D-I-TASSER Q8IXQ8-D1

D-I-TASSER results for Q8IXQ8-D1

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

Input Sequence in FASTA format

>Q8IXQ8 (177 residues)
MQKASHKNKKERGVSNKVKTSVHNLSKTQQTKLTVGSLGLGLIIIQHGPYLQITHLIRKG
AAANDGKLQPGDVLISVGHANVLGYTLREFLQLLQHITIGTVLQIKVYRDFINIPEEWQE
IYDLIPEAKFPVTSTPKKIELAKDESFTSSDDNENVDLDKRLQYYRYPWSTVHHPAR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MQKASHKNKKERGVSNKVKTSVHNLSKTQQTKLTVGSLGLGLIIIQHGPYLQITHLIRKGAAANDGKLQPGDVLISVGHANVLGYTLREFLQLLQHITIGTVLQIKVYRDFINIPEEWQEIYDLIPEAKFPVTSTPKKIELAKDESFTSSDDNENVDLDKRLQYYRYPWSTVHHPAR
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSSCCCCCCSSSSCCCCSSSSSSSCCCCHHHHHCCCCCCCSSSSSCCSSCCCCCHHHHHHHHHCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCC
Confidence	974100242213667777787667871699999867985557995399829999966999578719999992999999997799999999999972999986999997288899877664556676667888888988777778753348998753204531124688876678899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MQKASHKNKKERGVSNKVKTSVHNLSKTQQTKLTVGSLGLGLIIIQHGPYLQITHLIRKGAAANDGKLQPGDVLISVGHANVLGYTLREFLQLLQHITIGTVLQIKVYRDFINIPEEWQEIYDLIPEAKFPVTSTPKKIELAKDESFTSSDDNENVDLDKRLQYYRYPWSTVHHPAR
Prediction	855545644555646553544654454424040423650100002475410102302761204443404430200404442045231630041047156454030202243453445364145334546434554575454577543443755653525641642644544643458
	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                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSSCCCCCCSSSSCCCCSSSSSSSCCCCHHHHHCCCCCCCSSSSSCCSSCCCCCHHHHHHHHHCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCC
MQKASHKNKKERGVSNKVKTSVHNLSKTQQTKLTVGSLGLGLIIIQHGPYLQITHLIRKGAAANDGKLQPGDVLISVGHANVLGYTLREFLQLLQHITIGTVLQIKVYRDFINIPEEWQEIYDLIPEAKFPVTSTPKKIELAKDESFTSSDDNENVDLDKRLQYYRYPWSTVHHPAR

4wsiA

0.11

0.09

3.24

1.00

DEthreader

-----------------------GETVKIVRIEKARDIPLGATVRNEMDSVIISRIVKGGAAEKSGLLHEGDEVLEINGIEIRGKDVNEVFDLLSDM--HGTLTFVLIPSQQIKP--PP-A-KE----HVISEDPNWPG-IGPQGQNELRQRMNKFASAV-PHTT-RQFEDIFSDSQ

2kpkA

0.28

0.20

6.05

1.67

SPARKS-K

--------GAMGKPFFT-RNPSELKGKFIHTKLRKSSRGFGFTVVGGDEFLQIKSLVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCRG-------------------YPLPFDPDDPNTSLVTSVAILDKEP-----------------------

1u3bA

0.13

0.11

3.70

0.66

MapAlign

--------------------------EFKDVFIEKKGEILGVVIVESLPTVIIANMMHGGPAEKSGKLNIGDQIMSINGTSLVGLPLSTCQSIIKGLKNQSRVKLNIVRCPPVT--------TVLIRRPDLRYQLGFSVQNGIICSLMRGGIAERGGVRVGHRIIEINGQSVVKTM-

2kpkA

0.26

0.19

5.75

0.41

CEthreader

---------GAMGKPFFTRNPSELKGKFIHTKLRKSSRGFGFTVVGGDEFLQIKSLVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCRGYPLPFDPDDPNTSLVTSVAILDKEP------------------------------------------

2kpkA

0.29

0.21

6.36

1.36

MUSTER

---------GAMGKPFFTRNPSELKGKFIHTKLRKSSRGFGFTVVGGDEFLQIKSLVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCRGYP-----------LPFDPDDPNTSLVTSVAILDKEP-------------------------------

2xkxA

0.20

0.19

5.96

0.96

HHsearch

VREVTLK-EAGSIVRLYVMRRKPPAEKVMEIKLIKGPKGLGFSIAGGVNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKN--TYDVVYLKVAKPSNAYLSD------SYA---PP-DITTSYSQHLDNISHSSYLGTDYPTPTSPRRYSPVAKDLLPREPR

1wifA

0.71

0.47

13.48

1.25

FFAS-3D

-SSGSSGSKNEKEQLSKAKASVSSLNKVIQTKLTVGNLGLGLVVIQNGPYLQISHLINKGAAASDGILQPGDVLISVGHANVLGYTLREFLKLLQNITIGTVLQIKAYRGFLEIPQEWQ----------------------------------------------------------

7m4rA

0.15

0.13

4.38

1.02

EigenThreader

--------------------QYGGETVKIVRIEKARDIPLGATVRNEMDSVIISRIVKGGAAEKSGLLHEGDEVLEINGIEIRGKDVNEVFDLLS---DMHGTLTFVLIPSQETVINWWQAYREGDEDNQPLATYEEMSLYHQPANRKRDRFASAVPHTTRSRRDQVAGRDYHFVSR

2kpkA

0.36

0.18

5.21

1.58

CNFpred

--------------------------KFIHTKLRKSSRGFGFTVVGGDEFLQIKSLVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCRGY------------------------------------------------------------------

4wytA

0.21

0.13

4.14

0.83

DEthreader

----------------------EGPYPVEEIRLPRAGGPLGLSIVGHSPGVFISKVLPRGLAARS-GLRVGDRILAVNGQDVRDATHQEAVSALLRPC--LELSLLVRRDPA--------------------E-C----IRGGGHAGN----------ISKVGLRL----CDGFE--

(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	0.6628

(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	3r0hA	0.55	3.54	0.127	0.712	model1_3r0hA.pdb.gz
2	4wsiA	0.53	3.71	0.110	0.667	model1_4wsiA.pdb.gz
3	6irdC	0.51	3.20	0.162	0.638	model1_6irdC.pdb.gz
4	1obzB	0.51	3.14	0.103	0.610	model1_1obzB.pdb.gz
5	1u3bA	0.51	3.32	0.156	0.622	model1_1u3bA.pdb.gz
6	2kpkA	0.50	2.68	0.248	0.582	model1_2kpkA.pdb.gz
7	1fcfA	0.50	3.79	0.098	0.633	model1_1fcfA.pdb.gz
8	4wytA	0.50	3.34	0.211	0.616	model1_4wytA.pdb.gz
9	2dm8A	0.49	3.36	0.216	0.610	model1_2dm8A.pdb.gz
10	1wifA	0.49	2.80	0.608	0.582	model1_1wifA.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:0005102	0.62	receptor binding
GO:0003824	0.56	catalytic activity
GO:0016740	0.54	transferase activity
GO:0016301	0.53	kinase activity
GO:0035254	0.51	glutamate receptor binding
GO:0019904	0.51	protein domain specific binding
GO:0019201	0.50	nucleotide kinase activity
GO:0016776	0.50	phosphotransferase activity, phosphate group as acceptor
GO:0005198	0.50	structural molecule 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:0044699	0.90	single-organism process
GO:0009987	0.87	cellular process
GO:0044763	0.84	single-organism cellular process
GO:0016043	0.83	cellular component organization
GO:0065007	0.82	biological regulation
GO:0050789	0.77	regulation of biological process
GO:0050794	0.74	regulation of cellular process
GO:0051179	0.69	localization
GO:0032502	0.69	developmental process
GO:0022607	0.69	cellular component assembly
GO:0008104	0.66	protein localization
GO:0051641	0.65	cellular localization
GO:0048856	0.65	anatomical structure development
GO:0044767	0.64	single-organism developmental process
GO:0007165	0.63	signal transduction
GO:0007043	0.63	cell-cell junction assembly
GO:1902578	0.62	single-organism localization
GO:0070830	0.60	bicellular tight junction assembly
GO:0051128	0.58	regulation of cellular component organization
GO:0023051	0.57	regulation of signaling
GO:0010646	0.57	regulation of cell communication
GO:0048583	0.56	regulation of response to stimulus
GO:0048519	0.56	negative regulation of biological process
GO:0048518	0.56	positive regulation of biological process
GO:0007163	0.56	establishment or maintenance of cell polarity
GO:0051234	0.55	establishment of localization
GO:0048523	0.55	negative regulation of cellular process
GO:0048522	0.55	positive regulation of cellular process
GO:0032879	0.55	regulation of localization
GO:0032501	0.55	multicellular organismal process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0009966	0.55	regulation of signal transduction
GO:0080090	0.54	regulation of primary metabolic process
GO:0065008	0.54	regulation of biological quality
GO:0060255	0.54	regulation of macromolecule metabolic process
GO:0050793	0.54	regulation of developmental process
GO:0050790	0.54	regulation of catalytic activity
GO:0035088	0.54	establishment or maintenance of apical/basal cell polarity
GO:0051668	0.53	localization within membrane
GO:0019220	0.53	regulation of phosphate metabolic process
GO:1902531	0.52	regulation of intracellular signal transduction
GO:0043085	0.52	positive regulation of catalytic activity
GO:0035556	0.52	intracellular signal transduction
GO:0031399	0.52	regulation of protein modification process
GO:0022402	0.52	cell cycle process
GO:0009653	0.52	anatomical structure morphogenesis
GO:0051130	0.51	positive regulation of cellular component organization
GO:0051049	0.51	regulation of transport
GO:0044707	0.51	single-multicellular organism process
GO:0031325	0.51	positive regulation of cellular metabolic process
GO:0022603	0.51	regulation of anatomical structure morphogenesis
GO:0006996	0.51	organelle organization
GO:0006810	0.51	transport
GO:0051726	0.50	regulation of cell cycle
GO:0051050	0.50	positive regulation of transport
GO:0045937	0.50	positive regulation of phosphate metabolic process
GO:0042127	0.50	regulation of cell proliferation
GO:0010604	0.50	positive regulation of macromolecule metabolic process
GO:0009968	0.50	negative regulation of signal transduction
GO:0007154	0.50	cell communication
GO:0007010	0.50	cytoskeleton organization
GO:0003008	0.50	system 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:0016020	0.95	membrane
GO:0005886	0.92	plasma membrane
GO:0005737	0.85	cytoplasm
GO:0043226	0.81	organelle
GO:0030054	0.77	cell junction
GO:0044444	0.73	cytoplasmic part
GO:0043229	0.72	intracellular organelle
GO:0044459	0.71	plasma membrane part
GO:0032991	0.64	macromolecular complex
GO:0005911	0.64	cell-cell junction
GO:0043234	0.62	protein complex
GO:0098590	0.61	plasma membrane region
GO:0043227	0.61	membrane-bounded organelle
GO:0097458	0.60	neuron part
GO:0043232	0.59	intracellular non-membrane-bounded organelle
GO:0044456	0.54	synapse 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	1qavA	0.450	1.59	0.198	0.486	1.14.13.39	39,41,61,71,94
2	0.060	3khfB	0.420	2.35	0.116	0.486	2.7.11.1	41,68,93
3	0.060	1xl7A	0.380	5.75	0.069	0.718	2.3.1.137	NA
4	0.060	1soxA	0.394	5.76	0.079	0.740	1.8.3.1	NA
5	0.060	2zxqA	0.449	5.14	0.076	0.774	3.2.1.97	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	0.51	2i04A	0.441	1.31	0.366	0.463	1.36	III	complex1.pdb.gz	39,40,42,43,44,45,46,54,55,87,94
2	0.36	2awuB	0.436	1.37	0.329	0.463	1.35	III	complex2.pdb.gz	38,39,40,41,42,43,57,91
3	0.27	1l6oA	0.435	2.01	0.218	0.486	1.08	III	complex3.pdb.gz	39,40,41,42,43,44,45,46,47,48,86,92
4	0.16	2g2lB	0.438	1.25	0.341	0.463	0.85	III	complex4.pdb.gz	40,41,43,95
5	0.15	3jxtA	0.461	2.14	0.213	0.508	0.85	III	complex5.pdb.gz	41,42,56,58
6	0.13	2kawA	0.420	1.58	0.235	0.458	0.87	SUZ	complex6.pdb.gz	41,42,43,91,94,95
7	0.12	2ka9A	0.441	1.73	0.167	0.486	1.16	III	complex7.pdb.gz	40,41,42,43,57,87,91,94
8	0.12	1zubA	0.439	2.62	0.168	0.520	1.01	III	complex8.pdb.gz	40,41,42,43,44,45,54,55,77,89,93,96
9	0.10	3r0hG	0.526	3.59	0.124	0.689	0.96	III	complex9.pdb.gz	39,40,41,42,43,56,57,58,87,91,94,95
10	0.08	2kplA	0.478	2.31	0.264	0.548	1.02	III	complex10.pdb.gz	40,41,42,43,44,45,46,49,50,52,54,87,90,91,94,95

	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.