D-I-TASSER Q8TAM2-D2

D-I-TASSER results for Q8TAM2-D2

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

Input Sequence in FASTA format

>Q8TAM2 (128 residues)
DGPFINLSRLNLTKYSQKPKLAKALFEYIFHHENDVKTIHLEDVVLHLGIYPFLLRNKNH
IEKNALDLAALSTEHSQYKDWWWKVQIGKCYYRLGMYREAEKQFKSALKQQEMVDTFLYL
AKVYVSLD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| DGPFINLSRLNLTKYSQKPKLAKALFEYIFHHENDVKTIHLEDVVLHLGIYPFLLRNKNHIEKNALDLAALSTEHSQYKDWWWKVQIGKCYYRLGMYREAEKQFKSALKQQEMVDTFLYLAKVYVSLD
Prediction	CCCSCCHHHCCHHHHHHCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC
Confidence	99610034358899971615579999999997052456666555421013454434444331138999998640367888219999999999929907999999999992997699999999999729
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| DGPFINLSRLNLTKYSQKPKLAKALFEYIFHHENDVKTIHLEDVVLHLGIYPFLLRNKNHIEKNALDLAALSTEHSQYKDWWWKVQIGKCYYRLGMYREAEKQFKSALKQQEMVDTFLYLAKVYVSLD
Prediction	83442424413154117445103100210021244243344343325445444444544534552242234336467252110223203012214234501530450166373140002003103438
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCSCCHHHCCHHHHHHCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC
DGPFINLSRLNLTKYSQKPKLAKALFEYIFHHENDVKTIHLEDVVLHLGIYPFLLRNKNHIEKNALDLAALSTEHSQYKDWWWKVQIGKCYYRLGMYREAEKQFKSALKQQEMVDTFLYLAKVYVSLD

2c0mC

0.12

0.10

3.60

1.17

DEthreader

----K---GY--MAWQYLTTQAEEELVSFTNESLQRACLWVKELFLAVRL-------SG-EYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPYIRSRYNLGISCINLG

4cgvA

0.14

0.12

4.30

1.09

SPARKS-K

HVDSQKALVLKGNKYFKKYDEAIDCYTKGMDADPYNPVLPTNRASAYFRL---------KKFAVAESDCNLAVALNR-SYTKAYSRRGAARFALQKLEEAKKDYERVLELEPNFEATNELRKISQALA

6vfjB

0.15

0.12

4.22

1.20

FFAS-3D

------------ELAYKLGEYRIAIRAY-------RIALKRDPNNAEAWYNLGNAYYKQGRYREAIEYYQKALELDP-NNAEAWYNLGNAYYERGEYEEAIEYYRKALRLDPNADAMQNLLNAKMREE

3cvnA

0.11

0.09

3.39

1.17

DEthreader

-DINHARMLD-K---------DIAVHAALAVHAASLRAWLSEQLGSVN--L----FAAPNEYRECRTLLHAALEMNP-NDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDAQLWNKLGATLANGN

2vyiA

0.11

0.10

3.66

1.08

SPARKS-K

LEDSAEAERLKGNEQMKNFEAAVHFYGKAIELNPANAVYFCNRAAAYSKL---------GNYAGAVQDCERAICIDP-AYSKAYGRMGLALSSLNKHVEAVAYYKKALELDPNETYKSNLKIAELKLR

6vl6A

0.15

0.13

4.48

0.47

MapAlign

--LAEKMYKA-GNAMYRQYTIAIIAYTLALLKDPNNAEAWYNLGNAAY---------KKGEYDEAIEAYQKALE-LDPNNAEAWYNLGNAYYKQGDYDEAIEYYKKALRLDRNVDAIENLIEAEEKQ-

6vl6A

0.15

0.13

4.50

0.34

CEthreader

MGNLAEKMYKAGNAMYRQYTIAIIAYTLALLKDPNNAEAWYNLGNAAYKKGE---------YDEAIEAYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYKKALRLDPNVDAIENLIEAEEKQ-

6vbu8

0.35

0.34

10.27

0.85

MUSTER

SGPFINLSRLNLAKYAQKPKLAKALFEYIFHHENDLDLAALSTEHSQYKDWWWKVQYRLGLYREAEKQFKSALKQQ--EMVDTFLYLAKVYISLDQPLTALNLFKQGLDKFPEVTLLCGIARIYEEMN

6vbu8

0.38

11.11

0.59

HHsearch

SGPFINLSRLNLAKYAQKPKLAKALFEYIFHHENDVKTALLAALSTEHSQYKDWIGYRLGLYREAEKQFKSALKQQ-E-MVDTFLYLAKVYISLDQPLTALNLFKQGLDKFPEVTLLCGIARIYEEMN

5aemA3

0.19

0.12

4.02

1.17

FFAS-3D

---------------------------------------------ADLYFEAATALTRAEKYKEAIDFFTPLLSLEEWRTTDVFKPLARCYKEIESYETAKEFYELAIKSEPDLDIRVSLAEVYYRLN

(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	0.5871

(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	5dseA	0.67	3.28	0.109	0.859	model1_5dseA.pdb.gz
2	3cvnA	0.67	2.77	0.144	0.812	model1_3cvnA.pdb.gz
3	6af0A1	0.66	3.03	0.173	0.852	model1_6af0A1.pdb.gz
4	2pl2A	0.66	3.10	0.173	0.852	model1_2pl2A.pdb.gz
5	4eqfA	0.66	2.65	0.165	0.805	model1_4eqfA.pdb.gz
6	5nnpA	0.66	3.26	0.114	0.859	model1_5nnpA.pdb.gz
7	2c0mC	0.65	2.86	0.144	0.805	model1_2c0mC.pdb.gz
8	7cc7A	0.65	2.87	0.070	0.828	model1_7cc7A.pdb.gz
9	4a1sA	0.65	3.58	0.099	0.867	model1_4a1sA.pdb.gz
10	3ck9B	0.65	3.47	0.103	0.891	model1_3ck9B.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:0001103	1.00	RNA polymerase II repressing transcription factor binding
GO:0003824	0.61	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:0042384	1.00	cilium assembly
GO:0044707	0.93	single-multicellular organism process
GO:0007389	0.85	pattern specification process
GO:0006928	0.82	movement of cell or subcellular component
GO:0051234	0.70	establishment of localization
GO:0048856	0.62	anatomical structure development
GO:0009653	0.62	anatomical structure morphogenesis
GO:1902580	0.53	single-organism cellular localization
GO:0046907	0.53	intracellular transport
GO:0044765	0.53	single-organism transport
GO:0040011	0.53	locomotion

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:0044441	1.00	ciliary part
GO:0043231	1.00	intracellular membrane-bounded organelle
GO:0005929	1.00	cilium
GO:0036064	0.88	ciliary basal body
GO:0034464	0.86	BBSome
GO:0005634	0.82	nucleus
GO:0005813	0.74	centrosome
GO:0044444	0.52	cytoplasmic part

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	0.069	1tjcA	0.552	2.40	0.070	0.656	1.14.11.2	68
2	0.060	1w3bB	0.631	3.18	0.087	0.812	2.4.1.-	NA
3	0.060	1ujkB	0.456	4.57	0.076	0.797	3.4.23.46	NA
4	0.060	1gaiA	0.526	4.03	0.068	0.820	3.2.1.3	42
5	0.060	2c0lA	0.624	3.41	0.130	0.836	2.3.1.176	99

	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	3kd7E	0.567	2.36	0.157	0.648	0.94	III	complex1.pdb.gz	82,85,86,89,93,119
2	0.15	1fchB	0.661	2.72	0.154	0.812	0.47	III	complex2.pdb.gz	85,86,89,90,92,115,118,119
3	0.12	1na0B	0.623	3.18	0.136	0.789	0.79	IPT	complex3.pdb.gz	45,89,92,93
4	0.09	3axyJ	0.605	3.70	0.118	0.859	0.42	III	complex4.pdb.gz	38,82,85,92,93,118,119,122
5	0.09	1qz2A	0.621	3.11	0.106	0.789	0.41	III	complex5.pdb.gz	90,93,122,126
6	0.08	1o9fA	0.616	3.75	0.108	0.836	0.44	FSC	complex6.pdb.gz	89,92,93,118,119
7	0.07	3axyD	0.605	3.70	0.118	0.859	0.40	III	complex7.pdb.gz	86,89,96,122,125
8	0.03	2xcbA	0.615	3.11	0.163	0.797	0.78	III	complex8.pdb.gz	86,89,116,120

	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.