D-I-TASSER Q5T9L3-D3

D-I-TASSER results for Q5T9L3-D3

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

Input Sequence in FASTA format

>Q5T9L3 (175 residues)
TWMLLFGDIRQGIFYAMLLSFWIIFCGEHMMDQHERNHIAGYWKQVGPIAVGSFCLFIFD
MCERGVQLTNPFYSIWTTDIGTELAMAFIIVAGICLCLYFLFLCFMVFQVFRNISGKQSS
LPAMSKVRRLHYEGLIFRFKFLMLITLACAAMTVIFFIVSQVTEGHWKWGGVTVQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| TWMLLFGDIRQGIFYAMLLSFWIIFCGEHMMDQHERNHIAGYWKQVGPIAVGSFCLFIFDMCERGVQLTNPFYSIWTTDIGTELAMAFIIVAGICLCLYFLFLCFMVFQVFRNISGKQSSLPAMSKVRRLHYEGLIFRFKFLMLITLACAAMTVIFFIVSQVTEGHWKWGGVTVQ
Prediction	CSSSSHHHHHHHHHHHHHHHHHHHHHCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSCCCSSSSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHSSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCSCCC
Confidence	9154246778789999999999999224531552225636776764564124688999988751422149736773375102368999999999999999999999999999989999874315444420122215799999999999999999999998501243333773059
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| TWMLLFGDIRQGIFYAMLLSFWIIFCGEHMMDQHERNHIAGYWKQVGPIAVGSFCLFIFDMCERGVQLTNPFYSIWTTDIGTELAMAFIIVAGICLCLYFLFLCFMVFQVFRNISGKQSSLPAMSKVRRLHYEGLIFRFKFLMLITLACAAMTVIFFIVSQVTEGHWKWGGVTVQ
Prediction	7300002123301110203121110113101346646513412440110010010111131043224143201101236304400100023123013312321231102002304433532451564331303000333332133033113302211013324524042474538
	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                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSSHHHHHHHHHHHHHHHHHHHHHCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSCCCSSSSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHSSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCSCCC
TWMLLFGDIRQGIFYAMLLSFWIIFCGEHMMDQHERNHIAGYWKQVGPIAVGSFCLFIFDMCERGVQLTNPFYSIWTTDIGTELAMAFIIVAGICLCLYFLFLCFMVFQVFRNISGKQSSLPAMSKVRRLHYEGLIFRFKFLMLITLACAAMTVIFFIVSQVTEGHWKWGGVTVQ

5vjsA

0.04

2.04

1.17

DEthreader

QQQLAQEFQQLLQEIQQLGRELLKGELGILRSLQKLEDEEKHIELLETLQQTGQEAQQLLQELQQTGQ-ELWQLGGSGPELRQKHQQLAQKIQQLLQKHQQLGAKILEDEEKHIELLETILGGGD--ELRELLKGELQGIKQYRELQQLGQKAQQLVQKLQQTGQKLWQ-LG---

7kc4B

1.00

28.00

1.86

SPARKS-K

TWMLLFGDIRQGIFYAMLLSFWIIFCGEHMMDQHERNHIAGYWKQVGPIAVGSFCLFIFDMCERGVQLTNPFYSIWTTDIGTELAMAFIIVAGICLCLYFLFLCFMVFQVFRNISGKQSSLPAMSKVRRLHYEGLIFRFKFLMLITLACAAMTVIFFIVSQVTEGHWKWGGVTVQ

3jacA

0.10

3.61

0.74

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGWAFGKHSAATDIASSLSDDQVPLYLRKTVLGKLAFQ--VVLVVAIHIWMFFILPAVTCIYFALSAYQIRCGYPTRILGNFLTKKYNHLNL

3jacA

0.08

3.16

0.59

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

1xmeA2

0.09

0.08

3.09

0.61

MUSTER

PWNPAFVAPVLGLLGFIPGGAGGIVNASFTLDYVVHNTA-WVPGHFHLQVASLVTLTAMGSLYWLLPN---LTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNV----PRRAYIAQVPDAYPAVPMVFNVLAGIVLLVALLLFIYGLFSVLLS-----RERKPELAEA

7kc4B

1.00

28.00

7.26

HHsearch

TWMLLFGDIRQGIFYAMLLSFWIIFCGEHMMDQHERNHIAGYWKQVGPIAVGSFCLFIFDMCERGVQLTNPFYSIWTTDIGTELAMAFIIVAGICLCLYFLFLCFMVFQVFRNISGKQSSLPAMSKVRRLHYEGLIFRFKFLMLITLACAAMTVIFFIVSQVTEGHWKWGGVTVQ

7kc4B

1.00

28.00

1.33

FFAS-3D

TWMLLFGDIRQGIFYAMLLSFWIIFCGEHMMDQHERNHIAGYWKQVGPIAVGSFCLFIFDMCERGVQLTNPFYSIWTTDIGTELAMAFIIVAGICLCLYFLFLCFMVFQVFRNISGKQSSLPAMSKVRRLHYEGLIFRFKFLMLITLACAAMTVIFFIVSQVTEGHWKWGGVTVQ

4f4cA4

0.07

0.06

2.65

0.63

EigenThreader

KKAGVLKGLFLGISFGAMQASNFISFALAFYIGVGWVHALMFLVLAAAQGICSFLMTFFMGIASESLTRDLRNKLFRNVLSLATDVPNLRTAIDFRFSTVITTLVSMVAGIGLAFFYGRGRRFTG-----MRVLRVMYAITIST----STATSYFPEYAKATFAGGIIFGMLRKI

7kc4B

1.00

28.00

1.42

CNFpred

TWMLLFGDIRQGIFYAMLLSFWIIFCGEHMMDQHERNHIAGYWKQVGPIAVGSFCLFIFDMCERGVQLTNPFYSIWTTDIGTELAMAFIIVAGICLCLYFLFLCFMVFQVFRNISGKQSSLPAMSKVRRLHYEGLIFRFKFLMLITLACAAMTVIFFIVSQVTEGHWKWGGVTVQ

6w1wA

0.05

2.18

1.17

DEthreader

NVDTALNL-TDVYTDFLGISNYDATCNSLSRTEILRAV--MN-EFMQQKPKIFAQIITSFINYQTTFD---CAQN-QWIECLQLLQKTLKQNITLTNEAQQVFTKSYNQAKNAEELLASSIQGWLMIITKAIIQTLSNMSEEFLKIDDSLPALS-LLWQDELDKVNELINA-LQS

(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	0.7094

(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	5vjsA	0.79	2.77	0.047	0.971	model1_5vjsA.pdb.gz
2	7nmqA	0.73	3.64	0.063	0.977	model1_7nmqA.pdb.gz
3	6ezvX	0.72	3.53	0.035	0.960	model1_6ezvX.pdb.gz
4	6w1wA	0.72	3.56	0.035	0.977	model1_6w1wA.pdb.gz
5	4k1pA	0.70	3.44	0.054	0.949	model1_4k1pA.pdb.gz
6	6grjG1	0.69	3.38	0.041	0.914	model1_6grjG1.pdb.gz
7	1qoyA	0.69	3.70	0.029	0.960	model1_1qoyA.pdb.gz
8	2nrjA	0.69	4.02	0.046	0.966	model1_2nrjA.pdb.gz
9	5lp2B	0.68	3.83	0.059	0.937	model1_5lp2B.pdb.gz
10	6gy6A	0.68	3.92	0.047	0.954	model1_6gy6A.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:0017147	0.91	Wnt-protein 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:0065007	0.94	biological regulation
GO:0050794	0.93	regulation of cellular process
GO:0048518	0.87	positive regulation of biological process
GO:0048522	0.86	positive regulation of cellular process
GO:0044699	0.86	single-organism process
GO:0050714	0.85	positive regulation of protein secretion
GO:0030177	0.85	positive regulation of Wnt signaling pathway
GO:0044707	0.67	single-multicellular organism process
GO:0032502	0.67	developmental process
GO:0044767	0.66	single-organism developmental process
GO:0007389	0.66	pattern specification process
GO:0009653	0.54	anatomical structure morphogenesis
GO:0061357	0.51	positive regulation of Wnt protein secretion

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:0044444	1.00	cytoplasmic part
GO:0016020	0.93	membrane
GO:0044446	0.86	intracellular organelle part
GO:0044425	0.84	membrane part
GO:0044431	0.80	Golgi apparatus part
GO:0044459	0.75	plasma membrane part
GO:0044432	0.75	endoplasmic reticulum part
GO:0098590	0.74	plasma membrane region
GO:0044440	0.72	endosomal part
GO:0097458	0.71	neuron part
GO:0044433	0.71	cytoplasmic vesicle part
GO:0016021	0.64	integral component of membrane
GO:0031227	0.63	intrinsic component of endoplasmic reticulum membrane
GO:0005887	0.63	integral component of plasma membrane
GO:0045211	0.62	postsynaptic membrane
GO:0042734	0.62	presynaptic membrane
GO:0031594	0.62	neuromuscular junction
GO:0031302	0.62	intrinsic component of endosome membrane
GO:0031228	0.62	intrinsic component of Golgi membrane
GO:0030285	0.62	integral component of synaptic vesicle membrane
GO:0043226	0.58	organelle
GO:0043229	0.56	intracellular organelle
GO:0043227	0.56	membrane-bounded organelle
GO:0043231	0.55	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	1frvB	0.649	3.69	0.064	0.874	1.12.2.1	NA
2	0.060	3gtdA	0.594	4.18	0.069	0.903	4.2.1.2	NA
3	0.060	1jswB	0.576	4.43	0.037	0.909	4.3.1.1	NA
4	0.060	2pnrF	0.558	3.30	0.050	0.731	2.7.11.2	56,99
5	0.060	2occN	0.574	4.17	0.043	0.857	1.9.3.1	4,65

	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	0.03	1xly1	0.595	3.34	0.118	0.800	0.52	III	complex1.pdb.gz	37,38,41,42,44,45,48,49,86,87,91,92,94,98,101,104,105,108,112,115,116,119,120
2	0.03	1cc1L	0.643	3.35	0.060	0.840	0.70	H2S	complex2.pdb.gz	3,5,6,64
3	0.02	1e3dB	0.634	3.90	0.038	0.886	0.80	H2S	complex3.pdb.gz	8,61,64,65
4	0.01	1gzmA	0.616	3.88	0.059	0.834	0.51	UUU	complex4.pdb.gz	63,67,70,75,76

	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.