D-I-TASSER Q8IZU9-D5

D-I-TASSER results for Q8IZU9-D5

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

Input Sequence in FASTA format

>Q8IZU9 (117 residues)
GPPIISSTQTQHALHGEKGQIKCFIRSTPPPDRIAWSWKENVLESGTSGRYTVETISTEE
GVISTLTISNIVRADFQTIYNCTAWNSFGSDTEIIRLKEQGSEMKSGAGLEAESVPM

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| GPPIISSTQTQHALHGEKGQIKCFIRSTPPPDRIAWSWKENVLESGTSGRYTVETISTEEGVISTLTISNIVRADFQTIYNCTAWNSFGSDTEIIRLKEQGSEMKSGAGLEAESVPM
Prediction	CCCSSSCCCSSSSSCCCSSSSSSSSSSCCCCCSSSSSSCCSSCCCCCCCCSSSSSSSCCCCSSSSSSSCCCCHSHCCSSSSSSSSSCCCSSSSSSSSSSSCCCCCCCCCCCCCCCCC
Confidence	997674687199958936999999983179958999999999378999858999971699329999994985102774899999948950799999999778766778876333789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| GPPIISSTQTQHALHGEKGQIKCFIRSTPPPDRIAWSWKENVLESGTSGRYTVETISTEEGVISTLTISNIVRADFQTIYNCTAWNSFGSDTEIIRLKEQGSEMKSGAGLEAESVPM
Prediction	854424457434144455040303041514153020335754055765431313344475233020324614552434433131334244442403030545644554636465157
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCSSSCCCSSSSSCCCSSSSSSSSSSCCCCCSSSSSSCCSSCCCCCCCCSSSSSSSCCCCSSSSSSSCCCCHSHCCSSSSSSSSSCCCSSSSSSSSSSSCCCCCCCCCCCCCCCCC
GPPIISSTQTQHALHGEKGQIKCFIRSTPPPDRIAWSWKENVLESGTSGRYTVETISTEEGVISTLTISNIVRADFQTIYNCTAWNSFGSDTEIIRLKEQGSEMKSGAGLEAESVPM

6efyA3

0.26

0.22

6.85

1.33

DEthreader

FHPVIQVPQLVGAPLGTDVQIECHVEASPKS-INYWIKDTGEMIVT-SGKYHVQESSQSYETKMSMIVRKFQKDDV-GSYRCIAKNSLGEVDSSIRLYEIPH---------------

6eg0B3

0.20

0.18

5.74

1.10

SPARKS-K

PPMITVQNQLIGAVEGKGVTLDCESEAYPKS-INYWTRERGEIVPPGGKYSANVTEIGGYRNSMRLHINPLTQAEF-GSYRCVAKNSLGDTDGTIKLYRIPHHHHHH----------

6eg0B3

0.18

0.16

5.27

1.62

FFAS-3D

PPMITVQNQLIGAVEGKGVTLDCESEAYPKSINYWTRERGEI-VPPGGKYSANVTEIGGYRNSMRLHINPLTQA-EFGSYRCVAKNSLGDTDGTIKLYRIPHHHHH-----------

2rikA

0.24

0.22

6.93

1.56

CNFpred

APPFFDLPVSVDLALGESGTFKCHVTGT-APIKITWAKDNREIRP--GGNYKMTLV----ENTATLTVLKVTKGD-AGQYTCYASNVAGKDSCSAQLGVQEPPRFIKKLEPSRIVKQ

6efyA

0.26

0.22

6.85

1.33

DEthreader

FHPVIQVPQLVGAPLGTDVQIECHVEASPKS-INYWIKDTGEMIVT-SGKYHVQESSQSYETKMSMIVRKFQKDDV-GSYRCIAKNSLGEVDSSIRLYEIPH---------------

6efzA3

0.24

0.20

6.14

1.09

SPARKS-K

PPMIWIQNQLVGAALTQNITLECQSEAYPKS-INYWMKNDTIIVPGER--FVPETFESGYKITMRLTIYEVDIQDF-GAYRCVAKNSLGDTDGAIKLYHIP----------------

6efyA3

0.28

0.23

7.05

0.55

MapAlign

FHPVIQVNQLVGAPLGTDVQIECHVEASPKSI-NYWIKDGEMI--VTSGKYHVQESSQMYETKMSMIVRKFQKDDV-GSYRCIAKNSLGEVDSSIRLYEI-----------------

6efzA3

0.25

0.21

6.37

0.48

CEthreader

FPPMIWINQLVGAALTQNITLECQSEAYPKS-INYWMKNDTII--VPGERFVPETFESGYKITMRLTIYEVDIQDF-GAYRCVAKNSLGDTDGAIKLYHIP----------------

2cryA

0.95

0.89

24.94

0.94

MUSTER

GPPIISSTQTQHALHGEKGQIKCFIRSTPPPDRIAWSWKENVLESGTSGRYTVETISTEEGVISTLTISNIVRADFQTIYNCTAWNSFGSDTEIIRLKEQGSEMSGPSSG-------

3p3yA

0.25

0.22

6.91

0.39

HHsearch

RTPSFMYPSSQMVLRGMDLLLECIASGVPTP-DIAWYKKGGDLPS---DKAKFENFN------KALRITNVSEEDS-GEYFCLASNKMGSIRHTISVRVKAAPYWPKNLAPGEDGRL

(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	0.839

(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	6efyA3	0.79	1.13	0.273	0.846	model1_6efyA3.pdb.gz
2	6eg0B3	0.79	1.56	0.223	0.863	model1_6eg0B3.pdb.gz
3	3pxjA	0.78	2.71	0.250	0.940	model1_3pxjA.pdb.gz
4	6efzA3	0.77	1.16	0.247	0.829	model1_6efzA3.pdb.gz
5	3pxhA	0.76	2.73	0.243	0.932	model1_3pxhA.pdb.gz
6	3f8uD	0.76	2.33	0.095	0.906	model1_3f8uD.pdb.gz
7	3b43A	0.76	2.03	0.215	0.863	model1_3b43A.pdb.gz
8	3mtrA	0.76	2.41	0.198	0.880	model1_3mtrA.pdb.gz
9	2nziA	0.75	2.10	0.144	0.863	model1_2nziA.pdb.gz
10	6oilA	0.75	2.55	0.102	0.906	model1_6oilA.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:0042802	0.77	identical protein binding
GO:0046983	0.70	protein dimerization activity
GO:0042803	0.69	protein homodimerization activity
GO:0038023	0.69	signaling receptor activity
GO:0004888	0.68	transmembrane signaling receptor activity
GO:0008046	0.67	axon guidance receptor activity
GO:0003823	0.67	antigen 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:0009987	0.99	cellular process
GO:0044763	0.98	single-organism cellular process
GO:0044767	0.94	single-organism developmental process
GO:0048856	0.89	anatomical structure development
GO:0048869	0.88	cellular developmental process
GO:0065007	0.83	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0050794	0.81	regulation of cellular process
GO:0048513	0.81	animal organ development
GO:0009653	0.76	anatomical structure morphogenesis
GO:0048468	0.74	cell development
GO:0051128	0.73	regulation of cellular component organization
GO:2000026	0.72	regulation of multicellular organismal development
GO:0045595	0.70	regulation of cell differentiation
GO:0022603	0.70	regulation of anatomical structure morphogenesis
GO:0008038	0.68	neuron recognition
GO:0006928	0.68	movement of cell or subcellular component
GO:0070593	0.67	dendrite self-avoidance
GO:0051234	0.67	establishment of localization
GO:0010975	0.67	regulation of neuron projection development
GO:0050896	0.66	response to stimulus
GO:0050770	0.66	regulation of axonogenesis
GO:0048731	0.66	system development
GO:0044765	0.66	single-organism transport
GO:0060560	0.64	developmental growth involved in morphogenesis
GO:0048588	0.64	developmental cell growth
GO:0010033	0.64	response to organic substance
GO:0009628	0.64	response to abiotic stimulus
GO:0050976	0.63	detection of mechanical stimulus involved in sensory perception of touch
GO:0048846	0.63	axon extension involved in axon guidance
GO:0048814	0.63	regulation of dendrite morphogenesis
GO:0048666	0.63	neuron development
GO:0032490	0.63	detection of molecule of bacterial origin
GO:0021551	0.63	central nervous system morphogenesis
GO:0016319	0.63	mushroom body development
GO:0007422	0.63	peripheral nervous system development
GO:0007419	0.63	ventral cord development
GO:0007413	0.63	axonal fasciculation
GO:0007411	0.63	axon guidance
GO:0006909	0.63	phagocytosis

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:0044425	0.80	membrane part
GO:0031224	0.78	intrinsic component of membrane
GO:0097458	0.77	neuron part
GO:0016021	0.77	integral component of membrane
GO:0043005	0.75	neuron projection
GO:0030424	0.74	axon
GO:0030425	0.71	dendrite
GO:0044459	0.70	plasma membrane part
GO:0005887	0.68	integral component of plasma membrane
GO:0043025	0.64	neuronal cell body

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	0.237	2bk8A	0.718	1.65	0.196	0.803	2.7.11.1	NA
2	0.227	2dm7A	0.663	2.08	0.182	0.778	2.7.11.1	20,39,51
3	0.212	2edwA	0.671	1.90	0.170	0.769	2.7.11.1	11,43,75
4	0.160	2wwmD	0.742	1.47	0.240	0.821	2.7.11.1	NA
5	0.111	2eo1A	0.662	2.02	0.174	0.761	2.7.11.1	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	0.04	1tlk0	0.739	1.36	0.221	0.812	0.74	III	complex1.pdb.gz	26,28,30,32,34,35,43
2	0.04	3lexL	0.716	2.06	0.174	0.821	0.85	III	complex2.pdb.gz	33,41,44,46,85,86,88,90
3	0.04	2p5eD	0.739	2.02	0.150	0.855	0.73	III	complex3.pdb.gz	72,73,75,77,78
4	0.04	2pyeD	0.739	2.02	0.150	0.855	0.70	III	complex4.pdb.gz	12,13,14,17,18,19
5	0.03	2bnrD	0.733	1.99	0.162	0.838	0.61	III	complex5.pdb.gz	13,14,15,16,17,19
6	0.03	2f54K	0.734	2.03	0.161	0.846	0.60	III	complex6.pdb.gz	13,14,15,16,17,18,19
7	0.03	1ehlL	0.707	2.20	0.145	0.821	0.65	QNA	complex7.pdb.gz	28,32,90,91
8	0.03	2gsiE	0.718	2.06	0.128	0.821	0.66	III	complex8.pdb.gz	16,71,72,76
9	0.03	1q72H	0.696	2.62	0.106	0.855	0.77	COC	complex9.pdb.gz	31,33,85,86,89

	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.