D-I-TASSER Q7Z5U6-D1

D-I-TASSER results for Q7Z5U6-D1

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

Input Sequence in FASTA format

>Q7Z5U6 (97 residues)
MAVKWTGGHSSPVLCLNASKEGLLASGAEGGDLTAWGEDGTPLGHTRFQGADDVTSVLFS
PSCPTKLYASHGETISVLDVRSLKDSLDHFHVNEEEI

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MAVKWTGGHSSPVLCLNASKEGLLASGAEGGDLTAWGEDGTPLGHTRFQGADDVTSVLFSPSCPTKLYASHGETISVLDVRSLKDSLDHFHVNEEEI
Prediction	CCCSSCCCCCCCSSSSSSCCCCCSSSSCCCCSSSSSCCCCCSSSSSCCCCCCCSSSSSSCCCCCCSSSSSCCCSSSSSSCCCCCCCCSSCCCCCCCC
Confidence	9844136878977999986998188753898699990899730034168998679999889999199997899699996765556431012687779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MAVKWTGGHSSPVLCLNASKEGLLASGAEGGDLTAWGEDGTPLGHTRFQGADDVTSVLFSPSCPTKLYASHGETISVLDVRSLKDSLDHFHVNEEEI
Prediction	6534243415330200002461300011443302021354541443345354301000013734300000345302001063155215526346766
	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

                   |                   |                   |                   |

SS
Seq

CCCSSCCCCCCCSSSSSSCCCCCSSSSCCCCSSSSSCCCCCSSSSSCCCCCCCSSSSSSCCCCCCSSSSSCCCSSSSSSCCCCCCCCSSCCCCCCCC
MAVKWTGGHSSPVLCLNASKEGLLASGAEGGDLTAWGEDGTPLGHTRFQGADDVTSVLFSPSCPTKLYASHGETISVLDVRSLKDSLDHFHVNEEEI

1vyhT

0.20

6.27

1.50

DEthreader

DFERTLKGHTDSVQDISFDHSGLLASCSADMTIKLWDFGFECIRTMHGHD-HNVSSVSIMPNGDHIVSASRDKTIKMWEVQTGY-CVKTFTGHRDTV

1pevA3

0.12

0.10

3.65

1.73

SPARKS-K

---GNLTGQARAMNSVDFKPSRRIISGSDDNTVAIFEGPPFKFKSTFGEHTKFVHSVRYNPDGSLFASTGGDGTIVLYNGVDGTKTG----------

5cxcA

0.17

0.16

5.40

0.32

MapAlign

---LELYGHTGSVDWLDVDHSKHILTASADGAIGFWSAQRGPLGLWSI-HTAPATAAIFDRDRTVAYSASQDHTVRTLDLTTG-QVVSTLTLTHPLL

5cxcA4

0.19

0.18

5.66

0.26

CEthreader

----ELYGHTGSVDWLDVDGHSHILTASADGAIGFWSASKGPLGLWSI-HTAPATAAIFDPRRTVAYSASQDHTVRTLDLTTG-QVVSTLTLTHPL-

3j65q3

0.24

0.23

7.05

1.69

MUSTER

-------GHGSTILCSAFAPHTRMVTGAGDNTARIWDCDTQTPMHTLKGHYNWVLCVSWSPDGEVIATGSMDNTIRLWDPKSGQCLGDALRGHSKWI

6t9iD

0.17

0.16

5.43

0.59

HHsearch

YPLRIFAGHLNDVDCVSFHPNGYVFTGSSDKTCRMWDVSTGSVRLFLG-HTAPVISIAVCPDGRWLSTGSEDGIINVWDIGTGKRLK-QMRGHGNAI

4d6vA3

0.17

0.15

5.09

1.41

FFAS-3D

------DGHTEWVSCVRFSPNPVIISAGWDKTVKVWELSNCKLKTTHHGHTGYLNTLAVSPDGSLAASGGKDGITMLWDLNEGKH-LYSLDAG-DVI

6bk8M

0.16

0.15

5.16

0.43

EigenThreader

KVIRNYPGHPEGTTALKFLPKTLILSGGNDHTIKIWDFYYECLRDFQGH-NKPIKALRFTEDCQSFLSSSFDRSVKIWDTETGKVKTRLHLLSNSKI

5mzhA

0.19

6.00

1.51

CNFpred

RCLSVKQGHTDEVLDVAFDAATKMVSASADGSARLYHTLTGVCQHTLVGHEGEISKVAFNPQGTRLITASSDKTCRLWDCDTG-ECLQVLEGHTDEI

4j87A

0.20

6.27

1.50

DEthreader

DVKFVLEGHDRGVNWCAFHPLPLILSAGDDRLVKLWRMKAWEVDTCRGHF-NNVSCCLFHPHQELILSASEDKTIRVWDLNRRT-AVQTFRRADRAH

(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	0.8214

(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	1vyhT	0.91	1.11	0.200	0.979	model1_1vyhT.pdb.gz
2	2h9lA	0.91	1.10	0.200	0.979	model1_2h9lA.pdb.gz
3	3jcrD	0.91	1.11	0.158	0.979	model1_3jcrD.pdb.gz
4	6t9iD2	0.91	1.12	0.179	0.979	model1_6t9iD2.pdb.gz
5	2pbiD	0.91	1.23	0.188	0.990	model1_2pbiD.pdb.gz
6	3ow8A	0.90	1.15	0.189	0.979	model1_3ow8A.pdb.gz
7	1trjA	0.90	1.33	0.137	0.979	model1_1trjA.pdb.gz
8	2ymuA	0.90	1.11	0.223	0.969	model1_2ymuA.pdb.gz
9	6chgA	0.90	1.27	0.189	0.979	model1_6chgA.pdb.gz
10	6f3tA	0.90	1.19	0.137	0.979	model1_6f3tA.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	0.69	heterocyclic compound binding
GO:0097159	0.69	organic cyclic compound binding
GO:0003824	0.65	catalytic activity
GO:0003723	0.65	RNA binding
GO:0016740	0.60	transferase 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	0.96	cellular process
GO:0071704	0.88	organic substance metabolic process
GO:0044238	0.88	primary metabolic process
GO:0044237	0.88	cellular metabolic process
GO:0044260	0.86	cellular macromolecule metabolic process
GO:0006139	0.75	nucleobase-containing compound metabolic process
GO:0016070	0.74	RNA metabolic process
GO:0071840	0.68	cellular component organization or biogenesis
GO:0006396	0.68	RNA processing
GO:0044699	0.67	single-organism process
GO:0065007	0.66	biological regulation
GO:0016043	0.65	cellular component organization
GO:0050794	0.64	regulation of cellular process
GO:0044763	0.62	single-organism cellular process
GO:0019538	0.59	protein metabolic process
GO:0034470	0.58	ncRNA processing
GO:0006464	0.58	cellular protein modification process
GO:0043933	0.54	macromolecular complex subunit organization
GO:0080090	0.51	regulation of primary metabolic process
GO:0060255	0.51	regulation of macromolecule metabolic process
GO:0048522	0.51	positive regulation of cellular process
GO:0031323	0.51	regulation of cellular metabolic process
GO:0006325	0.51	chromatin organization
GO:0044767	0.50	single-organism developmental process
GO:0016570	0.50	histone modification

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:0044446	0.97	intracellular organelle part
GO:0032991	0.96	macromolecular complex
GO:0044428	0.89	nuclear part
GO:0043234	0.88	protein complex
GO:0043226	0.87	organelle
GO:0043229	0.86	intracellular organelle
GO:0043227	0.83	membrane-bounded organelle
GO:0043231	0.81	intracellular membrane-bounded organelle
GO:0005634	0.72	nucleus
GO:0044444	0.62	cytoplasmic part
GO:0030529	0.58	intracellular ribonucleoprotein 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	0.060	1v04A	0.756	2.27	0.120	0.949	3.1.1.2 3.1.8.1	NA
2	0.060	1v0eA	0.704	2.62	0.052	1.000	3.2.1.129	NA
3	0.060	1cruB	0.728	2.54	0.063	0.990	1.1.5.2	NA
4	0.060	2gc7A	0.772	2.12	0.117	0.969	1.4.99.3	22,61,65
5	0.060	3gvjA	0.741	2.28	0.065	0.959	3.2.1.129	37,39

	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	0.13	3pslA	0.912	1.08	0.211	0.979	0.58	III	complex1.pdb.gz	12,13,14,52,54,55,71
2	0.05	2yb8B	0.878	1.50	0.250	0.990	0.41	III	complex2.pdb.gz	30,32,43,44,45,47
3	0.05	1a0rB	0.883	1.54	0.198	0.990	0.66	FAR	complex3.pdb.gz	7,13,26,28,30,32,34,36
4	0.05	2xl2A	0.905	1.12	0.200	0.979	0.43	III	complex4.pdb.gz	4,18,40
5	0.04	2xl3B	0.904	1.14	0.200	0.979	0.41	III	complex5.pdb.gz	19,20,21,24,61,79
6	0.03	3sbpB	0.858	1.53	0.052	0.990	0.61	CUA	complex6.pdb.gz	30,51,55,71
7	0.03	3sbpD	0.858	1.53	0.052	0.990	0.50	IMD	complex7.pdb.gz	29,30,71,72

	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.