D-I-TASSER Q8TAL6-D1

D-I-TASSER results for Q8TAL6-D1

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

Input Sequence in FASTA format

>Q8TAL6 (211 residues)
MVFLKFFCMSFFCHLCQGYFDGPLYPEMSNGTLHHYFVPDGDYEENDDPEKCQLLFRVSD
HRRCSQGEGSQVGSLLSLTLREEFTVLGRQVEDAGRVLEGISKSISYDLDGEESYGKYLR
RESHQIGDAYSNSDKSLTELESKFKQGQEQDSRQESRLNEDFLGMLVHTRSLLKETLDIS
VGLRDKYELLALTIRSHGTRLGRLKNDYLKV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MVFLKFFCMSFFCHLCQGYFDGPLYPEMSNGTLHHYFVPDGDYEENDDPEKCQLLFRVSDHRRCSQGEGSQVGSLLSLTLREEFTVLGRQVEDAGRVLEGISKSISYDLDGEESYGKYLRRESHQIGDAYSNSDKSLTELESKFKQGQEQDSRQESRLNEDFLGMLVHTRSLLKETLDISVGLRDKYELLALTIRSHGTRLGRLKNDYLKV
Prediction	CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCSSSSSCCCCCCCCCCCHHHCSSSSSSSCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	9617999999998753244068888877899224554489986567893452588997157667986432135566666678899998887549999998767665214432678899999999999999888989999999987657776434303446899999999999999999982566279999999998201788877776349
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MVFLKFFCMSFFCHLCQGYFDGPLYPEMSNGTLHHYFVPDGDYEENDDPEKCQLLFRVSDHRRCSQGEGSQVGSLLSLTLREEFTVLGRQVEDAGRVLEGISKSISYDLDGEESYGKYLRRESHQIGDAYSNSDKSLTELESKFKQGQEQDSRQESRLNEDFLGMLVHTRSLLKETLDISVGLRDKYELLALTIRSHGTRLGRLKNDYLKV
Prediction	4432311200000220211272303241463302100013342655742530200010155451545654534533324034402112430650141053135325341534642252144315414631452543044034314545566454555144401310342352045224113435442400321043433413414542277
	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                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCSSSSSCCCCCCCCCCCHHHCSSSSSSSCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC
MVFLKFFCMSFFCHLCQGYFDGPLYPEMSNGTLHHYFVPDGDYEENDDPEKCQLLFRVSDHRRCSQGEGSQVGSLLSLTLREEFTVLGRQVEDAGRVLEGISKSISYDLDGEESYGKYLRRESHQIGDAYSNSDKSLTELESKFKQGQEQDSRQESRLNEDFLGMLVHTRSLLKETLDISVGLRDKYELLALTIRSHGTRLGRLKNDYLKV

4ev6A

0.07

2.79

0.48

CEthreader

PKDEELYKLSKKIGISVSDLQIGLDEQEIPRVEEDYLIIYKAPLFEEDITTTSLGIYIKNNLLLLISTKKPRIVFERGIGFLLYHILNEITRSYSRILMNLEDELKLLAGYDREVMEKILGLRKTLVYFHKSLIANRDVLVLLKRKYLPITTKEDRENFEDLYYDTLQLIDMSATYREVLTSMMDITLSLENIKMNQIMKILTMVTTIFAV

6nwdA

0.07

0.06

2.59

0.57

EigenThreader

TYGQFNLVYNAFSFAIAAMFASALF----------FFSAQALVGQRYRLALLVSAIVVSIAGYHYFRIFNSWDAAYVLENLPAKEARPLLIKLTVASVLMIATGYPGEISDDITTRIIWGTVSTIPFAYILYVLWVELSRSL---VRQ---PAAVQTLVRNMRWLLLLSWGVYPIAYLLPMLGVSGTSAAVGVQVGYTIADVLAKPVFGLL

4wheA

0.09

0.05

2.00

0.65

FFAS-3D

------------------------------------------------------------------------NANINALLEDPQKLVRLMIQEMEDTLVEVRSTSA-------RALAEKKQLTRRIEQASAREVEWQEKAELALLKEREDLARAALIEKQKLTDLIKSLEHEVTLVDDTLARMKKEIGELENKLSETRARQQALM------

6egcA

0.19

0.12

3.83

0.67

SPARKS-K

--------------------------------------------------------------------------TRTEIIRELERSLREQEELAKRLKELLRELERLQREGSDEDVRELLREIKELVEEIEKLAREQKYLVEELKRQGNEIIRELERSLREQEELAKRLKELLRELERLQRELREIKELVEEIEKEQKYLVEELKRQ----

4jehB

0.11

0.07

2.41

0.59

CNFpred

------------------------------------------------------------------------------EFFEQVEEIRGFIDKIAENVEEVKRKHSAILAPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSARIRKTQHSTLSRKFVEVMSEYNATQSDYR--ERCKGRIQRQLEITGRTTTSEELED

5nl6A

0.07

0.05

2.14

1.00

DEthreader

-----------------------------------------------QALKENAAKMGVEPSDEYH--Q-VKEQIN-ETKNYRGDKRAFIKEQGDLATLFGQINSKLRGMK-RPV--Y-VAPGLDPKSLEGYIANISEAERALRSKLNTAMRNCLIALRKAFADPANATDAKINEYRTFVTDSLQVATLKAKLEELKQ-VEAQLPPIEEAE

1mhsA

0.07

2.79

0.76

MapAlign

-GFVQEFQAGSIVDPEVVPGDILQVEEGTIIPADGRIVTDDFASSAVKRGEAFVVITATGDNTFVGRAAALVNAASGGSGHFTEVLNGIGTILLILVIFTLLIVWVSSFYRSNPIVQILEFTLAITIIGIIDALKTSRQIFHRMYAYVVYRIALSIHLEIFLGLWLGVVLAVGTWITVTTMYAVLFLQISLTENWLIFQLSGAIFLVDILA

1st6A

0.11

3.94

0.55

MUSTER

AMKRALALIDSKMNQAKGWLRDPNAPPGDAGEQAIRQILDGELCAGKERREILGTCKTLGQMTDQLADLRARGQGATPMAMQKAQQVSQGLDLLTAKVENAARKLEAMTNSKQAIAKKIDAAQNWLADPGSEGEEHIRGIMSEARKVAELEEPKERDDILRSLGEISALTAKLSDLRRHGKGDSPEARALAKQIATSLQNLQSKTNRAVAN

2efkA

0.16

0.09

3.17

0.42

HHsearch

---------------------------------------------------------------------------------GQFEVLERHTQWGLDLLDRYVKFVKERTEVEQAYAKQLRSEVNDFAGQRELVAENLSRVCLELTKYSKQERK-HFQEGRRAQQQLENGFKQLENSKRKFEKAAQTAEVAKQQAHLRSH-AEESKNEYAAQ

2v0oA

0.06

2.66

0.43

CEthreader

STKELADFVRERATIEEAYSRSMTKLAKSASNYSQLGTFAPVWDVFKTSTEKLANCHLDLVRKLQEKEVQKYGEEQVKSHKKTKEEVAGTLEAVQTIQSITQALQKSKSKKATDTYKLYVEKYALAKADFEQKMTETAQKFQDIEETHLIHIKEIIGSLSNAIKEIHLQIGQVHEEFINNMANTTVESLIQKFAESKGTGKERPGLIEFEE

(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	0.4858

(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	7jh5A	0.57	4.42	0.053	0.820	model1_7jh5A.pdb.gz
2	2l6xA	0.56	4.48	0.067	0.791	model1_2l6xA.pdb.gz
3	4ui9I	0.56	4.61	0.082	0.844	model1_4ui9I.pdb.gz
4	4uosA	0.56	2.52	0.092	0.668	model1_4uosA.pdb.gz
5	5xbjA	0.55	3.41	0.103	0.692	model1_5xbjA.pdb.gz
6	4hyjA	0.55	4.19	0.071	0.763	model1_4hyjA.pdb.gz
7	4xtlA	0.54	4.50	0.028	0.763	model1_4xtlA.pdb.gz
8	4qi1A	0.54	4.25	0.090	0.739	model1_4qi1A.pdb.gz
9	1xioA	0.53	4.17	0.061	0.744	model1_1xioA.pdb.gz
10	3a7kA	0.53	4.29	0.064	0.720	model1_3a7kA.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:1904264	1.00	ubiquitin protein ligase activity involved in ERAD pathway
GO:0044822	1.00	poly(A) RNA binding
GO:0098641	0.64	cadherin binding involved in cell-cell adhesion
GO:0003700	0.64	transcription factor activity, sequence-specific DNA 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:0044699	0.96	single-organism process
GO:0009987	0.66	cellular process
GO:0032502	0.64	developmental process
GO:0044767	0.63	single-organism developmental process
GO:0009653	0.63	anatomical structure morphogenesis
GO:0035118	0.62	embryonic pectoral fin morphogenesis
GO:0044763	0.60	single-organism cellular process
GO:0065007	0.55	biological regulation
GO:0050789	0.55	regulation of biological process
GO:0008152	0.55	metabolic process
GO:0071704	0.50	organic substance metabolic process

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:0044444	0.99	cytoplasmic part
GO:0043227	0.89	membrane-bounded organelle
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0005783	0.53	endoplasmic reticulum

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	0.066	1c17M	0.464	3.35	0.070	0.597	3.6.3.14	57
2	0.060	2q80A	0.473	4.75	0.045	0.725	2.5.1.29 2.5.1.10 2.5.1.1	205
3	0.060	2ewgA	0.511	4.22	0.057	0.706	2.5.1.10	NA
4	0.060	3m9uA	0.481	4.68	0.052	0.692	2.5.1.10	NA
5	0.060	1mo7A	0.272	5.80	0.015	0.483	3.6.3.9	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	3qbgB	0.529	4.25	0.064	0.720	0.62	22B	complex1.pdb.gz	9,13,16
2	0.01	2zzlA	0.522	4.27	0.069	0.711	0.72	SOG	complex2.pdb.gz	25,26,27,30
3	0.01	2at9A	0.520	4.30	0.084	0.730	0.48	2DP	complex3.pdb.gz	11,15,16,22
4	0.01	1jv6A	0.518	4.45	0.079	0.739	0.44	LI1	complex4.pdb.gz	11,14,15
5	0.01	1cwqB	0.517	4.28	0.070	0.716	0.45	TRD	complex5.pdb.gz	10,13,17,23,24
6	0.01	1brrA	0.524	4.17	0.069	0.725	0.46	ARC	complex6.pdb.gz	12,19,20
7	0.01	1kg8A	0.477	4.42	0.089	0.687	0.42	LI1	complex7.pdb.gz	13,17,26
8	0.01	1o0aA	0.505	4.17	0.059	0.697	0.41	LI1	complex8.pdb.gz	9,10,17,33
9	0.01	1c8sA	0.434	4.48	0.065	0.621	0.47	LI1	complex9.pdb.gz	115,119,181
10	0.01	3qbgA	0.535	4.33	0.058	0.725	0.42	22B	complex10.pdb.gz	8,12,16

	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.