D-I-TASSER Q9H306

D-I-TASSER results for Q9H306

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

Summary of the Protein

Uniprot ID: Q9H306
Protein Name: Matrix metalloproteinase-27
Gene Name: MMP27

Input Sequence in FASTA format

>Q9H306 (513 residues)
MKRLLLLFLFFITFSSAFPLVRMTENEENMQLAQAYLNQFYSLEIEGNHLVQSKNRSLID
DKIREMQAFFGLTVTGKLDSNTLEIMKTPRCGVPDVGQYGYTLPGWRKYNLTYRIINYTP
DMARAAVDEAIQEGLEVWSKVTPLKFTKISKGIADIMIAFRTRVHGRCPRYFDGPLGVLG
HAFPPGPGLGGDTHFDEDENWTKDGAGFNLFLVAAHEFGHALGLSHSNDQTALMFPNYVS
LDPRKYPLSQDDINGIQSIYGGLPKEPAKPKEPTIPHACDPDLTFDAITTFRREVMFFKG
RHLWRIYYDITDVEFELIASFWPSLPADLQAAYENPRDKILVFKDENFWMIRGYAVLPDY
PKSIHTLGFPGRVKKIDAAVCDKTTRKTYFFVGIWCWRFDEMTQTMDKGFPQRVVKHFPG
ISIRVDAAFQYKGFFFFSRGSKQFEYDIKTKNITRIMRTNTWFQCKEPKNSSFGFDINKE
KAHSGGIKILYHKSLSLFIFGIVHLLKNTSIYQ

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	Q9H306-D1	1-261	261		MKRLLLLFLFFITFSSAFPLVRMTENEENMQLAQAYLNQFYSLEIEGNHLVQSKNRSLIDDKIREMQAFFGLTVTGKLDSNTLEIMKTPRCGVPDVGQYGYTLPGWRKYNLTYRIINYTPDMARAAVDEAIQEGLEVWSKVTPLKFTKISKGIADIMIAFRTRVHGRCPRYFDGPLGVLGHAFPPGPGLGGDTHFDEDENWTKDGAGFNLFLVAAHEFGHALGLSHSNDQTALMFPNYVSLDPRKYPLSQDDINGIQSIYG
2	Q9H306-D2	262-513	252		GLPKEPAKPKEPTIPHACDPDLTFDAITTFRREVMFFKGRHLWRIYYDITDVEFELIASFWPSLPADLQAAYENPRDKILVFKDENFWMIRGYAVLPDYPKSIHTLGFPGRVKKIDAAVCDKTTRKTYFFVGIWCWRFDEMTQTMDKGFPQRVVKHFPGISIRVDAAFQYKGFFFFSRGSKQFEYDIKTKNITRIMRTNTWFQCKEPKNSSFGFDINKEKAHSGGIKILYHKSLSLFIFGIVHLLKNTSIYQ

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.81

(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	1gxdA	0.60	5.72	0.297	0.842	model1_1gxdA.pdb.gz
2	1su3B	0.59	5.08	0.372	0.766	model1_1su3B.pdb.gz
3	4fu4A	0.55	4.27	0.380	0.665	model1_4fu4A.pdb.gz
4	5wlcLH	0.45	7.31	0.049	0.710	model1_5wlcLH.pdb.gz
5	2mzeA	0.44	2.18	0.447	0.468	model1_2mzeA.pdb.gz
6	4nsxA	0.44	6.76	0.037	0.665	model1_4nsxA.pdb.gz
7	5wyjBE	0.44	6.78	0.049	0.655	model1_5wyjBE.pdb.gz
8	5i2tA	0.43	6.69	0.052	0.651	model1_5i2tA.pdb.gz
9	1slmA	0.43	0.93	0.596	0.435	model1_1slmA.pdb.gz
10	5oqlO	0.43	7.07	0.038	0.659	model1_5oqlO.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:0008233	0.97	peptidase activity
GO:0070011	0.95	peptidase activity, acting on L-amino acid peptides
GO:0008237	0.91	metallopeptidase activity
GO:0004175	0.89	endopeptidase activity
GO:0004222	0.85	metalloendopeptidase activity
GO:0046872	0.70	metal ion binding
GO:0004252	0.67	serine-type endopeptidase activity
GO:0008270	0.64	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:0044699	0.94	single-organism process
GO:0009987	0.91	cellular process
GO:0044763	0.88	single-organism cellular process
GO:0065007	0.78	biological regulation
GO:0071704	0.77	organic substance metabolic process
GO:0032501	0.76	multicellular organismal process
GO:0050789	0.75	regulation of biological process
GO:0044707	0.75	single-multicellular organism process
GO:0043170	0.75	macromolecule metabolic process
GO:0016043	0.73	cellular component organization
GO:0050794	0.72	regulation of cellular process
GO:0030198	0.70	extracellular matrix organization
GO:0022617	0.67	extracellular matrix disassembly
GO:0044710	0.64	single-organism metabolic process
GO:0009056	0.64	catabolic process
GO:0030574	0.62	collagen catabolic process
GO:0050896	0.61	response to stimulus
GO:0048518	0.61	positive regulation of biological process
GO:0048522	0.59	positive regulation of cellular process
GO:0032502	0.59	developmental process
GO:0044767	0.56	single-organism developmental process
GO:0048583	0.54	regulation of response to stimulus
GO:0048519	0.53	negative regulation of biological process
GO:0048523	0.52	negative regulation of cellular process
GO:0006950	0.51	response to stress
GO:0042221	0.50	response to chemical

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	0.78	cell part
GO:0044424	0.62	intracellular part
GO:0044421	0.59	extracellular region part
GO:0044444	0.43	cytoplasmic part
GO:0005576	0.42	extracellular region
GO:0044446	0.32	intracellular organelle part
GO:0043226	0.32	organelle
GO:0005615	0.32	extracellular space
GO:0044425	0.31	membrane part
GO:0043227	0.31	membrane-bounded organelle
GO:0016020	0.30	membrane

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	0.580	1fblA	0.571	4.04	0.421	0.692	3.4.24.7	217,234
2	0.287	1l6jA	0.416	1.45	0.463	0.425	3.4.24.35	217,234
3	0.275	1su3B	0.588	5.08	0.372	0.766	3.4.24.7	217,234
4	0.183	3ba0A	0.366	1.37	0.234	0.374	3.4.24.65	217,234
5	0.070	3hdaP	0.356	5.92	0.150	0.479	3.4.24.-	217

	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	0.06	1g4kA	0.316	1.76	0.593	0.326	0.22	HQQ	complex1.pdb.gz	93,94,95,96,226
2	0.06	1cizA	0.316	1.77	0.593	0.326	0.18	DPS	complex2.pdb.gz	225,226,235,236,237,238
3	0.06	3usnA	0.308	2.13	0.593	0.326	0.16	ATT	complex3.pdb.gz	91,92,93,94
4	0.06	2usnA	0.309	1.85	0.579	0.320	0.14	IN8	complex4.pdb.gz	62,92,94,99
5	0.05	1eakA	0.435	2.05	0.484	0.454	0.13	III	complex5.pdb.gz	68,69,182,225
6	0.04	1gxd3	0.597	5.72	0.297	0.842	0.12	III	complex6.pdb.gz	90,91,92
7	0.04	1gxd0	0.597	5.72	0.297	0.842	0.11	III	complex7.pdb.gz	32,161,180,181,182

	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.