D-I-TASSER Q9BXJ3-D1

D-I-TASSER results for Q9BXJ3-D1

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

Input Sequence in FASTA format

>Q9BXJ3 (155 residues)
MLPLLLGLLGPAACWALGPTPGPGSSELRSAFSAARTTPLEGTSEMAVTFDKVYVNIGGD
FDVATGQFRCRVPGAYFFSFTAGKAPHKSLSVMLVRNRDEVQALAFDEQRRPGARRAASQ
SAMLQLDYGDTVWLRLHGAPQYALGAPGATFSGYL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MLPLLLGLLGPAACWALGPTPGPGSSELRSAFSAARTTPLEGTSEMAVTFDKVYVNIGGDFDVATGQFRCRVPGAYFFSFTAGKAPHKSLSVMLVRNRDEVQALAFDEQRRPGARRAASQSAMLQLDYGDTVWLRLHGAPQYALGAPGATFSGYL
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSCCCCCCCCCCSSSCCSSSSCCCCCCCCCCCSSSCCCCSSSSSSSSSSSCCCCSSSSSSSSCCCCSSSSSSSCCCCCCCCCSSSSSSSSSSCCCCSSSSSSCCCCSCCCCCCCCSSSSSC
Confidence	98899898899999899999998888650579999689988899935873779984898721688869827781899999985138958999999467622799984168988621443269999479949999990883104789973787519
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MLPLLLGLLGPAACWALGPTPGPGSSELRSAFSAARTTPLEGTSEMAVTFDKVYVNIGGDFDVATGQFRCRVPGAYFFSFTAGKAPHKSLSVMLVRNRDEVQALAFDEQRRPGARRAASQSAMLQLDYGDTVWLRLHGAPQYALGAPGATFSGYL
Prediction	74544734524524634626527456532000102134535257623030330321344403443130203341201010123234423010101334433311121334554433312220303045413000103534334444421143344
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSCCCCCCCCCCSSSCCSSSSCCCCCCCCCCCSSSCCCCSSSSSSSSSSSCCCCSSSSSSSSCCCCSSSSSSSCCCCCCCCCSSSSSSSSSSCCCCSSSSSSCCCCSCCCCCCCCSSSSSC
MLPLLLGLLGPAACWALGPTPGPGSSELRSAFSAARTTPLEGTSEMAVTFDKVYVNIGGDFDVATGQFRCRVPGAYFFSFTAGKAPHKSLSVMLVRNRDEVQALAFDEQRRPGARRAASQSAMLQLDYGDTVWLRLHGAPQYALGAPGATFSGYL

5hkjA

0.26

0.25

7.55

1.33

DEthreader

---LGFSGGMVTSGFLLFPDG--SAKAQKIAFSATRTINVPLRRDQTIRFDHVITNMNNNYEPRSGKFTCKVPGLYYFTYHASSR--GNLCVNLMRGAQKVVTFCDYAY--N-TFQVTTGGMVLKLEQGENVFLQATDKN-SLLGMENSIFSGFL

4oulA

0.39

0.32

9.34

2.13

SPARKS-K

----------------------------RVAFSAARTSNLAPTLDQPIVFDLLLNNLGETFDLQLGRFNCPVNGTYVFIFHMLKLANVPLYVNLMKNEEVLVSAYANDGAPD--HETASNHAILQLFQGDQIWLRLHRGAIYGSSWKYSTFSGYL

4oulA

0.41

0.32

9.50

1.00

MapAlign

----------------------------RVAFSAARTSNLAPTLDQPIVFDLLLNNLGETFDLQLGRFNCPVNGTYVFIFHMLKLANVPLYVNLMKNEEVL-VSAYANDGA-PDHETASNHAILQLFQGDQIWLRLHRG--AIYGSKYSTFSGYL

1gr3A

0.30

0.24

7.25

0.75

CEthreader

--------------------------MPVSAFTVILSKAY-PAIGTPIPFDKILYNRQQHYDPRTGIFTCQIPGIYYFSYHVHVKG-THVWVGLYKNGTPVMYTYDEYTKGY--LDQASGSAIIDLTENDQVWLQLPNAESNGLYSVHSSFSGFL

5kcaA5

0.34

0.28

8.32

1.85

MUSTER

------------------------SGSAKVAFSAIRSTNHEPSETMIIYFDQVLVNIGNNFDSERSTFIAPRKGIYSFNFHVVKVYRQTIQVSLMLNGWPVISAFAG--DQDVTREAASNGVLIQMEKGDRAYLKLERGNLMG-GWKYSTFSGFL

4oulA

0.41

0.33

9.69

2.42

HHsearch

----------------------------RVAFSAARTSNLAPTLDQPIVFDLLLNNLGETFDLQLGRFNCPVNGTYVFIFHMLKLANVPLYVNLMKNEEVLVS-AYANDGAPD-HETASNHAILQLFQGDQIWLRLHRGAIYGSSWKYSTFSGYL

4oulA

0.39

0.32

9.34

1.75

FFAS-3D

----------------------------RVAFSAARTSNLAPTLDQPIVFDLLLNNLGETFDLQLGRFNCPVNGTYVFIFHMLLAVNVPLYVNLMKNEEVLVSAYA--NDGAPDHETASNHAILQLFQGDQIWLRLHRGAIYGSSWKYSTFSGYL

1rj7E

0.09

0.08

2.95

1.08

EigenThreader

----------------------GTRENQPAVVHLQGQGSANDLSGGVLNDWSRTMNPKVFLHPRSGELEVLVDGTYFIYSQVEVYYTDFASYEVVVDEKPFLQCTRSIETGKTNYNTCYTAGVCLLKARQKIAVKMVHADISINMSKTTFFGAIR

5hkjA

0.28

0.22

6.71

2.03

CNFpred

----------------------------KIAFSATRTINVPLRRDQTIRFDHVITNMNNNYEPRSGKFTCKVPGLYYFTYHASSR--GNLCVNLMRGRAQKVVTFCDYA---NTFQVTTGGMVLKLEQGENVFLQATDKNSLLGMGANSIFSGFL

4douA

0.29

0.27

8.25

1.33

DEthreader

---LFTSGSVLSTGFLLYHDTN-P-YVYRSAFSVGLETY--IP-NMPIRFTKIFYNQQNHYDGSTGKFHCNIPGLYYFAYHITVY-MKDVKVSLFKKDKAMLF-TYDQYQEN-NVDQASGSVLLHLEVGDQVWLQVYGGERNGLYADDSTFTGFL

(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	0.8438

(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	5hkjA	0.84	2.12	0.250	0.942	model1_5hkjA.pdb.gz
2	4douA	0.84	1.83	0.259	0.929	model1_4douA.pdb.gz
3	5kcaA	0.83	2.13	0.289	0.942	model1_5kcaA.pdb.gz
4	4oulA	0.76	1.07	0.398	0.793	model1_4oulA.pdb.gz
5	1gr3A	0.76	1.32	0.280	0.806	model1_1gr3A.pdb.gz
6	2jg8B	0.76	1.24	0.282	0.800	model1_2jg8B.pdb.gz
7	4f3jA	0.75	1.53	0.333	0.813	model1_4f3jA.pdb.gz
8	1o91A	0.75	1.45	0.306	0.800	model1_1o91A.pdb.gz
9	4d7yA	0.74	1.25	0.328	0.787	model1_4d7yA.pdb.gz
10	2jg8A	0.72	1.89	0.285	0.793	model1_2jg8A.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	0.54	heterocyclic compound binding
GO:0097159	0.54	organic cyclic compound binding
GO:0003824	0.53	catalytic activity
GO:0005102	0.52	receptor binding
GO:0003723	0.50	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:0065007	0.86	biological regulation
GO:0044699	0.86	single-organism process
GO:0050789	0.85	regulation of biological process
GO:0048518	0.78	positive regulation of biological process
GO:0050794	0.76	regulation of cellular process
GO:0009987	0.76	cellular process
GO:0048583	0.75	regulation of response to stimulus
GO:0048584	0.71	positive regulation of response to stimulus
GO:0008152	0.70	metabolic process
GO:0048523	0.68	negative regulation of cellular process
GO:0044763	0.68	single-organism cellular process
GO:0019222	0.68	regulation of metabolic process
GO:0048522	0.67	positive regulation of cellular process
GO:0031323	0.67	regulation of cellular metabolic process
GO:0071704	0.66	organic substance metabolic process
GO:0060255	0.66	regulation of macromolecule metabolic process
GO:0051239	0.66	regulation of multicellular organismal process
GO:0080090	0.65	regulation of primary metabolic process
GO:0023051	0.65	regulation of signaling
GO:0010646	0.65	regulation of cell communication
GO:0051240	0.64	positive regulation of multicellular organismal process
GO:0032268	0.64	regulation of cellular protein metabolic process
GO:0009966	0.64	regulation of signal transduction
GO:2000026	0.63	regulation of multicellular organismal development
GO:0050896	0.63	response to stimulus
GO:0023056	0.63	positive regulation of signaling
GO:0010647	0.63	positive regulation of cell communication
GO:0051128	0.62	regulation of cellular component organization
GO:0031326	0.62	regulation of cellular biosynthetic process
GO:0010468	0.62	regulation of gene expression
GO:0051094	0.61	positive regulation of developmental process
GO:0045595	0.61	regulation of cell differentiation
GO:0044238	0.61	primary metabolic process
GO:0032502	0.61	developmental process
GO:0031324	0.61	negative regulation of cellular metabolic process
GO:0009967	0.61	positive regulation of signal transduction
GO:2000112	0.60	regulation of cellular macromolecule biosynthetic process
GO:0022603	0.60	regulation of anatomical structure morphogenesis
GO:0010720	0.60	positive regulation of cell development
GO:0010605	0.60	negative regulation of macromolecule metabolic process
GO:0051171	0.59	regulation of nitrogen compound metabolic process
GO:0032269	0.59	negative regulation of cellular protein metabolic process
GO:0031327	0.59	negative regulation of cellular biosynthetic process
GO:0010629	0.58	negative regulation of gene expression
GO:2000113	0.57	negative regulation of cellular macromolecule biosynthetic process
GO:0051172	0.57	negative regulation of nitrogen compound metabolic process
GO:0044767	0.56	single-organism developmental process
GO:0048856	0.55	anatomical structure development
GO:0002682	0.54	regulation of immune system process
GO:0051130	0.52	positive regulation of cellular component organization
GO:0051962	0.51	positive regulation of nervous system development
GO:0090263	0.50	positive regulation of canonical Wnt signaling pathway
GO:0061003	0.50	positive regulation of dendritic spine morphogenesis
GO:0031399	0.50	regulation of protein modification process
GO:0019220	0.50	regulation of phosphate 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	0.93	cell part
GO:0044424	0.88	intracellular part
GO:0044421	0.87	extracellular region part
GO:0043226	0.79	organelle
GO:0043227	0.78	membrane-bounded organelle
GO:0005576	0.73	extracellular region
GO:0044444	0.69	cytoplasmic part
GO:0005615	0.64	extracellular space
GO:0043229	0.61	intracellular organelle
GO:0043231	0.60	intracellular membrane-bounded organelle
GO:0016020	0.54	membrane
GO:0031988	0.51	membrane-bounded vesicle
GO:0032991	0.50	macromolecular 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	1h6yA	0.542	2.82	0.103	0.690	3.2.1.8	NA
2	0.066	1w0nA	0.492	2.90	0.120	0.645	3.2.1.55	126
3	0.060	1pov0	0.521	3.93	0.068	0.748	3.4.22.29	104,134,150
4	0.060	1wmdA	0.517	3.72	0.071	0.729	3.4.21.-	NA
5	0.060	1novC	0.519	4.62	0.041	0.839	3.4.23.44	60

	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	0.07	3lkjA	0.673	2.39	0.116	0.781	1.18	LKJ	complex1.pdb.gz	75,77,123,125,153,155
2	0.06	2az5B	0.669	2.36	0.124	0.781	0.69	307	complex2.pdb.gz	74,76,122,123,124,153
3	0.05	2wnuF	0.736	1.55	0.301	0.793	0.52	UUU	complex3.pdb.gz	67,95,99,133
4	0.03	3lkjC	0.654	2.30	0.109	0.768	0.74	LKJ	complex4.pdb.gz	28,30,32,77,78,119,120,155
5	0.02	1osgA	0.697	2.24	0.095	0.813	0.53	III	complex5.pdb.gz	66,92,94
6	0.02	1oqeE	0.697	2.29	0.087	0.813	0.51	III	complex6.pdb.gz	66,82,91,92,93,101

	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.