D-I-TASSER P30039-D2

D-I-TASSER results for P30039-D2

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

Input Sequence in FASTA format

>P30039 (139 residues)
YPAHPQDFHEVEDLIKTAIGNTLVQDICYSPDTQKLLVRLSDVYNRSFLENLKVNTENLL
QVENTGKVKGLILTLKGEPGGQTQAFDFYSRYFAPWVGVAEDPVTGSAHAVLSSYWSQHL
GKKEMHAFQCSHRGGELGI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| YPAHPQDFHEVEDLIKTAIGNTLVQDICYSPDTQKLLVRLSDVYNRSFLENLKVNTENLLQVENTGKVKGLILTLKGEPGGQTQAFDFYSRYFAPWVGVAEDPVTGSAHAVLSSYWSQHLGKKEMHAFQCSHRGGELGI
Prediction	CCCCCCCCCCCCHHHHHHCCCCCSSSSSSCCCCCSSSSSSCCCCCHHHHHHCCCCHHHHHHHHCCCCCCSSSSSSCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCSSSSSSCCCCCCSSSC
Confidence	9789974577428999971999248998337887599998478999999857999999998531269728999835788777788418996236556899887652233348999999869981899981588717849
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| YPAHPQDFHEVEDLIKTAIGNTLVQDICYSPDTQKLLVRLSDVYNRSFLENLKVNTENLLQVENTGKVKGLILTLKGEPGGQTQAFDFYSRYFAPWVGVAEDPVTGSAHAVLSSYWSQHLGKKEMHAFQCSHRGGELGI
Prediction	7545446636136203711624304203214624100000243633630550432262045037725020000003144555554110000111243414131021210020031026315464030200163515157
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCHHHHHHCCCCCSSSSSSCCCCCSSSSSSCCCCCHHHHHHCCCCHHHHHHHHCCCCCCSSSSSSCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCSSSSSSCCCCCCSSSC
YPAHPQDFHEVEDLIKTAIGNTLVQDICYSPDTQKLLVRLSDVYNRSFLENLKVNTENLLQVENTGKVKGLILTLKGEPGGQTQAFDFYSRYFAPWVGVAEDPVTGSAHAVLSSYWSQHLGKKEMHAFQCSHRGGELGI

1ym5A2

0.19

0.18

5.82

1.33

DEthreader

PMADYESISSMIADYEKAIGLKFIKPPALLHGPEWIVALVE-D--AETCFNANPNFAMLAHQTKQNDHVGIILAGPKKEA-A-IKNSYEMRAFAPVINVYEDPVCGSGSVALARYLQEYKFTTDITISEGGKRNGLMLA

1s7jA2

0.30

0.27

8.07

2.50

SPARKS-K

FPYILPERIPILPEYEAALGTK-IYEAYLG---RDLFFVLKD---EETVAKITPDFSALKAL---DLGVGVIVTASGDS------VDFVSRTFFPKLRINEDPVCGSAHANLIPYWGKRLNQTTLSAYQVSPRGGFLTC

1ym5A2

0.19

0.18

5.81

1.05

MapAlign

--MADYESIEMIADYEKAIGLKFIKPPALLHTPEWIVALVE--D-AETCFNANPNFAMLAHQTKQNDHVGIILAGPKKEA--AIKNSYEMRAFAPVINVYEDPVCGSGSVALARYLQEVYKFTDITISERLKRNGLMLA

1ym5A2

0.19

6.01

1.00

CEthreader

MADYESISSEMIADYEKAIGLKFIKPPALLHGPEWIVALVED---AETCFNANPNFAMLAHQTKQNDHVGIILAGPKKEA--AIKNSYEMRAFAPVINVYEDPVCGSGSVALARYLQEVYKTTDITISEGGKRNGLMLA

1s7jA2

0.30

0.26

7.87

1.98

MUSTER

FPYILPERIPILPEYEAALGTKIYEAYL-----RDLFFVL---KDEETVAKITPDFSALKAL---DLGVGVIVTASGD------SVDFVSRTFFPKLRINEDPVCGSAHANLIPYWGKRLNQTTLSAYQVSPRGGFLTC

1s7jA2

0.30

0.27

8.07

2.79

HHsearch

FPYILPERIPILPEYEAALGTKIYE---AYLG-RDLFFVLKD---EETVAKITPDFSALKALDL---GVGVIVTASG------DSVDFVSRTFFPKLRINEDPVCGSAHANLIPYWGKRLNQTTLSAYQVSPRGGFLTC

1s7jA2

0.27

0.24

7.29

1.78

FFAS-3D

FPYILPERIPILPEYEAALGTKIYEAYL----GRDLFFVL---KDEETVAKITPDFSALKALDLGVGVIVTA---------SGDSVDFVSRTFFPKLRINEDPVCGSAHANLIPYWGKRLNQTTLSAYQVSPRGGFLTC

1ym5A2

0.19

0.18

5.82

1.12

EigenThreader

FKAPMADYESIIADYEKAIGLFIKPPALLHTGPEWIVALV---EDAETCFNANPNFAMLAHQTKQNDHVGIILAGPKKEAAIK--NSYEMRAFAPVINVYEDPVCGSGSVALARYLQEVYKFTTDITIEGGRLKRLASI

1ym5A

0.19

0.18

5.81

1.60

CNFpred

MADYESISSEMIADYEKAIGLKFIPPALLHTGPEWIVALVE---DAETCFNANPNFAMLAHQTKQNDHVGIILAGPKK--EAAIKNSYEMRAFAPVINVYEDPVCGSGSVALARYLQEVY-TTDITISEGGRRNGLMLA

1ym5A

0.19

0.18

5.82

1.33

DEthreader

PMADYESISSMIADYEKAIGLKFIKPPALLHGPEWIVALVE-D--AETCFNANPNFAMLAHQTKQNDHVGIILAGPKKEA-A-IKNSYEMRAFAPVINVYEDPVCGSGSVALARYLQEYKFTTDITISEGGKRNGLMLA

(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	0.8401

(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	1ym5A2	0.86	1.70	0.194	0.964	model1_1ym5A2.pdb.gz
2	1qyaB2	0.84	1.74	0.191	0.942	model1_1qyaB2.pdb.gz
3	1s7jA2	0.80	1.56	0.293	0.885	model1_1s7jA2.pdb.gz
4	1u1wB2	0.79	1.78	0.200	0.899	model1_1u1wB2.pdb.gz
5	3ednA	0.77	2.54	0.208	0.935	model1_3ednA.pdb.gz
6	4dunA	0.76	1.96	0.352	0.878	model1_4dunA.pdb.gz
7	1u0kA	0.72	2.46	0.153	0.892	model1_1u0kA.pdb.gz
8	4owtA3	0.39	4.90	0.055	0.676	model1_4owtA3.pdb.gz
9	5fmgH	0.37	4.72	0.010	0.604	model1_5fmgH.pdb.gz
10	3r0xA	0.37	5.51	0.066	0.727	model1_3r0xA.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:0003824	0.54	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:0060394	1.00	negative regulation of pathway-restricted SMAD protein phosphorylation
GO:0060392	1.00	negative regulation of SMAD protein import into nucleus
GO:0050680	1.00	negative regulation of epithelial cell proliferation
GO:0030512	1.00	negative regulation of transforming growth factor beta receptor signaling pathway
GO:0030277	1.00	maintenance of gastrointestinal epithelium
GO:0010719	1.00	negative regulation of epithelial to mesenchymal transition
GO:0010633	1.00	negative regulation of epithelial cell migration
GO:0009987	0.51	cellular process
GO:0008152	0.51	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:0043226	0.90	organelle
GO:0043227	0.89	membrane-bounded organelle
GO:0070062	0.85	extracellular exosome
GO:0005737	0.85	cytoplasm
GO:0044444	0.51	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	0.060	1s9rA	0.499	4.27	0.076	0.770	3.5.3.6	60
2	0.060	1l1lA	0.477	4.99	0.062	0.878	1.17.4.2	NA
3	0.060	3fveA	0.638	3.00	0.096	0.820	5.1.1.7	NA
4	0.060	1f2jA	0.464	5.03	0.038	0.813	4.1.2.13	NA
5	0.060	1xfbA	0.466	4.99	0.061	0.813	4.1.2.13	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	0.14	1u1wA	0.794	1.77	0.200	0.899	0.47	3HA	complex1.pdb.gz	92,102,104,105,106,107
2	0.02	3hnfB	0.481	5.14	0.096	0.899	0.49	TTP	complex2.pdb.gz	71,72,102,106,107,108,109
3	0.02	2wghB	0.489	4.98	0.115	0.892	0.73	DTP	complex3.pdb.gz	17,18,19,62,71,72,73
4	0.01	3hncA	0.375	5.40	0.052	0.741	0.46	TTP	complex4.pdb.gz	19,22,52,57,58,71
5	0.01	3as2A	0.475	4.66	0.039	0.813	0.56	POY	complex5.pdb.gz	70,94,102,107,108
6	0.01	3hneB	0.447	4.85	0.031	0.784	0.49	TTP	complex6.pdb.gz	106,134,136,137

	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.