D-I-TASSER results for A0A286YFK9

Summary of the Protein

Uniprot ID: A0A286YFK9


Protein Name: Small integral membrane protein 38


Gene Name: SMIM38

Input Sequence in FASTA format

>A0A286YFK9 (51 residues)
MTSWPGGSFGPDPLLALLVVILLARLILWSCLGTYIDYRLAQRRPQKPKQD

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

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	Sequence
1	A0A286YFK9-D1	1-51	51	MTSWPGGSFGPDPLLALLVVILLARLILWSCLGTYIDYRLAQRRPQKPKQD

Top 1 final models from D-I-TASSER

Rank^a	Estimated TM-score^b
1	0.6409


(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.
1	1rh1A	0.76	2.05	0.020	0.961
2	5u1dB	0.76	2.36	0.039	0.961
3	3rx6A	0.76	1.80	0.039	0.922
4	3zbhA	0.75	1.70	0.111	0.882
5	7ad3B	0.75	1.96	0.061	0.961
6	3i9wA	0.75	2.17	0.137	0.941
7	6gauA2	0.75	2.68	0.120	0.980
8	6h7wB	0.75	1.57	0.039	0.902
9	1ki1D	0.75	2.24	0.039	0.961
10	4fm3A	0.75	1.34	0.078	0.882



(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:0046872	0.54	metal ion binding
GO:0019207	0.54	kinase regulator activity
GO:0008047	0.54	enzyme activator activity
GO:0005198	0.54	structural molecule activity
GO:0005088	0.54	Ras guanyl-nucleotide exchange factor activity






(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:

Biological Process (BP)


GO term	Cscore^GO	Name
GO:1902533	0.54	positive regulation of intracellular signal transduction
GO:1901215	0.54	negative regulation of neuron death
GO:0072583	0.54	clathrin-mediated endocytosis
GO:0051896	0.54	regulation of protein kinase B signaling
GO:0051345	0.54	positive regulation of hydrolase activity
GO:0046578	0.54	regulation of Ras protein signal transduction
GO:0045937	0.54	positive regulation of phosphate metabolic process
GO:0043523	0.54	regulation of neuron apoptotic process
GO:0043087	0.54	regulation of GTPase activity
GO:0043068	0.54	positive regulation of programmed cell death
GO:0043066	0.54	negative regulation of apoptotic process
GO:0042325	0.54	regulation of phosphorylation
GO:0036465	0.54	synaptic vesicle recycling
GO:0007266	0.54	Rho protein signal transduction
GO:0007169	0.54	transmembrane receptor protein tyrosine kinase signaling pathway






(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:

Cellular Component (CC)


GO term	Cscore^GO	Name
GO:0044464	0.83	cell part
GO:0016020	0.75	membrane
GO:0044424	0.62	intracellular part






(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:

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	0.201	3brvC	0.617	1.69	0.024	0.726	2.7.11.10	17
2	0.194	1z8yN	0.552	1.28	0.083	0.706	3.4.21.90	19,24
3	0.189	2k1lA	0.459	1.95	0.162	0.608	2.7.10.1	9,17,21
4	0.186	2k9yA	0.525	2.03	0.135	0.706	2.7.10.1	5,23
5	0.178	2jwaA	0.590	2.34	0.125	0.726	2.7.10.1	18



(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	Predicted binding site residues
1	0.09	2xcrB	0.702	2.71	0.078	0.922	0.61	RXV	3,6,15
2	0.08	2xcsD	0.704	2.58	0.078	0.863	0.50	RXV	4,6,10
3	0.06	2yl4A	0.744	2.23	0.039	0.941	0.43	ACP	10,11,12,13



(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.

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.