D-I-TASSER Q6AI08-D2

D-I-TASSER results for Q6AI08-D2

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

Input Sequence in FASTA format

>Q6AI08 (88 residues)
SWTHREILQALAALVYCNGSKCQKYLPELLGNTGLLMKLSDLAQSDPEVRRAAVHCMANL
CLSVPGQPYLEEPYQNVCFQAFLTILQS

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| SWTHREILQALAALVYCNGSKCQKYLPELLGNTGLLMKLSDLAQSDPEVRRAAVHCMANLCLSVPGQPYLEEPYQNVCFQAFLTILQS
Prediction	CCCHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCSSSSCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHC
Confidence	9647999999999997275589998898618776233214877899899999999999887538899999558899999999999829
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| SWTHREILQALAALVYCNGSKCQKYLPELLGNTGLLMKLSDLAQSDPEVRRAAVHCMANLCLSVPGQPYLEEPYQNVCFQAFLTILQS
Prediction	8342340142013011432640352055114653223301444455361341013011410142575331666243201310143158
	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

CCCHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCSSSSCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHC
SWTHREILQALAALVYCNGSKCQKYLPELLGNTGLLMKLSDLAQSDPEVRRAAVHCMANLCLSVPGQPYLEEPYQNVCFQAFLTILQS

5ifeC2

0.17

0.16

5.22

1.33

DEthreader

LNVQNGVLKSLSFLFEYIGEMGKDYIYAVT---PLLEDALMD--RDLVHRQTASAVVQHMSLGV-YGFG-CEDSLNHLLNYVWPNVFE

5ifeC

0.16

0.15

4.91

0.77

SPARKS-K

LNVQNGVLKSLSFLFEYIGEMGKDYIYAVTPLLEDALM-----DRDLVHRQTASAVVQHMSLGVYGFGC--EDSLNHLLNYVWPNVFE

3ea5B

0.11

0.10

3.67

0.58

MapAlign

PKVATNCSWTIINLVEQLASPIYNFYPALV---DGLIGAANRIDNEFNARASAFSALTTMVEYA--TDTV-AETSASISTFVMDKL--

3w3tA2

0.12

0.11

4.03

0.38

CEthreader

LDDKVSAMELLQSYATLLRGQFAVYVKEVMEE--IALPSLDFY-LHDGVRAAGATLIPILLSCLLAATEELVLLWHKASSKLIGGLMS

5ifeC

0.19

0.17

5.52

0.66

MUSTER

LNVQNGVLKSLSFLFEYIGEMGKDYIYAVTP---LLEDALM--DRDLVHRQTASAVVQHMSLGVYGFGC--EDSLNHLLNYVWPNVFE

1u6gC1

0.23

0.16

4.99

0.80

HHsearch

MSTTRTYIQCIAAISRQAGHRIGEYLEKIIP---LVVKFCN--VDDDELREYCIQAFESFVRRCPK----------------------

3opbA3

0.15

0.14

4.61

0.65

FFAS-3D

--DNYEALLALTNLASSETSDGEEVCKHIVSTKVYWSTIENLLDENVPLQRSTLELISNMM---SHPLTIAAKFSLRNFNILVKLLQ-

6xteA4

0.13

0.12

4.32

0.57

EigenThreader

KLVLEQVVTSIASVADTAEEKFVPYYDLFMP---SLKHIVENAVQLRLLRGKTIECISLIGLAVG--KEKFMQDASDVMQLLLKTQTD

3w3vA

0.11

0.10

3.73

0.73

CNFpred

DDALASVFESLIELVELAPKLFKDMFDQII---QFTDMVIKNKDLEPPARTTALELLTVFSENAPQMCKSNQNYGQTLVMVTLIMMTE

5ifeC

0.17

0.16

5.22

1.33

DEthreader

LNVQNGVLKSLSFLFEYIGEMGKDYIYAVT---PLLEDALMD--RDLVHRQTASAVVQHMSLGV--YGFGCEDSLNHLLNYVWPNVFE

(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	0.7406

(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	5ifeC2	0.82	1.31	0.185	0.920	model1_5ifeC2.pdb.gz
2	1u6gC	0.80	1.61	0.120	0.943	model1_1u6gC.pdb.gz
3	5lqwQ	0.79	1.47	0.152	0.898	model1_5lqwQ.pdb.gz
4	6bcuW3	0.78	1.82	0.123	0.920	model1_6bcuW3.pdb.gz
5	3w3tA5	0.78	1.68	0.111	0.920	model1_3w3tA5.pdb.gz
6	3ea5B	0.76	1.75	0.160	0.920	model1_3ea5B.pdb.gz
7	1qgkA1	0.76	1.79	0.138	0.909	model1_1qgkA1.pdb.gz
8	1wa5B	0.75	2.11	0.145	0.943	model1_1wa5B.pdb.gz
9	1qbkB2	0.70	2.22	0.152	0.898	model1_1qbkB2.pdb.gz
10	1b3uA	0.69	1.80	0.095	0.841	model1_1b3uA.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:0044822	1.00	poly(A) RNA 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:0009987	0.75	cellular process
GO:0065007	0.71	biological regulation
GO:0050789	0.70	regulation of biological process
GO:0050794	0.67	regulation of cellular process
GO:0008152	0.66	metabolic process
GO:0071704	0.64	organic substance metabolic process
GO:0019222	0.64	regulation of metabolic process
GO:0060255	0.63	regulation of macromolecule metabolic process
GO:0044238	0.63	primary metabolic process
GO:0044237	0.63	cellular metabolic process
GO:0043170	0.63	macromolecule metabolic process
GO:0080090	0.62	regulation of primary metabolic process
GO:0044260	0.62	cellular macromolecule metabolic process
GO:0031323	0.62	regulation of cellular metabolic process
GO:0016043	0.59	cellular component organization
GO:0051246	0.57	regulation of protein metabolic process
GO:0044267	0.56	cellular protein metabolic process
GO:0031399	0.56	regulation of protein modification process
GO:0006996	0.56	organelle organization
GO:0006810	0.56	transport
GO:1903047	0.55	mitotic cell cycle process
GO:0051726	0.55	regulation of cell cycle
GO:0051028	0.55	mRNA transport
GO:0043933	0.55	macromolecular complex subunit organization
GO:0022607	0.55	cellular component assembly
GO:0018193	0.55	peptidyl-amino acid modification
GO:0006405	0.55	RNA export from nucleus
GO:1903320	0.54	regulation of protein modification by small protein conjugation or removal
GO:0071427	0.54	mRNA-containing ribonucleoprotein complex export from nucleus
GO:0051783	0.54	regulation of nuclear division
GO:0043623	0.54	cellular protein complex assembly
GO:0030162	0.54	regulation of proteolysis
GO:0016926	0.54	protein desumoylation
GO:0010564	0.54	regulation of cell cycle process
GO:0007346	0.54	regulation of mitotic cell cycle
GO:0007067	0.54	mitotic nuclear division
GO:0044699	0.51	single-organism 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	1.00	cell part
GO:0044424	0.96	intracellular part
GO:0044446	0.90	intracellular organelle part
GO:0043229	0.89	intracellular organelle
GO:0043231	0.82	intracellular membrane-bounded organelle
GO:0016020	0.81	membrane
GO:0005634	0.75	nucleus
GO:0044428	0.70	nuclear part
GO:0005737	0.69	cytoplasm
GO:0032991	0.65	macromolecular complex
GO:0043234	0.62	protein complex
GO:0044444	0.56	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	3gzkA	0.626	2.86	0.072	0.920	3.2.1.4	NA
2	0.060	1ihgA	0.614	2.98	0.073	0.920	5.2.1.8	NA
3	0.060	1nxcA	0.613	2.56	0.130	0.864	3.2.1.113	NA
4	0.060	1j0mA	0.618	3.09	0.024	0.898	4.2.2.12	NA
5	0.060	1ujkB	0.664	2.31	0.114	0.898	3.4.23.46	12,51

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.04	2jdq0	0.735	1.99	0.207	0.932	0.57	III	complex1.pdb.gz	23,26,70
	2	0.01	1qgk1	0.253	2.26	0.051	0.295	0.47	III	complex2.pdb.gz	19,20,21,30,31,37,38,41,45,46

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.