D-I-TASSER P41002-D2

D-I-TASSER results for P41002-D2

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

Input Sequence in FASTA format

>P41002 (130 residues)
AVSKQQVFSVQKGLNDTMRYILIDWLVEVATMKDFTSLCLHLTVECVDRYLRRRLVPRYR
LQLLGIACMVICTRFISKEILTIREAVWLTDNTYKYEDLVRMMGEIVSALEGKIRVPTVV
DYKEVLLTLV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| AVSKQQVFSVQKGLNDTMRYILIDWLVEVATMKDFTSLCLHLTVECVDRYLRRRLVPRYRLQLLGIACMVICTRFISKEILTIREAVWLTDNTYKYEDLVRMMGEIVSALEGKIRVPTVVDYKEVLLTLV
Prediction	CCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCSCCCCCHHHHHHHHHHHC
Confidence	9996166650889999999999999999999979985899999999999852267756787789999999999733478999999999977999999999999999999198416889899999999969
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| AVSKQQVFSVQKGLNDTMRYILIDWLVEVATMKDFTSLCLHLTVECVDRYLRRRLVPRYRLQLLGIACMVICTRFISKEILTIREAVWLTDNTYKYEDLVRMMGEIVSALEGKIRVPTVVDYKEVLLTLV
Prediction	8455551254057034610320010003003424134301220020001001333144431200000001001333344314042003005420447243511344562052403200022004120314
	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

CCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCSCCCCCHHHHHHHHHHHC
AVSKQQVFSVQKGLNDTMRYILIDWLVEVATMKDFTSLCLHLTVECVDRYLRRRLVPRYRLQLLGIACMVICTRFISKEILTIREAVWLTDNTYKYEDLVRMMGEIVSALEGKIRVPTVVDYKEVLLTLV

2w96A

0.29

0.28

8.45

1.50

DEthreader

---V-SYFKCQKEVLPSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPEELLQMELLLVNKLKWNLAAMTPHDFIEHFLSKM

6gu2B1

0.26

0.25

7.85

1.86

SPARKS-K

QAVRPKYLLGR-EVTGNMRAILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQNNSVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQIRQMEMKILRALNFGLGRPLPLHFLRRASKIG

1g3nC

0.18

5.75

0.95

MapAlign

---DSVFGTFQQSLTSHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQELIDQEKELLEKLAWRTEAVLATDVTSFLLLK-

1g3nC

0.18

5.98

0.66

CEthreader

LTSDSVFGTFQQSLTSHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQELIDQEKELLEKLAWRTEAVLATDVTSFLLLKL

3ddpD

0.30

9.10

1.59

MUSTER

CKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLAFDLAAPTINQFLTQYFLHQ

1w98B

0.24

7.44

2.04

HHsearch

YLRDQHFLEQHPLLQPKMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDEILTMELMIMKALKWRLSPLTIVSWLNVYMQVA

1g3nC

0.19

0.18

5.98

2.46

FFAS-3D

-TSDSVFGTFQQSLTSHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQELIDQEKELLEKLAWRTEAVLATDVTSFLLLKL

1w98B

0.23

7.22

1.22

EigenThreader

RDQH--FLEQHPLLQPKMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQNVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDEILTMELMIMKALKWRLSPLTIVSWLNVYMQVA

5l2wB

0.24

7.42

1.26

CNFpred

--RDQHFLEQHPLLQPKMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQNVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDEILTMELMIMKALKWRLSPLTIVSWLNVYMQVA

3ddpD

0.30

0.29

8.86

1.50

DEthreader

---V-GYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLAFDLAAPTINQFLTQYFLHS

(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	0.9154

(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	3ddpD	0.96	0.91	0.295	0.992	model1_3ddpD.pdb.gz
2	2w96A	0.96	0.86	0.295	0.992	model1_2w96A.pdb.gz
3	1g3nC	0.96	0.88	0.202	0.992	model1_1g3nC.pdb.gz
4	2jgzB	0.95	0.99	0.273	0.985	model1_2jgzB.pdb.gz
5	1w98B	0.94	1.05	0.233	0.992	model1_1w98B.pdb.gz
6	2eufA	0.91	1.35	0.198	0.969	model1_2eufA.pdb.gz
7	3g33D1	0.86	1.06	0.224	0.892	model1_3g33D1.pdb.gz
8	2i53A	0.83	2.38	0.070	0.992	model1_2i53A.pdb.gz
9	2w2hA	0.82	2.75	0.109	0.992	model1_2w2hA.pdb.gz
10	1f5qD1	0.76	2.14	0.127	0.846	model1_1f5qD1.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:1901363	0.44	heterocyclic compound binding
GO:0097159	0.44	organic cyclic compound binding
GO:0098772	0.36	molecular function regulator
GO:0019899	0.36	enzyme binding
GO:0019900	0.35	kinase binding
GO:0019887	0.35	protein kinase regulator activity
GO:0019901	0.34	protein kinase binding
GO:0016538	0.34	cyclin-dependent protein serine/threonine kinase regulator activity
GO:0003824	0.32	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:0009987	0.93	cellular process
GO:0065007	0.90	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0051726	0.71	regulation of cell cycle
GO:0010564	0.55	regulation of cell cycle process
GO:0044699	0.54	single-organism process
GO:0048519	0.52	negative regulation of biological process
GO:0022402	0.52	cell cycle process
GO:0048523	0.51	negative regulation of cellular process
GO:0008152	0.51	metabolic process
GO:0071704	0.50	organic substance metabolic process
GO:0048518	0.50	positive regulation of biological 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:0043229	0.90	intracellular organelle
GO:0043231	0.83	intracellular membrane-bounded organelle
GO:0005634	0.80	nucleus
GO:0032991	0.68	macromolecular complex
GO:0044422	0.66	organelle part
GO:0044446	0.64	intracellular organelle part
GO:0043234	0.64	protein complex
GO:1902494	0.57	catalytic complex
GO:1990234	0.56	transferase complex
GO:0044444	0.52	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	0.098	1xo2A	0.902	1.49	0.197	0.969	2.7.11.22	54,71,73
2	0.060	3kb9A	0.537	4.63	0.072	0.892	4.2.3.37	NA
3	0.060	3b8cB	0.522	4.05	0.051	0.831	3.6.3.6	55,106
4	0.060	2r8qA	0.525	4.57	0.039	0.885	3.1.4.17	NA
5	0.060	1tazA	0.514	4.68	0.102	0.892	3.1.4.17	71

	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	0.34	2cchB	0.960	0.94	0.302	0.992	1.23	III	complex1.pdb.gz	18,21,22,25,28,29,32,33,58,61,62,85,88,89,90,91,93
2	0.32	1h28D	0.959	0.89	0.302	0.992	1.01	III	complex2.pdb.gz	18,25,28,33,58,59,60,62
3	0.08	3qhrB	0.961	0.90	0.302	0.992	1.34	III	complex3.pdb.gz	28,32,33,34,35,62,77,79,85,88,89,91,93
4	0.03	1jkw0	0.782	2.88	0.100	1.000	0.92	III	complex4.pdb.gz	70,71,74,75,82,83,96,97,100,101,103,104,107,112

	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.