D-I-TASSER A0A1B0GUV8-D1

D-I-TASSER results for A0A1B0GUV8-D1

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

Input Sequence in FASTA format

>A0A1B0GUV8 (181 residues)
MALEKGPLLLLALGLGLAGAQKALEEVPVQPGFNAQKVEGRWLTLQLAANHADLVSPADP
LRLALHSIRTRDGGDVDFVLFWKGEGVCKETNITVHPTQLQGQYQGSFEGGSMHVCFVST
DYSNLILYVRFEDDEITNLWVLLARRMLEDPKWLGRYLEYVEKFHLQKAPVFNIDGPCPP
P

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MALEKGPLLLLALGLGLAGAQKALEEVPVQPGFNAQKVEGRWLTLQLAANHADLVSPADPLRLALHSIRTRDGGDVDFVLFWKGEGVCKETNITVHPTQLQGQYQGSFEGGSMHVCFVSTDYSNLILYVRFEDDEITNLWVLLARRMLEDPKWLGRYLEYVEKFHLQKAPVFNIDGPCPPP
Prediction	CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCSSSSSSSSSSCCHHHHCCCCCCSSSSSSSSSCCCCCSSSSSSSSCCCSSSSSSSSSSSCCCCCSSSSSCCCCSSSSSSSSCCCCSSSSSSSSCCCCSSSSSSSSSCCCCCCHHHHHHHHHHHHHHCCCHHHSSSCCCCCCCC
Confidence	9631369999999999986222245687688998567525649999975781340037861689999999699959999999619917999999998588988998327964899999518987999999638955999999968999999999999999999198967778668989989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MALEKGPLLLLALGLGLAGAQKALEEVPVQPGFNAQKVEGRWLTLQLAANHADLVSPADPLRLALHSIRTRDGGDVDFVLFWKGEGVCKETNITVHPTQLQGQYQGSFEGGSMHVCFVSTDYSNLILYVRFEDDEITNLWVLLARRMLEDPKWLGRYLEYVEKFHLQKAPVFNIDGPCPPP
Prediction	6525313011111000000023337714336515374133311000001325533666441411123030377240201021346531442323044375414031435454220100204342000002156644221010103447246711640251067370466201505771468
	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                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCSSSSSSSSSSCCHHHHCCCCCCSSSSSSSSSCCCCCSSSSSSSSCCCSSSSSSSSSSSCCCCCSSSSSCCCCSSSSSSSSCCCCSSSSSSSSCCCCSSSSSSSSSCCCCCCHHHHHHHHHHHHHHCCCHHHSSSCCCCCCCC
MALEKGPLLLLALGLGLAGAQKALEEVPVQPGFNAQKVEGRWLTLQLAANHADLVSPADPLRLALHSIRTRDGGDVDFVLFWKGEGVCKETNITVHPTQLQGQYQGSFEGGSMHVCFVSTDYSNLILYVRFEDDEITNLWVLLARRMLEDPKWLGRYLEYVEKFHLQKAPVFNIDGPCPPP

3qkgA

0.16

0.14

4.59

1.33

DEthreader

----------------------D--NIQVQENFNISRIYGKWYNLAIGSTSPWLKIMDR-MTVSTLVLGEGTEAEISMTSTRWRKGVCEETSGAYEKTDTDGKFLYHKKWITMESYVVHTNYEYAIFLTKKFSRHPTITAKLYGRAPQLRETLLQDFRVVAQGVGIPEDSIFTMADRGECV

5x7yA

0.18

0.15

5.03

2.37

SPARKS-K

--------------------------DVVKGNFDISKISGDWYSILLASDIKEKIEENGSMRVFVKDIEVLSNSSLIFTMHTKVNGKCTKISLICNKTEKDGEYDVVHDG-YNLFRIIETAYEDYIIFHLNNQEQEFQLMELYGRKPDVSPKVKEKFVRYCQGMEIPKENILDLTQVCLQA

3fiqB

0.13

0.10

3.66

1.08

MapAlign

--------------------------HENLD-ISPSEVNGDWRTLYIVADNVEKVAEGGSLRAYFQHMECGECQELKIIFNVKLDSECQTHTVVGQKH-EDGRYTTDY-SGRNYFHVLKKTDDIIFFHNVNVDGKETNVILVAGKREDLNKAQKQELRKLAEEYNIPNENTQHLVPCNQ--

3qkgA

0.17

0.14

4.75

0.79

CEthreader

------------------------DNIQVQENFNISRIYGKWYNLAIGSTSPWLKKIMDRMTVSTLVLGEGTEAEISMTSTRWRKGVCEETSGAYEKTDTDGKFLYHKSKITMESYVVHTNYEYAIFLTKKFSHGPTITAKLYGRAPQLRETLLQDFRVVAQGVGIPEDSIFTMADRGECV

5x7yA

0.18

0.15

5.03

1.92

MUSTER

--------------------------DVVKGNFDISKISGDWYSILLASDIKEKIEENGSMRVFVKDIEVLSNSSLIFTMHTKVNGKCTKISLICNKTEKDGEYDVVHDG-YNLFRIIETAYEDYIIFHLNNQEQEFQLMELYGRKPDVSPKVKEKFVRYCQGMEIPKENILDLVDRCLQA

5x7yA

0.18

0.15

5.03

1.91

HHsearch

--------------------------DVVKGNFDISKISGDWYSILLASDIKEKIEENGSMRVFVKDIEVLSNSSLIFTMHTKVNGKCTKISLICNKTEKDGEYDVVHDGY-NLFRIIETAYEDYIFHLNNVNEQEFQLMELYGRKPDVSPKVKEKFVRYCQGMEIPKENILDLTDRCLQA

5x7yA

0.18

0.15

5.02

2.28

FFAS-3D

---------------------------VVKGNFDISKISGDWYSILLASDIKEKIEENGSMRVFVKDIEVLSNSSLIFTMHTKVNGKCTKISLICNKTEKDGEYDVVHDG-YNLFRIIETAYEDYIIFHLNNQEQEFQLMELYGRKPDVSPKVKEKFVRYCQGMEIPKENILDLTQVCLQ-

2e4jA

0.16

0.14

4.76

1.28

EigenThreader

---------------------GSQGHDTVQPNFQQDKFLGRWYSAGLASNSSWFREKKAVLYMCKTVVAPSTEGGLNLTSTFLRKNQAETKIMVLQPAGAPGHYTYSSSGSIHSVSVVEANDEYALLFSRGTKGQDFRMATLYSRTQTLKDELKEKFTTFSKAQGLTEEDIVFLPQPDKAI

1ew3A

0.18

0.15

5.02

2.28

CNFpred

---------------------------VAIRNFDISKISGEWYSIFLASDVKEKIEENGSMRVFVDVIRALDNSSLYAEYQTKVNGECTEFPMVFDKTEEDGVYSLNYD-GYNVFRISEFENDEHIILYLVNFDRPFQLFEFYAREPDVSPEIKEEFVKIVQKRGIVKENIIDLTDRCFQL

5ez2A

0.13

0.12

3.99

1.33

DEthreader

---------------KP-GRC-P--KPAVQEDFDAARYLGVWYDIQRLP-N--KF---QKGECATATYSLSPGVGFSVFNRERLAGTIKSVIGSAIAEDCEAKLQFFHNAAPVPYWVLSTDYNYALVYSCINLGSHAAYASIVSRQPTLPEETIKKLQGTMSSFGVGVDTLLTTQDACSMN

(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	0.7652

(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	3qkgA	0.78	2.24	0.166	0.867	model1_3qkgA.pdb.gz
2	1gm6A	0.77	1.67	0.191	0.834	model1_1gm6A.pdb.gz
3	5nghA	0.77	1.75	0.212	0.840	model1_5nghA.pdb.gz
4	2qosC	0.77	1.94	0.200	0.856	model1_2qosC.pdb.gz
5	1epbB	0.76	2.11	0.124	0.845	model1_1epbB.pdb.gz
6	1ew3A	0.76	1.69	0.197	0.829	model1_1ew3A.pdb.gz
7	1df3A	0.74	2.08	0.194	0.834	model1_1df3A.pdb.gz
8	2hzqA	0.74	2.60	0.161	0.856	model1_2hzqA.pdb.gz
9	1aqbA	0.73	2.63	0.135	0.851	model1_1aqbA.pdb.gz
10	2xstA	0.73	1.86	0.228	0.801	model1_2xstA.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:0036094	0.85	small molecule binding
GO:0005215	0.84	transporter activity
GO:0043167	0.66	ion binding
GO:0005506	0.62	iron ion binding
GO:0008289	0.59	lipid binding
GO:0003824	0.56	catalytic 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	0.94	single-organism process
GO:0009987	0.91	cellular process
GO:0044763	0.90	single-organism cellular process
GO:0065007	0.86	biological regulation
GO:0050896	0.84	response to stimulus
GO:0006950	0.76	response to stress
GO:0008152	0.75	metabolic process
GO:0065008	0.72	regulation of biological quality
GO:0044710	0.72	single-organism metabolic process
GO:0048878	0.71	chemical homeostasis
GO:0006810	0.71	transport
GO:0050789	0.70	regulation of biological process
GO:0006952	0.68	defense response
GO:0044765	0.66	single-organism transport
GO:0071704	0.63	organic substance metabolic process
GO:0045087	0.63	innate immune response
GO:0015891	0.63	siderophore transport
GO:0006879	0.63	cellular iron ion homeostasis
GO:0006811	0.63	ion transport
GO:0044238	0.62	primary metabolic process
GO:0044237	0.62	cellular metabolic process
GO:0006629	0.60	lipid metabolic process
GO:0050794	0.59	regulation of cellular process
GO:0044281	0.59	small molecule metabolic process
GO:0042221	0.59	response to chemical
GO:0048519	0.55	negative regulation of biological process
GO:0051716	0.54	cellular response to stimulus
GO:0051239	0.54	regulation of multicellular organismal process
GO:0048523	0.54	negative regulation of cellular process
GO:0060255	0.52	regulation of macromolecule metabolic process
GO:0016043	0.51	cellular component organization

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:0005576	1.00	extracellular region
GO:0044421	0.95	extracellular region part
GO:0005615	0.94	extracellular space
GO:0044464	0.78	cell part
GO:0043227	0.76	membrane-bounded organelle
GO:0044424	0.73	intracellular part
GO:0044444	0.68	cytoplasmic part
GO:0043231	0.61	intracellular membrane-bounded organelle

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	0.212	2e4jA	0.683	3.05	0.152	0.840	5.3.99.2	30,47,104,127,145
2	0.060	1qqwB	0.448	3.95	0.033	0.624	1.11.1.6	NA
3	0.060	1ei5A	0.470	3.60	0.085	0.635	3.4.11.19	NA
4	0.060	2gq3A	0.429	5.39	0.056	0.724	2.3.3.9	NA
5	0.060	3gh4A	0.427	5.43	0.037	0.735	3.2.1.52	121

	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	0.17	1fenA	0.724	2.75	0.134	0.856	0.84	AZE	complex1.pdb.gz	60,61,68,78,84,91,106,115
2	0.16	3uexA	0.742	2.36	0.190	0.845	0.81	STE	complex2.pdb.gz	35,68,76,93,115,117
3	0.14	1epbB	0.763	2.11	0.124	0.845	0.99	REA	complex3.pdb.gz	33,35,38,42,78,106,108,113,117,125,127,129,141,143
4	0.06	2gj5A	0.747	2.16	0.188	0.845	0.84	VD3	complex4.pdb.gz	60,61,63,78,82,84,92,107,127,129
5	0.03	1epa0	0.737	2.23	0.119	0.829	1.01	III	complex5.pdb.gz	147,150,152,154,155,158,168,169,172,173,176

	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.