D-I-TASSER P35222-D4

D-I-TASSER results for P35222-D4

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

Input Sequence in FASTA format

>P35222 (135 residues)
NQESKLIILASGGPQALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALG
LHLTDPSQRLVQNCLWTLRNLSDAATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNL
TCNNYKNKMMVCQVG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| NQESKLIILASGGPQALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALGLHLTDPSQRLVQNCLWTLRNLSDAATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNKMMVCQVG
Prediction	CHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHCC
Confidence	889999999909979999999249959999999999999947951089999909779999998299999999999999998432443556750699999998299978999999999998539989999998766
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| NQESKLIILASGGPQALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALGLHLTDPSQRLVQNCLWTLRNLSDAATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNKMMVCQVG
Prediction	877224203627114300400553735501220030021002347134301624004101410536345013100100210133454444144004200410637445023100000010014276014302738
	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 DeepPotential. 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

CHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHCC
NQESKLIILASGGPQALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALGLHLTDPSQRLVQNCLWTLRNLSDAATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNKMMVCQVG

4rv1A

0.25

7.79

1.50

DEthreader

PDEAIKAIVDAGGVEVLVKLLT-STDSEVQKEAARALANIASGPSAIKAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIASGPDEIKAIDGGVEVLVKLLTSTDSEVQKEAARALANIASGPDEAIKAIVDAG

4rv1A

0.26

7.99

1.36

SPARKS-K

PDEAIKAIVDAGGVEVLVKLL-TSTDSEVQKEAARALANIASGDEAIKAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIASGPIKAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIASGPDEAIKAIVDAG

4rv1A2

0.25

0.24

7.59

0.63

MapAlign

-DEAIKAIVDAGGVEVLVKLLT-STDSEVQKEAARALANIAGPDEAIKAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIAGPDEAIKAIVGGVEVLVKLLTSTDSEVQKEAARALANIASGPTSAIKAIVDAG

4rv1A

0.25

0.24

7.59

0.41

CEthreader

PDEAIKAIVDAGGVEVLVKLLT-STDSEVQKEAARALANIAGPDEAIKAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIASGPDEAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIASGPTSAIKAIVDAG

2z6gA

1.00

28.00

1.19

MUSTER

NQESKLIILASGGPQALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALGLHLTDPSQRLVQNCLWTLRNLSDAATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNKMMVCQVG

4r0zA

0.41

12.20

0.94

HHsearch

DAPSKITFLSLLGPQILVSILREYDHRKLIYTVVRCIRSLSVCPSNKPALISLGCLPALYVELCTKDERSQTAILVAMRNLSDSATNEENLTQLIIKLLEIIRVANDGMTACACGTLSNLTCNNTRNKQTVCSHG

3tt9A2

0.18

0.16

5.33

1.60

FFAS-3D

DNDNKLEVAELNGVPRLLQVLKQTRDLETKKQITGLLWNLSSNDKLKNLMITEALLTLTENIIGLLDFDIFYNVTGCLRNMSSGRKAMRRCDGLIDSLVHYVYQPDDKATENCVCILHNLSYQLE----------

3dadA2

0.13

4.59

0.67

EigenThreader

DKDLVPEFVHSEGLSCLIRVGAA-ADHNYQSYILRALGQLMLFVDGMLGVVAHDTIQWLYTLCASLSRLVVKTALKLLLVFVEYSNNAPLFIRAVNNLVSILEEADPELLVYTVTLINKTLAALPDSFYDVTDAL

2gl7A

1.00

28.00

1.18

CNFpred

NQESKLIILASGGPQALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALGLHLTDPSQRLVQNCLWTLRNLSDAATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNKMMVCQVG

4rv1A2

0.25

7.79

1.50

DEthreader

PDEAIKAIVDAGGVEVLVKLL-TSTDSEVQKEAARALANIASGPEAIKAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIASGPDEIKAIDGGVEVLVKLLTSTDSEVQKEAARALANIASGPTSAIKAIVDAG

(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	0.9253

(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 DeepPotential, 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	4rv1A	0.95	0.93	0.239	0.993	model1_4rv1A.pdb.gz
2	4hxtA	0.94	1.03	0.246	0.993	model1_4hxtA.pdb.gz
3	3l6xA	0.93	1.18	0.224	0.993	model1_3l6xA.pdb.gz
4	4db6A	0.93	1.21	0.261	0.993	model1_4db6A.pdb.gz
5	1wa5B2	0.93	1.23	0.179	0.993	model1_1wa5B2.pdb.gz
6	4d49A	0.92	1.25	0.187	0.993	model1_4d49A.pdb.gz
7	4plqA	0.92	1.31	0.261	0.993	model1_4plqA.pdb.gz
8	4r0zA	0.92	1.42	0.410	0.993	model1_4r0zA.pdb.gz
9	5xjgA	0.91	1.36	0.231	0.993	model1_5xjgA.pdb.gz
10	4rxhB	0.91	1.39	0.157	0.993	model1_4rxhB.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:0045296	0.88	cadherin binding
GO:0019899	0.76	enzyme binding
GO:0045294	0.74	alpha-catenin binding
GO:0019903	0.73	protein phosphatase 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:0044699	0.99	single-organism process
GO:0032502	0.84	developmental process
GO:0065007	0.83	biological regulation
GO:0050789	0.83	regulation of biological process
GO:0044767	0.81	single-organism developmental process
GO:0050794	0.79	regulation of cellular process
GO:0009987	0.73	cellular process
GO:0009653	0.73	anatomical structure morphogenesis
GO:0007155	0.66	cell adhesion
GO:0044763	0.63	single-organism cellular process
GO:0048856	0.58	anatomical structure development
GO:0048518	0.56	positive regulation of biological process
GO:0007165	0.56	signal transduction
GO:0002009	0.55	morphogenesis of an epithelium
GO:0007166	0.54	cell surface receptor signaling pathway
GO:0044707	0.53	single-multicellular organism process
GO:0016055	0.53	Wnt signaling pathway
GO:0019222	0.51	regulation of metabolic process
GO:0080090	0.50	regulation of primary metabolic process
GO:0060255	0.50	regulation of macromolecule metabolic process
GO:0048519	0.50	negative regulation of biological process
GO:0031323	0.50	regulation of cellular 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:0044464	0.99	cell part
GO:0044424	0.98	intracellular part
GO:0043231	0.95	intracellular membrane-bounded organelle
GO:0005634	0.94	nucleus
GO:0043234	0.80	protein complex
GO:0005737	0.79	cytoplasm
GO:0044425	0.78	membrane part
GO:0098797	0.77	plasma membrane protein complex
GO:0016342	0.76	catenin 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	0.066	1ujkB	0.596	3.61	0.114	0.844	3.4.23.46	89
2	0.060	1js4A	0.547	3.98	0.068	0.881	3.2.1.4	NA
3	0.060	1h19A	0.547	4.22	0.069	0.852	3.3.2.6	64
4	0.060	1z1wA	0.609	3.91	0.073	0.896	3.4.11.-	NA
5	0.060	2q1fA	0.593	3.94	0.079	0.911	4.2.2.21	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	0.51	1jppB	0.875	1.76	1.000	1.000	1.32	III	complex1.pdb.gz	38,47,76,79,83,115,119,122,123,128
2	0.15	1i7x0	0.905	1.50	1.000	1.000	1.27	III	complex2.pdb.gz	19,51,52,53,54,57,86,87,89,90
3	0.15	2gl7A	0.899	1.57	1.000	1.000	0.80	III	complex3.pdb.gz	62,65,67,69,70,77,81,84
4	0.15	2gl7D	0.886	1.68	1.000	1.000	0.83	III	complex4.pdb.gz	56,61,63,77,81
5	0.15	2gl7D	0.886	1.68	1.000	1.000	0.83	III	complex5.pdb.gz	26,28,31,69
6	0.08	1q1tC	0.902	1.47	0.187	0.993	0.83	III	complex6.pdb.gz	35,38,41,42,47,73,76,79,80,83,112,115,119
7	0.06	1o6oA	0.828	2.33	0.104	0.993	0.90	III	complex7.pdb.gz	51,56,57,61,90,93,94
8	0.05	2jdq0	0.897	1.51	0.149	0.993	1.04	III	complex8.pdb.gz	57,60,61,64,88,91,92,93,96,126,127,133

	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.