D-I-TASSER A8MYJ7-D4

D-I-TASSER results for A8MYJ7-D4

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

Input Sequence in FASTA format

>A8MYJ7 (162 residues)
GPGTVVPELRSLKPEAQALITQGLYSHCRALLSQLPDTGAPLEDKDTQGLLAVGEALIKI
DSGQPHWHLLLADILMAQGSYEEAGTHLEKALHRAPTSEAARARLGLLQLKKGDVPGAAR
DLQSLAEVDAPDLSCLLHLLEASERQSLAQAAAQEAGTLLDA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GPGTVVPELRSLKPEAQALITQGLYSHCRALLSQLPDTGAPLEDKDTQGLLAVGEALIKIDSGQPHWHLLLADILMAQGSYEEAGTHLEKALHRAPTSEAARARLGLLQLKKGDVPGAARDLQSLAEVDAPDLSCLLHLLEASERQSLAQAAAQEAGTLLDA
Prediction	CCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	953267999834289999999999999999999998713001118999999999999984989989999999999990999999999999997499989999999999999299999999999999739122799999974999870699999999999719
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GPGTVVPELRSLKPEAQALITQGLYSHCRALLSQLPDTGAPLEDKDTQGLLAVGEALIKIDSGQPHWHLLLADILMAQGSYEEAGTHLEKALHRAPTSEAARARLGLLQLKKGDVPGAARDLQSLAEVDAPDLSCLLHLLEASERQSLAQAAAQEAGTLLDA
Prediction	854322440371475044214311253035125412635431556416401510430161237324102210301344451650152045007341732401232020103444264026104400733174041014204444445215400630441278
	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                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
GPGTVVPELRSLKPEAQALITQGLYSHCRALLSQLPDTGAPLEDKDTQGLLAVGEALIKIDSGQPHWHLLLADILMAQGSYEEAGTHLEKALHRAPTSEAARARLGLLQLKKGDVPGAARDLQSLAEVDAPDLSCLLHLLEASERQSLAQAAAQEAGTLLDA

1qz2A

0.15

0.13

4.35

1.17

DEthreader

EMEEKLEQSTIVK--E---------------R-------GTVYEGKYKQALLQYKKIVSWLEQRLASHLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLFRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAREKKLYANMFE

4xi0A

0.16

0.15

5.15

1.51

SPARKS-K

---AMGDKAKLYRNISQRCLRRGSPEEALRYLKEWARHEKNDNLGDYQRAVTVFDKVLKLRPNHFMASYRKGAVLLKIKQYKLALPVLEAVVAAAPADARAYYLLGLAYDGDEQLEKGIEAMQKAVDLDPEEIKYHQHLGFMNVRHKTAAEHFTKVMELERS

3sf4A

0.14

4.64

0.50

MapAlign

-----EASCLELALEGERLCKSGDCRAGVSFFEAAVQVGTYFYLHDYAKALEYHHHDLTLAQLEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISKVGARALYNLGNVYHAKGALQAAVDFYEENLSLVRAAGRAFGNLGNTHYLLRDAVIAHEQRLLIAKE

2vq2A

0.13

0.12

4.31

0.33

CEthreader

----ANQVSNIKTQLAMEYMRGQDYRQATASIEDALKSDPKNYLKVNDKAQESFRQALSIKPDSAEINNNYGWFLCRLNRPAESMAYFDKALATYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLGDADYYFKKYQSR

3as4A

0.12

4.33

1.08

MUSTER

RDKGISHAKAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEANPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEALPHFKKANEL

5nnpA

0.15

0.14

4.80

0.63

HHsearch

------TREANLFRTVIRHYEDKQYKRGLKAAEQILKKNPKHGDGKTEEAFALAKEALTIDMKSYICWHVYGILYRTNKNFDEAIKAYKFALKLEPESHQIQRDLAVLQIQMRDYAGYVQSRLNMLKARPQIRQNWTALAIAYHLEGNLEKAETTYEKSLTT

4ui9C3

0.12

0.11

3.94

1.99

FFAS-3D

--------IENMDTFSNLLYVRSMKSELSYLAHNLCEIDKYSLRSQHEKAALYFQRALKLNPRYLGAWTLMGHEYMEMKNTSAAIQAYRHAIEVNKRDYRAWYGLGQTYEILKMPFYCLYYYRRAHQLRPNDSRMLVALGECYEKLNQLVEAKKCYWRAYA-

6b85J

0.20

6.33

0.62

EigenThreader

KIWRTIMLLLVFAILLSAIIWYQITTNQLLLIALMLVVIALSLLNRLSLAAEAYKKAIELDPNDALAWLLLGSVLEKLKRLDEAAEAYKKAIELKPNDASAWKELGKVLEKLGRLDEAAEAYKKAIELDPEDAEAWKELGKVLEKLDEAAEAYKKAIELDPN

3cv0A

0.12

0.11

3.94

1.13

CNFpred

--------IAVHAALAVSHTNEHNANAALASLRAWLLSQPQYE-NEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYM

6vbu42

0.16

0.14

4.53

1.17

DEthreader

-------T-ELLTTLGLLYLQLGIYQKAFEHLGNLTYPTIAGMMHDFDVALTKYKVVACAVIESPPLWNNIGMCFFGKKKYVAAISCLKRANYLAPLDWKILYNLGLVHLTMQQYASAFHFLSAAINFQPKMGELYMLLAVALTNLED--------------

(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	0.7956

(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	5udiA	0.85	2.18	0.149	0.982	model1_5udiA.pdb.gz
2	2vq2A	0.85	2.07	0.130	0.957	model1_2vq2A.pdb.gz
3	5dseA	0.84	2.30	0.105	0.957	model1_5dseA.pdb.gz
4	1w3bA	0.83	2.11	0.130	0.957	model1_1w3bA.pdb.gz
5	4a1sA	0.82	2.21	0.120	0.932	model1_4a1sA.pdb.gz
6	3vtxA	0.81	2.34	0.112	0.926	model1_3vtxA.pdb.gz
7	4xi0A	0.81	2.51	0.161	0.938	model1_4xi0A.pdb.gz
8	3sf4A	0.81	2.45	0.120	0.932	model1_3sf4A.pdb.gz
9	6vbu4	0.81	2.35	0.105	0.957	model1_6vbu4.pdb.gz
10	4ui9C	0.81	2.64	0.111	0.963	model1_4ui9C.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:0046872	1.00	metal ion binding
GO:0003824	0.60	catalytic activity
GO:0042277	0.55	peptide binding
GO:0019899	0.55	enzyme binding
GO:0005048	0.54	signal sequence binding
GO:0051020	0.52	GTPase 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:0038061	1.00	NIK/NF-kappaB signaling
GO:0009987	0.83	cellular process
GO:0044699	0.63	single-organism process
GO:0044763	0.62	single-organism cellular process
GO:0016043	0.62	cellular component organization
GO:0071704	0.60	organic substance metabolic process
GO:0044238	0.60	primary metabolic process
GO:0044237	0.60	cellular metabolic process
GO:0051234	0.58	establishment of localization
GO:0046907	0.57	intracellular transport
GO:1902580	0.56	single-organism cellular localization
GO:0044765	0.56	single-organism transport
GO:0006886	0.56	intracellular protein transport
GO:1902582	0.55	single-organism intracellular transport
GO:0051128	0.55	regulation of cellular component organization
GO:0006996	0.55	organelle organization
GO:1902589	0.54	single-organism organelle organization
GO:0080090	0.54	regulation of primary metabolic process
GO:0060255	0.54	regulation of macromolecule metabolic process
GO:0048523	0.54	negative regulation of cellular process
GO:0034613	0.54	cellular protein localization
GO:0031323	0.54	regulation of cellular metabolic process
GO:2000112	0.53	regulation of cellular macromolecule biosynthetic process
GO:0044710	0.53	single-organism metabolic process
GO:0022615	0.53	protein to membrane docking
GO:0019219	0.53	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.53	regulation of gene expression
GO:0072594	0.52	establishment of protein localization to organelle
GO:0048522	0.52	positive regulation of cellular process
GO:0006355	0.52	regulation of transcription, DNA-templated
GO:1901093	0.51	regulation of protein homotetramerization
GO:1901091	0.51	negative regulation of protein tetramerization
GO:0072663	0.51	establishment of protein localization to peroxisome
GO:0072659	0.51	protein localization to plasma membrane
GO:0046834	0.51	lipid phosphorylation
GO:0046488	0.51	phosphatidylinositol metabolic process
GO:0044743	0.51	intracellular protein transmembrane import
GO:0032463	0.51	negative regulation of protein homooligomerization
GO:0015919	0.51	peroxisomal membrane transport
GO:0010604	0.51	positive regulation of macromolecule metabolic process
GO:0045893	0.50	positive regulation of transcription, DNA-templated
GO:0006357	0.50	regulation of transcription from RNA polymerase II promoter

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:0005634	1.00	nucleus
GO:0044444	0.78	cytoplasmic part
GO:0005737	0.72	cytoplasm
GO:0032991	0.68	macromolecular complex
GO:0044422	0.66	organelle part
GO:0044446	0.65	intracellular organelle part
GO:0043234	0.65	protein complex
GO:0016020	0.53	membrane

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	0.376	1tjcA	0.499	1.90	0.148	0.543	1.14.11.2	71,89,92
2	0.066	1klxA	0.479	3.71	0.157	0.660	3.5.2.6	90
3	0.060	1w3bA	0.834	2.11	0.130	0.957	2.4.1.-	89
4	0.060	3gzkA	0.586	3.98	0.093	0.883	3.2.1.4	NA
5	0.060	1hn0A	0.586	4.68	0.112	0.969	4.2.2.20	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	0.15	1na0B	0.654	2.00	0.222	0.722	1.11	IPT	complex1.pdb.gz	76,107,110,111,138
2	0.15	3kd7B	0.584	1.11	0.242	0.611	1.18	III	complex2.pdb.gz	69,73,76,77,103,104,107,111
3	0.06	1qz2A	0.673	2.17	0.146	0.759	0.93	III	complex3.pdb.gz	70,73,100,104,133

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.