D-I-TASSER Q495T6

D-I-TASSER results for Q495T6

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

Summary of the Protein

Uniprot ID: Q495T6
Protein Name: Membrane metallo-endopeptidase-like 1
Gene Name: MMEL1

Input Sequence in FASTA format

>Q495T6 (779 residues)
MGKSEGPVGMVESAGRAGQKRPGFLEGGLLLLLLLVTAALVALGVLYADRRGKQLPRLAS
RLCFLQEERTFVKRKPRGIPEAQEVSEVCTTPGCVIAAARILQNMDPTTEPCDDFYQFAC
GGWLRRHVIPETNSRYSIFDVLRDELEVILKAVLENSTAKDRPAVEKARTLYRSCMNQSV
IEKRGSQPLLDILEVVGGWPVAMDRWNETVGLEWELERQLALMNSQFNRRVLIDLFIWND
DQNSSRHIIYIDQPTLGMPSREYYFNGGSNRKVREAYLQFMVSVATLLREDANLPRDSCL
VQEDMVQVLELETQLAKATVPQEERHDVIALYHRMGLEELQSQFGLKGFNWTLFIQTVLS
SVKIKLLPDEEVVVYGIPYLQNLENIIDTYSARTIQNYLVWRLVLDRIGSLSQRFKDTRV
NYRKALFGTMVEEVRWRECVGYVNSNMENAVGSLYVREAFPGDSKSMVRELIDKVRTVFV
ETLDELGWMDEESKKKAQEKAMSIREQIGHPDYILEEMNRRLDEEYSNLNFSEDLYFENS
LQNLKVGAQRSLRKLREKVDPNLWIIGAAVVNAFYSPNRNQIVFPAGILQPPFFSKEQPQ
ALNFGGIGMVIGHEITHGFDDNGRNFDKNGNMMDWWSNFSTQHFREQSECMIYQYGNYSW
DLADEQNVNGFNTLGENIADNGGVRQAYKAYLKWMAEGGKDQQLPGLDLTHEQLFFINYA
QVWCGSYRPEFAIQSIKTDVHSPLKYRVLGSLQNLAAFADTFHCARGTPMHPKERCRVW

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	Q495T6-D1	1-779	779		MGKSEGPVGMVESAGRAGQKRPGFLEGGLLLLLLLVTAALVALGVLYADRRGKQLPRLASRLCFLQEERTFVKRKPRGIPEAQEVSEVCTTPGCVIAAARILQNMDPTTEPCDDFYQFACGGWLRRHVIPETNSRYSIFDVLRDELEVILKAVLENSTAKDRPAVEKARTLYRSCMNQSVIEKRGSQPLLDILEVVGGWPVAMDRWNETVGLEWELERQLALMNSQFNRRVLIDLFIWNDDQNSSRHIIYIDQPTLGMPSREYYFNGGSNRKVREAYLQFMVSVATLLREDANLPRDSCLVQEDMVQVLELETQLAKATVPQEERHDVIALYHRMGLEELQSQFGLKGFNWTLFIQTVLSSVKIKLLPDEEVVVYGIPYLQNLENIIDTYSARTIQNYLVWRLVLDRIGSLSQRFKDTRVNYRKALFGTMVEEVRWRECVGYVNSNMENAVGSLYVREAFPGDSKSMVRELIDKVRTVFVETLDELGWMDEESKKKAQEKAMSIREQIGHPDYILEEMNRRLDEEYSNLNFSEDLYFENSLQNLKVGAQRSLRKLREKVDPNLWIIGAAVVNAFYSPNRNQIVFPAGILQPPFFSKEQPQALNFGGIGMVIGHEITHGFDDNGRNFDKNGNMMDWWSNFSTQHFREQSECMIYQYGNYSWDLADEQNVNGFNTLGENIADNGGVRQAYKAYLKWMAEGGKDQQLPGLDLTHEQLFFINYAQVWCGSYRPEFAIQSIKTDVHSPLKYRVLGSLQNLAAFADTFHCARGTPMHPKERCRVW

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6558

(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	1r1hA	0.89	0.51	0.549	0.888	model1_1r1hA.pdb.gz
2	3dwbA	0.83	1.57	0.406	0.847	model1_3dwbA.pdb.gz
3	3zukA	0.80	2.08	0.291	0.829	model1_3zukA.pdb.gz
4	4iuwA	0.76	2.54	0.228	0.801	model1_4iuwA.pdb.gz
5	6rowA	0.73	2.13	0.259	0.759	model1_6rowA.pdb.gz
6	4z24A	0.22	8.21	0.035	0.344	model1_4z24A.pdb.gz
7	3iygQ	0.20	8.18	0.056	0.325	model1_3iygQ.pdb.gz
8	2f2fB	0.16	6.74	0.044	0.225	model1_2f2fB.pdb.gz
9	3akfA1	0.16	6.51	0.017	0.216	model1_3akfA1.pdb.gz
10	3skqA	0.15	6.03	0.058	0.196	model1_3skqA.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:0003824	0.99	catalytic activity
GO:0070011	0.98	peptidase activity, acting on L-amino acid peptides
GO:0008237	0.96	metallopeptidase activity
GO:0004175	0.86	endopeptidase activity
GO:0004222	0.81	metalloendopeptidase activity
GO:0046872	0.62	metal ion binding
GO:0046914	0.60	transition metal ion binding
GO:0033218	0.52	amide binding
GO:0008270	0.52	zinc ion 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:0008152	0.91	metabolic process
GO:0071704	0.90	organic substance metabolic process
GO:0044238	0.90	primary metabolic process
GO:0009987	0.90	cellular process
GO:0043170	0.89	macromolecule metabolic process
GO:0044699	0.88	single-organism process
GO:0019538	0.88	protein metabolic process
GO:0006508	0.87	proteolysis
GO:0044237	0.82	cellular metabolic process
GO:0032502	0.79	developmental process
GO:0044763	0.78	single-organism cellular process
GO:0006807	0.78	nitrogen compound metabolic process
GO:0048856	0.77	anatomical structure development
GO:0044767	0.77	single-organism developmental process
GO:0034641	0.77	cellular nitrogen compound metabolic process
GO:1901564	0.75	organonitrogen compound metabolic process
GO:0006518	0.74	peptide metabolic process
GO:0048869	0.71	cellular developmental process
GO:0048513	0.66	animal organ development
GO:0032501	0.66	multicellular organismal process
GO:0065007	0.65	biological regulation
GO:0003008	0.64	system process
GO:0046483	0.60	heterocycle metabolic process
GO:0044710	0.59	single-organism metabolic process
GO:0050896	0.58	response to stimulus
GO:0044281	0.58	small molecule metabolic process
GO:0050877	0.55	neurological system process
GO:0042221	0.55	response to chemical
GO:0009628	0.55	response to abiotic stimulus
GO:0051716	0.54	cellular response to stimulus
GO:0034097	0.54	response to cytokine
GO:0009416	0.54	response to light stimulus
GO:0007600	0.54	sensory perception
GO:0072338	0.53	cellular lactam metabolic process
GO:0071310	0.53	cellular response to organic substance
GO:0070141	0.53	response to UV-A
GO:0034644	0.53	cellular response to UV
GO:0010224	0.53	response to UV-B
GO:0007569	0.53	cell aging
GO:0050789	0.50	regulation of biological 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	0.92	intracellular part
GO:0016020	0.84	membrane
GO:0044444	0.82	cytoplasmic part
GO:0043226	0.72	organelle
GO:0043229	0.70	intracellular organelle
GO:0043227	0.69	membrane-bounded organelle
GO:0043231	0.66	intracellular membrane-bounded organelle
GO:0005886	0.60	plasma membrane
GO:0005737	0.55	cytoplasm
GO:0031988	0.51	membrane-bounded vesicle

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	0.223	1r1jA	0.885	0.56	0.549	0.888	3.4.24.11	NA
2	0.205	3dwbA	0.826	1.57	0.406	0.847	3.4.24.71	NA
3	0.060	3cskA	0.292	7.91	0.037	0.447	3.4.14.4	NA
4	0.060	2vdcF	0.309	8.59	0.036	0.499	1.4.1.13	NA
5	0.060	1q16A	0.275	8.72	0.031	0.445	1.7.99.4	63

	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	0.09	2yb9A	0.885	0.55	0.549	0.888	0.61	HA0	complex1.pdb.gz	676,723,725,727,744,747

	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.