D-I-TASSER Q8TF40-D3

D-I-TASSER results for Q8TF40-D3

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

Input Sequence in FASTA format

>Q8TF40 (158 residues)
IAIGVIFSLSKDEDENNKFNEFFFSHFPLFESHMNKLKSAIEQAMKMSRRSADASQRSLA
YNRIVDALNEFRTTICNLYTMPRIGEPVWLTMMSGTPEKNHLCYRFMKEFTFLMENASKN
QFLPALITAVLTNHLAWVPTVMPNGQPPIKIFLEKHSS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| IAIGVIFSLSKDEDENNKFNEFFFSHFPLFESHMNKLKSAIEQAMKMSRRSADASQRSLAYNRIVDALNEFRTTICNLYTMPRIGEPVWLTMMSGTPEKNHLCYRFMKEFTFLMENASKNQFLPALITAVLTNHLAWVPTVMPNGQPPIKIFLEKHSS
Prediction	CSSSSSSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCC
Confidence	92799983587712788999999997999999999999999999864123200122238999999999999999999970766688556664158741227999999999999852465226999999999853567765068999983356776169
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| IAIGVIFSLSKDEDENNKFNEFFFSHFPLFESHMNKLKSAIEQAMKMSRRSADASQRSLAYNRIVDALNEFRTTICNLYTMPRIGEPVWLTMMSGTPEKNHLCYRFMKEFTFLMENASKNQFLPALITAVLTNHLAWVPTVMPNGQPPIKIFLEKHSS
Prediction	41000001043576435402410230032043204402420251144444444444434112301501440242024002133043210010233355334104300530151044354410112101000333331121034464343432464378
	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 AttentionPotential. 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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSSSSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCC
IAIGVIFSLSKDEDENNKFNEFFFSHFPLFESHMNKLKSAIEQAMKMSRRSADASQRSLAYNRIVDALNEFRTTICNLYTMPRIGEPVWLTMMSGTPEKNHLCYRFMKEFTFLMENASKNQFLPALITAVLTNHLAWVPTVMPNGQPPIKIFLEKHSS

2fji1

0.09

0.08

2.94

1.00

DEthreader

----SIQINHDIDPI--CPGGLVEYLIAVSNDQMKAADYAVAISSKYGKLV-SKVYEKQITNHLEGTLDGFAEVAQCSSLG--LITLMFDDL-RKPQQIADTLDEYLLDIKPQM--------NSVLFVNFIDNVIGETIIKFDEIYQLFVKVLDNESK

6nzdI

0.61

0.56

16.13

1.26

SPARKS-K

IAISIIFSLCEKEEAQRNFQDFFFSHFPLFESHMNRLKSAIEKA-------------QFYVSRLMEALGEFRGTIWNLYSVPRIAEPVWLTMMSGTLEKNQLCQRFLKEFTLLIEQINKNQFFAALLTAVLTYHLAWVPTVMGAIGSPVRTVVKQKDL

6nzdI

0.63

0.56

16.10

1.33

MUSTER

IAISIIFSLCEKEEAQRNFQDFFFSHFPLFESHMNRLKSAIEKA--------------FYVSRLMEALGEFRGTIWNLYSVPRIAEPVWLTMMSGTLEKNQLCQRFLKEFTLLIEQINKNQFFAALLTAVLTYHLAWVPTVM---NPLWAQLGDLYGA

6nzdI

0.64

0.57

16.27

5.95

HHsearch

IAISIIFSLCEKEEAQRNFQDFFFSHFPLFESHMNRLKSAIEKA-------------QFYVSRLMEALGEFRGTIWNLYSVPRIAEPVWLTMMSGTLEKNQLCQRFLKEFTLLIEQINKNQFFAALLTAVLTYHLAWVPTVM----NPLWAQLDLYGA

6nzdI

0.62

0.55

15.76

1.48

FFAS-3D

-AISIIFSLCEKEEAQRNFQDFFFSHFPLFESHMNRLKSAIEKA-------------QFYVSRLMEALGEFRGTIWNLYSVPRIAEPVWLTMMSGTLEKNQLCQRFLKEFTLLIEQINKNQFFAALLTAVLTYHLAWVPTVMNP---LWAQLGDLYGA

5twvB

0.04

1.89

1.00

DEthreader

--------IGAAIILLAPVQYFVATKLSQAQRTTLEHSNERLKQTNEMLRGLYAESIFSRVEVTRRKEMTSLRAFAVYTSI--SIFM-NTAIPAAILFHILVTPLFL-S---------RSDNTIDQHIPSTLECLSRSTLLCAVSLNWMVRNLADMEI

5yfpC

0.06

2.46

1.00

DEthreader

----IQIHDIDPE-I---D-ECPGGLVEYLIAVSNDQMKAADYVAISSKYGKSKYEKQITNHLEGTLDGFAEVAQCSSLGL-TLMFDDLRKPYQEIWSQAQQIDTLDEYLLDIK-PQM-NSVLFVNFIDNVIGETIIKFLTFAMDFEIFYQLFVLESK

5k7vA

0.12

0.11

4.01

0.64

SPARKS-K

KAIEAIYRLADNHTT----DTFMARAIAAIANLAVTAILAIAALASNHT---TEEFMARAISAIAELAKKAIEAIYRLAD--NHTTD--KFMAAAIEAIALLATLAILAIALLASNHTTEEFMAKAISAIAELAKKAIEAILADNHTSPTYIEKAIEA

5v8kA

0.11

4.07

0.68

MapAlign

VAAMVSFILVLSPDALFVARMHLLMGKALVAQFHFFALIATLWGLHMAFYGILGPPTGLAGNHVAFGAVFFLGGIFHYFEKDWEAVLSVSCQVMGIMFWIGGVFHGAHFAFLPIFVSEFVAAHAIAGGLHFTMVPMWRMVFFSKVSPWTTKVGMKAK-

2q13A1

0.06

2.53

0.56

CEthreader

TRSLLGVFEEDATAISNYMNQLYQAMHRIYDAQNELSAATHLTSKLLKESSTLQQFSKVIDELSSCHAVLSTQLADAMMFPITQFKERDLKEILTLKEVFQIASNDHDAAINRYSRLSKKR-ENDKVKYEVTEDVYTSRKKQHQTMMHYFCALNTLQY

(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	0.6527

(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 AttentionPotential, 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	5a7dL	0.61	3.34	0.074	0.842	model1_5a7dL.pdb.gz
2	5yfpC	0.61	3.81	0.068	0.886	model1_5yfpC.pdb.gz
3	3mmiA	0.61	3.63	0.077	0.854	model1_3mmiA.pdb.gz
4	4y21A	0.61	3.43	0.072	0.842	model1_4y21A.pdb.gz
5	7arhE	0.61	3.80	0.041	0.823	model1_7arhE.pdb.gz
6	6yjjA	0.59	4.25	0.087	0.911	model1_6yjjA.pdb.gz
7	3swhA	0.59	3.35	0.060	0.829	model1_3swhA.pdb.gz
8	5h11A	0.59	3.57	0.079	0.835	model1_5h11A.pdb.gz
9	5u71A1	0.59	3.90	0.038	0.867	model1_5u71A1.pdb.gz
10	4av3A	0.59	4.38	0.057	0.892	model1_4av3A.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:0005085	0.96	guanyl-nucleotide exchange factor 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:0080090	1.00	regulation of primary metabolic process
GO:0060255	1.00	regulation of macromolecule metabolic process
GO:0031323	1.00	regulation of cellular metabolic process
GO:0000122	0.98	negative regulation of transcription from RNA polymerase II promoter
GO:0009987	0.87	cellular process
GO:0048518	0.84	positive regulation of biological process
GO:0048522	0.83	positive regulation of cellular process
GO:0010604	0.83	positive regulation of macromolecule metabolic process
GO:0032270	0.82	positive regulation of cellular protein metabolic process
GO:0007165	0.82	signal transduction
GO:0006950	0.81	response to stress
GO:0001934	0.81	positive regulation of protein phosphorylation
GO:0035556	0.80	intracellular signal transduction
GO:0033554	0.80	cellular response to stress
GO:0044699	0.65	single-organism process
GO:0044763	0.57	single-organism cellular process
GO:0008152	0.57	metabolic process
GO:0048583	0.53	regulation of response to stimulus
GO:0023051	0.53	regulation of signaling
GO:0050790	0.52	regulation of catalytic activity
GO:0032006	0.52	regulation of TOR signaling
GO:0002682	0.52	regulation of immune system process
GO:0050793	0.51	regulation of developmental process
GO:0032269	0.51	negative regulation of cellular protein metabolic process
GO:0032007	0.51	negative regulation of TOR signaling
GO:0030162	0.51	regulation of proteolysis
GO:0030154	0.51	cell differentiation
GO:0009605	0.51	response to external stimulus
GO:0007154	0.51	cell communication
GO:0002376	0.51	immune system process
GO:2000973	0.50	regulation of pro-B cell differentiation
GO:0071704	0.50	organic substance metabolic process
GO:0043154	0.50	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0031929	0.50	TOR signaling
GO:0009267	0.50	cellular response to starvation
GO:0002904	0.50	positive regulation of B cell apoptotic process
GO:0002327	0.50	immature B cell differentiation

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:0005737	1.00	cytoplasm
GO:0043226	0.56	organelle
GO:0043229	0.55	intracellular organelle
GO:0043231	0.53	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	0.060	2uw1B	0.522	5.03	0.039	0.873	1.14.99.6	NA
2	0.060	3lssB	0.509	3.88	0.048	0.715	6.1.1.11	108
3	0.060	3epsA	0.496	3.78	0.059	0.728	2.7.11.5	NA
4	0.060	2vuaA	0.289	5.47	0.046	0.506	3.4.24.69	NA
5	0.060	1y2mB	0.531	4.10	0.092	0.785	4.3.1.24	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	2d0uA	0.576	4.16	0.085	0.861	0.20	HEM	complex1.pdb.gz	88,133,134,135
2	0.01	2nw8A	0.572	4.15	0.085	0.854	0.26	HEM	complex2.pdb.gz	134,138,142
3	0.01	3ebiA	0.490	4.05	0.038	0.753	0.10	BEY	complex3.pdb.gz	1,5,6,19,23
4	0.01	3q43A	0.494	4.30	0.062	0.772	0.12	D66	complex4.pdb.gz	1,5,19,22,23
5	0.01	3bk9C	0.572	4.02	0.043	0.804	0.24	HEM	complex5.pdb.gz	30,78,114,122,156
6	0.01	2nwbA	0.541	4.20	0.072	0.791	0.10	HEM	complex6.pdb.gz	106,109,148,152,153

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.