D-I-TASSER A0A1B0GVR7-D1

D-I-TASSER results for A0A1B0GVR7-D1

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

Input Sequence in FASTA format

>A0A1B0GVR7 (95 residues)
MVGKNMSKSLTLKNPGRVAYDSGGIKMFWEKKIEHHARHLQNEDIRVRRSALNKLRVGWA
EQLEGRNKMLQGPGRCPDRVPEATESLHTKDKKAA

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MVGKNMSKSLTLKNPGRVAYDSGGIKMFWEKKIEHHARHLQNEDIRVRRSALNKLRVGWAEQLEGRNKMLQGPGRCPDRVPEATESLHTKDKKAA
Prediction	CCCCCHHHHHCCCCCCSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHCC
Confidence	96520123213578855786106788999999999999999899999999999999999999999997335644323356403677888775219
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MVGKNMSKSLTLKNPGRVAYDSGGIKMFWEKKIEHHARHLQNEDIRVRRSALNKLRVGWAEQLEGRNKMLQGPGRCPDRVPEATESLHTKDKKAA
Prediction	74455155335264341211335304521453155145446446533653015414650442144445417436534742452344135436658
	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

                   |                   |                   |                   |

SS
Seq

CCCCCHHHHHCCCCCCSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHCC
MVGKNMSKSLTLKNPGRVAYDSGGIKMFWEKKIEHHARHLQNEDIRVRRSALNKLRVGWAEQLEGRNKMLQGPGRCPDRVPEATESLHTKDKKAA

5t4oI

0.05

0.04

2.05

1.17

DEthreader

--------LAERKDLDLAKASATDQLKKAKAEAQVIIEQANKRRSQILDEAKAEAEQERTKIVAQAQAEIEAKRARELQVILAVAGAEKIIESKL

5xftA

0.15

4.98

0.48

CEthreader

LLEASGGKVPVIKPDAPYMPDSDVIVVHLEKQHPEGAKLFPNFRAILIGPAAEVADKVAALEEQLAGMDDYLRQHEAQGPLFGGQHLNGTDCSLA

5araT

0.06

2.71

0.52

EigenThreader

EQKIAQLEEVKQASIKQIQDAIDMEKSQQALVQKRHYLFDVQRNNIAMALEVTYRERLHRVYREVKNRLDYHISVQNMMRQKEQEHMINWVEKRV

1rm1C1

0.14

0.06

2.17

0.49

FFAS-3D

----------------------AEASRVYEIIVESVVNEVREDNAGIDEQTLQDLKNIWQKKLTET-----------------------------

1rw6A2

0.09

0.08

3.26

0.87

SPARKS-K

NDRRRLALENYITALQAVPPRPRHVFNMLKKYVRAEQKDRQHTLKHFEHVKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDEL-

2dlaA

0.13

0.07

2.57

0.42

CNFpred

----------------VYLKRIRIWSKAFERNVERGVNMLYEIRDELPRKVLGEIQAFAEEEFGRKFGEIQ------------------------

1ciiA

0.08

3.27

1.17

DEthreader

IKITTAEEWLRLLRNKITSAESAVNSARNNLSARTNEQKHANDALNALLKEKENIRNQLSGINQKIAEEKRKELKKDINFTEFLKSVSEKYGGIW

3ayfA1

0.04

2.14

0.68

MapAlign

QKYGLMDYGTVLGHGSYMGPDYTAEALKVYTEGMQDYKIREQVIKEMVLTDAQVYGLEKVRDYYRDVFTNGDGWGLKKGLIKESDMPKANRAWVA

5wahA

0.14

4.67

0.68

MUSTER

KTAGETSATDTGKREKQLQQWKNNLKNDVDNTHEQKNEFKTKIDETNDSDALLELENQFNETNRLLHIKQHEEVEKDKKAKQQ-KTLKQSDTKV-

1vt4I

0.14

4.67

0.44

HHsearch

KDVQDMPKSILSKHIIMSKDAVSTLRLFWTLLS-KQEEMVPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS-RLQPQALLELRPAKTWVA

(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	0.5401

(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	7ko4P	0.64	2.90	0.080	0.905	model1_7ko4P.pdb.gz
2	6f1tX	0.63	2.99	0.082	0.895	model1_6f1tX.pdb.gz
3	3w3aG	0.62	3.40	0.065	0.926	model1_3w3aG.pdb.gz
4	6r17A	0.62	2.74	0.024	0.863	model1_6r17A.pdb.gz
5	2ocyA	0.62	3.18	0.057	0.884	model1_2ocyA.pdb.gz
6	1ciiA2	0.61	3.16	0.098	0.905	model1_1ciiA2.pdb.gz
7	2otoB	0.61	3.07	0.080	0.874	model1_2otoB.pdb.gz
8	4zryA	0.61	2.88	0.072	0.874	model1_4zryA.pdb.gz
9	5hmoA	0.61	3.02	0.094	0.884	model1_5hmoA.pdb.gz
10	6z47G	0.61	3.36	0.106	0.884	model1_6z47G.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:0060089	0.37	molecular transducer activity
GO:0019215	0.33	intermediate filament binding
GO:1901981	0.32	phosphatidylinositol phosphate binding
GO:0098811	0.32	transcriptional repressor activity, RNA polymerase II activating transcription factor binding
GO:0042623	0.32	ATPase activity, coupled
GO:0035639	0.32	purine ribonucleoside triphosphate binding
GO:0032559	0.32	adenyl ribonucleotide binding
GO:0032550	0.32	purine ribonucleoside binding
GO:0008092	0.32	cytoskeletal protein binding
GO:0005198	0.32	structural molecule activity
GO:0001134	0.32	transcription factor activity, transcription factor recruiting
GO:0001083	0.32	transcription factor activity, RNA polymerase II basal transcription factor binding
GO:0001071	0.32	nucleic acid binding transcription factor activity
GO:0000987	0.32	core promoter proximal region sequence-specific DNA binding
GO:0000977	0.32	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000146	0.32	microfilament motor 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:1902589	0.92	single-organism organelle organization
GO:0044767	0.92	single-organism developmental process
GO:0032501	0.92	multicellular organismal process
GO:0007010	0.92	cytoskeleton organization
GO:0060047	0.88	heart contraction
GO:0055008	0.88	cardiac muscle tissue morphogenesis
GO:0045214	0.88	sarcomere 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:0044464	1.00	cell part
GO:0016020	0.83	membrane
GO:0044424	0.78	intracellular part
GO:0043229	0.72	intracellular organelle
GO:0043231	0.67	intracellular membrane-bounded organelle
GO:0044446	0.61	intracellular organelle part
GO:0044444	0.56	cytoplasmic part
GO:0044430	0.50	cytoskeletal part
GO:0005886	0.50	plasma membrane
GO:0005737	0.50	cytoplasm

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	0.140	2h8nA	0.500	2.54	0.015	0.684	3.5.1.98	60,64
2	0.060	1mc0A	0.399	4.13	0.023	0.695	3.1.4.17	NA
3	0.060	1y2mB	0.485	3.96	0.045	0.821	4.3.1.24	NA
4	0.060	3b8cB	0.442	3.69	0.067	0.716	3.6.3.6	65
5	0.060	1zvuA	0.430	3.22	0.057	0.642	5.99.1.-	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	0.02	1ik9B	0.520	3.73	0.035	0.832	1.25	III	complex1.pdb.gz	60,61,63,64,67,68,71
2	0.01	2w6dB	0.593	3.36	0.070	0.884	0.55	CPL	complex2.pdb.gz	63,64,66
3	0.01	1l4aB	0.526	2.91	0.027	0.747	1.18	III	complex3.pdb.gz	52,55,58,62,65,69
4	0.01	1ujw1	0.398	2.85	0.034	0.568	0.59	III	complex4.pdb.gz	56,57,58,59,60,62,63,65,66,67,70
5	0.01	1w7i0	0.400	3.96	0.045	0.653	0.90	III	complex5.pdb.gz	47,50,52,54,55,57,58,59,60,62,63,66,69

	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.