D-I-TASSER Q6P1M3

D-I-TASSER results for Q6P1M3

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

Summary of the Protein

Uniprot ID: Q6P1M3
Protein Name: LLGL scribble cell polarity complex component 2
Gene Name: LLGL2

Input Sequence in FASTA format

>Q6P1M3 (1020 residues)
MRRFLRPGHDPVRERLKRDLFQFNKTVEHGFPHQPSALGYSPSLRILAIGTRSGAIKLYG
APGVEFMGLHQENNAVTQIHLLPGQCQLVTLLDDNSLHLWSLKVKGGASELQEDESFTLR
GPPGAAPSATQITVVLPHSSCELLYLGTESGNVFVVQLPAFRALEDRTISSDAVLQRLPE
EARHRRVFEMVEALQEHPRDPNQILIGYSRGLVVIWDLQGSRVLYHFLSSQQLENIWWQR
DGRLLVSCHSDGSYCQWPVSSEAQQPEPLRSLVPYGPFPCKAITRILWLTTRQGLPFTIF
QGGMPRASYGDRHCISVIHDGQQTAFDFTSRVIGFTVLTEADPAATFDDPYALVVLAEEE
LVVIDLQTAGWPPVQLPYLASLHCSAITCSHHVSNIPLKLWERIIAAGSRQNAHFSTMEW
PIDGGTSLTPAPPQRDLLLTGHEDGTVRFWDASGVCLRLLYKLSTVRVFLTDTDPNENFS
AQGEDEWPPLRKVGSFDPYSDDPRLGIQKIFLCKYSGYLAVAGTAGQVLVLELNDEAAEQ
AVEQVEADLLQDQEGYRWKGHERLAARSGPVRFEPGFQPFVLVQCQPPAVVTSLALHSEW
RLVAFGTSHGFGLFDHQQRRQVFVKCTLHPSDQLALEGPLSRVKSLKKSLRQSFRRMRRS
RVSSRKRHPAGPPGEAQEGSAKAERPGLQNMELAPVQRKIEARSAEDSFTGFVRTLYFAD
TYLKDSSRHCPSLWAGTNGGTIYAFSLRVPPAERRMDEPVRAEQAKEIQLMHRAPVVGIL
VLDGHSVPLPEPLEVAHDLSKSPDMQGSHQLLVVSEEQFKVFTLPKVSAKLKLKLTALEG
SRVRRVSVAHFGSRRAEDYGEHHLAVLTNLGDIQVVSLPLLKPQVRYSCIRREDVSGIAS
CVFTKYGQGFYLISPSEFERFSLSTKWLVEPRCLVDSAETKNHRPGNGAGPKKAPSRARN
SGTQSDGEEKQPGLVMERALLSDERVLKEIQSTLEGDRGSGNWRSHRAAVGCSLSNGGAE

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q6P1M3-D1	1-424,697-711,778-1020	682		MRRFLRPGHDPVRERLKRDLFQFNKTVEHGFPHQPSALGYSPSLRILAIGTRSGAIKLYGAPGVEFMGLHQENNAVTQIHLLPGQCQLVTLLDDNSLHLWSLKVKGGASELQEDESFTLRGPPGAAPSATQITVVLPHSSCELLYLGTESGNVFVVQLPAFRALEDRTISSDAVLQRLPEEARHRRVFEMVEALQEHPRDPNQILIGYSRGLVVIWDLQGSRVLYHFLSSQQLENIWWQRDGRLLVSCHSDGSYCQWPVSSEAQQPEPLRSLVPYGPFPCKAITRILWLTTRQGLPFTIFQGGMPRASYGDRHCISVIHDGQQTAFDFTSRVIGFTVLTEADPAATFDDPYALVVLAEEELVVIDLQTAGWPPVQLPYLASLHCSAITCSHHVSNIPLKLWERIIAAGSRQNAHFSTMEWPIDGQRKIEARSAEDSFTGGILVLDGHSVPLPEPLEVAHDLSKSPDMQGSHQLLVVSEEQFKVFTLPKVSAKLKLKLTALEGSRVRRVSVAHFGSRRAEDYGEHHLAVLTNLGDIQVVSLPLLKPQVRYSCIRREDVSGIASCVFTKYGQGFYLISPSEFERFSLSTKWLVEPRCLVDSAETKNHRPGNGAGPKKAPSRARNSGTQSDGEEKQPGLVMERALLSDERVLKEIQSTLEGDRGSGNWRSHRAAVGCSLSNGGAE
2	Q6P1M3-D2	425-696	272		GTSLTPAPPQRDLLLTGHEDGTVRFWDASGVCLRLLYKLSTVRVFLTDTDPNENFSAQGEDEWPPLRKVGSFDPYSDDPRLGIQKIFLCKYSGYLAVAGTAGQVLVLELNDEAAEQAVEQVEADLLQDQEGYRWKGHERLAARSGPVRFEPGFQPFVLVQCQPPAVVTSLALHSEWRLVAFGTSHGFGLFDHQQRRQVFVKCTLHPSDQLALEGPLSRVKSLKKSLRQSFRRMRRSRVSSRKRHPAGPPGEAQEGSAKAERPGLQNMELAPV
3	Q6P1M3-D3	712-777	66		FVRTLYFADTYLKDSSRHCPSLWAGTNGGTIYAFSLRVPPAERRMDEPVRAEQAKEIQLMHRAPVV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.47

(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	6n8pA	0.70	3.48	0.862	0.761	model1_6n8pA.pdb.gz
2	2oajA	0.63	5.42	0.116	0.754	model1_2oajA.pdb.gz
3	5oqlO	0.50	5.52	0.086	0.604	model1_5oqlO.pdb.gz
4	5wyjBC	0.49	5.16	0.104	0.580	model1_5wyjBC.pdb.gz
5	5wlcLO	0.49	4.94	0.085	0.578	model1_5wlcLO.pdb.gz
6	4nsxA	0.48	4.76	0.077	0.569	model1_4nsxA.pdb.gz
7	5oqlA	0.48	4.85	0.094	0.572	model1_5oqlA.pdb.gz
8	2ymuA	0.47	4.85	0.114	0.551	model1_2ymuA.pdb.gz
9	5teeA	0.45	5.79	0.101	0.558	model1_5teeA.pdb.gz
10	5i2tA	0.45	5.49	0.096	0.553	model1_5i2tA.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:0000149	1.00	SNARE binding
GO:0019905	0.99	syntaxin binding
GO:0017137	0.99	Rab GTPase binding
GO:0005096	0.99	GTPase activator 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:0050794	0.98	regulation of cellular process
GO:0017157	0.93	regulation of exocytosis
GO:0050708	0.89	regulation of protein secretion
GO:0044699	0.83	single-organism process
GO:0009987	0.83	cellular process
GO:0044763	0.77	single-organism cellular process
GO:0051179	0.72	localization
GO:0016043	0.72	cellular component organization
GO:0051234	0.71	establishment of localization
GO:0048583	0.71	regulation of response to stimulus
GO:0023051	0.71	regulation of signaling
GO:0010646	0.71	regulation of cell communication
GO:1902578	0.69	single-organism localization
GO:0009966	0.69	regulation of signal transduction
GO:0048869	0.68	cellular developmental process
GO:0008593	0.68	regulation of Notch signaling pathway
GO:1902580	0.67	single-organism cellular localization
GO:0051656	0.67	establishment of organelle localization
GO:0051649	0.67	establishment of localization in cell
GO:0030029	0.66	actin filament-based process
GO:0051294	0.65	establishment of spindle orientation
GO:0032878	0.65	regulation of establishment or maintenance of cell polarity
GO:0030866	0.65	cortical actin cytoskeleton organization
GO:0030154	0.65	cell differentiation
GO:0022008	0.64	neurogenesis

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	0.98	intracellular part
GO:0016020	0.95	membrane
GO:0044444	0.92	cytoplasmic part
GO:0043226	0.92	organelle
GO:0043229	0.91	intracellular organelle
GO:0005886	0.90	plasma membrane
GO:0044422	0.72	organelle part
GO:0044446	0.71	intracellular organelle part
GO:0044430	0.66	cytoskeletal part
GO:0043232	0.65	intracellular non-membrane-bounded organelle
GO:0030864	0.63	cortical actin cytoskeleton

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	2pffB	0.206	8.68	0.048	0.313	2.3.1.86	336
2	0.060	1gjqA	0.306	4.53	0.077	0.351	1.7.99.1 1.7.2.1	NA
3	0.060	1g72A	0.305	4.82	0.082	0.353	1.1.99.8	50
4	0.060	1gthA	0.302	9.33	0.049	0.483	1.3.1.2	NA
5	0.060	3h09B	0.287	9.11	0.033	0.449	3.4.21.72	423

	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	1nirB	0.279	5.28	0.083	0.333	0.25	HEC	complex1.pdb.gz	28,30,49
2	0.04	1gjqA	0.306	4.53	0.077	0.351	0.24	HEC	complex2.pdb.gz	30,31,33,47
3	0.01	1n90B	0.279	5.28	0.083	0.333	0.19	HEC	complex3.pdb.gz	32,35,38,379
4	0.01	1n15A	0.279	5.29	0.083	0.333	0.19	HEC	complex4.pdb.gz	30,49,51,53,54,55,56
5	0.01	1flgB	0.300	5.53	0.069	0.362	0.12	PQQ	complex5.pdb.gz	49,65,917,918
6	0.01	1vt4I	0.421	6.83	0.002	0.560	0.13	DTP	complex6.pdb.gz	31,54,57,58,382
7	0.01	1kv9A	0.310	5.24	0.058	0.366	0.11	PQQ	complex7.pdb.gz	32,59,60,61,62
8	0.01	3sfzA	0.400	7.49	0.054	0.555	0.19	ADP	complex8.pdb.gz	31,32,52,53,54,464
9	0.01	1h4j0	0.320	5.02	0.083	0.373	0.20	III	complex9.pdb.gz	34,58,62,65,67,313,315,325,326,327,328,356
10	0.01	1shy1	0.273	5.16	0.051	0.322	0.21	III	complex10.pdb.gz	90,91,92

	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.