D-I-TASSER P49356-D1

D-I-TASSER results for P49356-D1

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

Input Sequence in FASTA format

>P49356 (199 residues)
MASPSSFTYYCPPSSSPVWSEPLYSLRPEHARERLQDDSVETVTSIEQAKVEEKIQEVFS
SYKFNHLVPRLVSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRA
LHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQ
HFGSGAMLHDVVLGVPENA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MASPSSFTYYCPPSSSPVWSEPLYSLRPEHARERLQDDSVETVTSIEQAKVEEKIQEVFSSYKFNHLVPRLVSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQHFGSGAMLHDVVLGVPENA
Prediction	CCCCCCCCCCCCCCCCCCCCCCHHHHCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCSSCCCCCC
Confidence	9987776443577776433420444153567888899999974025799877751078899999998386311699999999999558877870678899875413679999999986665135663224555424899999999998288889867898999861367999999999178787767888621488779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MASPSSFTYYCPPSSSPVWSEPLYSLRPEHARERLQDDSVETVTSIEQAKVEEKIQEVFSSYKFNHLVPRLVSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQHFGSGAMLHDVVLGVPENA
Prediction	7445551441333643433454042045752454135400420212523421231110100000010053045032630140014203546100213443442100010000003002422445554445343201126103400030123641002431754101100000000000022572663424000003668
	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                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCHHHHCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCSSCCCCCC
MASPSSFTYYCPPSSSPVWSEPLYSLRPEHARERLQDDSVETVTSIEQAKVEEKIQEVFSSYKFNHLVPRLVSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQHFGSGAMLHDVVLGVPENA

1ft1B

0.59

0.55

15.72

1.17

DEthreader

-DGSVDVRSYCSVALTNIITPDLFEGTAEWIARCQNWEGGI-------MEAH--GGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAGDPALSMSH-WMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQHFGMLHDVV--MGV-PENV

1ft1B

0.67

0.66

18.75

2.08

SPARKS-K

GEVDVRSAYCAASVASLTNIIDLFEGTAEWIARCQNWEGGIGGVPGM----EAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQHFGSGAMLHDVVMGVPENV

1ft1B

0.68

0.64

18.17

0.97

MapAlign

---------DGSFLMHVGGEVDVRSAYCAASVACQNWEGGIGGVPGME--AH--GGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQHFGSGAMLHDVVMGVPENV

1ft1B

0.67

0.66

18.75

0.84

CEthreader

GEVDVRSAYCAASVASLIITPDLFEGTAEWIARCQNWEGGIGGVPG----MEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQHFGSGAMLHDVVMGVPENV

1ft1B

0.67

0.66

18.75

1.71

MUSTER

GEVDVRSAYCAASVASLIITPDLFEGTAEWIARCQNWEGGIGGV----PGMEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQHFGSGAMLHDVVMGVPENV

3q73B

0.30

0.29

8.84

2.99

HHsearch

GEVDVRGTYCLLVVATLLDTPELLHNVDKFVSACQTYEGGFARV----SMAEAHGGYTSCSLNSHFLLTSVPLIDANAALRWTVLQQGEEGGGFRGRTNKLVDGCYSWWVGGGAPVAEELVRREKSR--KVIPPIFNRVALQEFTLVAAQQSTGGLRDKPGKRPDQYHTCNNLSGLSIAQHKMSHSPSTEIIVGGKDNR

1tnzL

0.14

0.13

4.44

1.65

FFAS-3D

-SGH-IAMTYTGLSCLIILGDDLSRVDKEACLAGL-----RALQLEDGSGSENDMRFVYCASCICYMLNNWSGMDMKKAISYIRRSMSY-DNGLAQGAGLESHGGSTFCGIASLCLMGKLEEVFSEKELNKIFQYTNFEKNRNYILSTQDRLVGGFAKWPDSHPDALHAYFGICGLSLMEESGICKVHP----------

4l9pB

0.30

8.99

1.13

EigenThreader

FTVCEGGEEDVRGAYCAMVVHALLDLPEYLSR--CQTYEGGISGSPGSEAHGAYAFCALACLCLRPEVVVPRYMNIATLLPWLSARQYAPEGGFSGRTNKLVDGCYSHWVWPLVQAALDGTQPLAGPKRSSVGNLYSREGLTRYILSCCQCKLGGLRDKPGKHPDSYHTCYALTGLSTVQASDGQGSDIGVFTENDRLV

1jcqB

0.71

0.67

19.14

2.06

CNFpred

-----RSAYCAASVASNIITPDLFEGTAEWIARCQNWEGGIGGVPG----MEAHGGYTFCGLAALVILKRERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQHFGSGAMLHDVVLGVPENA

4l9pB

0.34

0.31

9.19

1.17

DEthreader

--DGGEDVRYCVVHLLDLPLATFTDGLPEYLSRCQTYEGGI-------SEAH--GAYAFCALACLCLLGVVRYMNIATLLPWLSARQYAPEGGFSGRTNKLVDGCYSHWVGNCWPLVQAALDGTRSS-VG---NLYSREGLTRYILSCCQCKLGGLRDKPGKHPDSYHTCYALTGLSTVQYYHDPNFASDGVFT--NDR

(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	0.8013

(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	1ft1B	0.96	0.75	0.667	0.980	model1_1ft1B.pdb.gz
2	3q73B	0.90	1.98	0.318	0.970	model1_3q73B.pdb.gz
3	4l9pB	0.89	2.03	0.301	0.965	model1_4l9pB.pdb.gz
4	4ydeB	0.85	2.14	0.293	0.925	model1_4ydeB.pdb.gz
5	3draB	0.78	2.21	0.222	0.859	model1_3draB.pdb.gz
6	1dceB	0.76	2.14	0.164	0.839	model1_1dceB.pdb.gz
7	3sqcA	0.65	3.31	0.117	0.809	model1_3sqcA.pdb.gz
8	1tnzL2	0.64	2.47	0.123	0.734	model1_1tnzL2.pdb.gz
9	1zvrA2	0.37	5.89	0.029	0.683	model1_1zvrA2.pdb.gz
10	1kbiA2	0.34	5.18	0.078	0.573	model1_1kbiA2.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:0008318	1.00	protein prenyltransferase activity
GO:0004660	0.70	protein farnesyltransferase activity
GO:0004661	0.54	protein geranylgeranyltransferase 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:0018342	0.99	protein prenylation
GO:0018343	0.73	protein farnesylation
GO:0018344	0.53	protein geranylgeranylation

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:1990234	1.00	transferase complex
GO:0044424	1.00	intracellular part
GO:0044444	0.88	cytoplasmic part
GO:0005965	0.59	protein farnesyltransferase complex

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	0.222	1ft1B	0.965	0.75	0.667	0.980	2.5.1.58 2.5.1.-	106
2	0.112	1dceB	0.761	2.14	0.164	0.839	2.5.1.60 2.5.1.-	106
3	0.105	1n4pB	0.760	1.92	0.244	0.824	2.5.1.59 2.5.1.-	106
4	0.060	1hzfA	0.663	3.61	0.097	0.874	3.4.21.43	NA
5	0.060	1i8qA	0.637	4.13	0.088	0.909	4.2.2.1	109

	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	0.79	3eu5B	0.965	0.73	0.667	0.980	0.99	GBO	complex1.pdb.gz	6,54,56,57,97,100,106,109,167
2	0.76	3e37B	0.966	0.71	0.682	0.980	0.80	ED5	complex2.pdb.gz	56,57,60,103,105,109,165,167,168
3	0.75	3e32B	0.965	0.74	0.667	0.980	0.83	ED2	complex3.pdb.gz	103,105,165,167,168
4	0.67	2h6gB	0.965	0.73	0.682	0.980	0.96	GER	complex4.pdb.gz	6,9,10,54,56,60,103,105,106,109,171
5	0.46	1ft2B	0.965	0.73	0.667	0.980	1.10	FPP	complex5.pdb.gz	56,60,97,100,106
6	0.39	2h6hB	0.966	0.73	0.677	0.980	0.87	III	complex6.pdb.gz	103,105,158,161,162,163,167,168
7	0.12	2h6iB	0.965	0.73	0.677	0.980	1.09	SUC	complex7.pdb.gz	87,88,92,137,140
8	0.11	1d8dB	0.964	0.75	0.667	0.980	0.82	ZN	complex8.pdb.gz	103,105,173

	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.