabolic process
GO:0070647	0.74	protein modification by small protein conjugation or removal
GO:0070646	0.73	protein modification by small protein removal
GO:0080090	0.71	regulation of primary metabolic process
GO:0050896	0.71	response to stimulus
GO:0031323	0.71	regulation of cellular metabolic process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0048518	0.69	positive regulation of biological process
GO:0048522	0.68	positive regulation of cellular process
GO:0009893	0.67	positive regulation of metabolic process
GO:0031325	0.66	positive regulation of cellular metabolic process
GO:0016579	0.66	protein deubiquitination
GO:0010604	0.66	positive regulation of macromolecule metabolic process
GO:0006807	0.66	nitrogen compound metabolic process
GO:0006139	0.65	nucleobase-containing compound metabolic process
GO:0090304	0.64	nucleic acid metabolic process
GO:0016043	0.64	cellular component organization
GO:0006950	0.64	response to stress
GO:0006974	0.62	cellular response to DNA damage stimulus
GO:0051171	0.61	regulation of nitrogen compound metabolic process
GO:0043933	0.61	macromolecular complex subunit organization
GO:0006281	0.61	DNA repair
GO:0048583	0.59	regulation of response to stimulus
GO:0019219	0.59	regulation of nucleobase-containing compound metabolic process
GO:0045935	0.58	positive regulation of nucleobase-containing compound metabolic process
GO:0080134	0.57	regulation of response to stress
GO:0006325	0.57	chromatin organization
GO:0022402	0.56	cell cycle process
GO:0070536	0.55	protein K63-linked deubiquitination
GO:0016578	0.55	histone deubiquitination
GO:0080135	0.54	regulation of cellular response to stress
GO:0048584	0.54	positive regulation of response to stimulus
GO:0006302	0.54	double-strand break repair
GO:0009628	0.53	response to abiotic stimulus
GO:0000075	0.53	cell cycle checkpoint
GO:0045739	0.52	positive regulation of DNA repair
GO:0031572	0.52	G2 DNA damage checkpoint
GO:0070537	0.51	histone H2A K63-linked deubiquitination
GO:0010212	0.51	response to ionizing radiation

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:0044424	1.00	intracellular part
GO:0032991	0.93	macromolecular complex
GO:0043234	0.92	protein complex
GO:0043226	0.90	organelle
GO:0043231	0.89	intracellular membrane-bounded organelle
GO:0005634	0.85	nucleus
GO:0044446	0.83	intracellular organelle part
GO:0044428	0.80	nuclear part
GO:0070531	0.60	BRCA1-A complex
GO:0070552	0.59	BRISC complex

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	0.220	2znvD	0.565	2.97	0.185	0.680	3.1.2.15	120,124,173
2	0.060	2e3zA	0.426	5.62	0.056	0.730	3.2.1.21	NA
3	0.060	1xfbA	0.423	5.48	0.056	0.698	4.1.2.13	NA
4	0.060	3kx6A	0.428	5.68	0.036	0.721	4.1.2.13	NA
5	0.060	1fbaA	0.421	5.81	0.031	0.721	4.1.2.13	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	2cvtA	0.451	5.47	0.035	0.739	0.55	ANP	complex1.pdb.gz	19,36,39,40,120
2	0.01	2cvwA	0.462	5.12	0.045	0.734	0.43	TTP	complex2.pdb.gz	125,126,127,156,167
3	0.01	1xjfA	0.438	5.06	0.019	0.689	0.41	DTP	complex3.pdb.gz	136,137,138,149,150,151
4	0.01	2cvxA	0.461	5.23	0.045	0.739	0.47	DGT	complex4.pdb.gz	39,40,41

	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.