D-I-TASSER Q96GJ1

D-I-TASSER results for Q96GJ1

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

Summary of the Protein

Uniprot ID: Q96GJ1
Protein Name: tRNA (uracil(54)-C(5))-methyltransferase homolog
Gene Name: TRMT2B

Input Sequence in FASTA format

>Q96GJ1 (504 residues)
MAGLKRRVPLHSLRYFISMVGLFSKPGLLPWYARNPPGWSQLFLGTVCKGDFTRVIATKC
QKGQKSQKKPSHLGPLDGSWQERLADVVTPLWRLSYEEQLKVKFAAQKKILQRLESYIQM
LNGVSVTTAVPKSERLSCLLHPIIPSPVINGYRNKSTFSVNRGPDGNPKTVGFYLGTWRD
GNVVCVQSNHLKNIPEKHSQVAQYYEVFLRQSPLEPCLVFHEGGYWRELTVRTNSQGHTM
AIITFHPQKLSQEELHVQKEIVKEFFIRGPGAACGLTSLYFQESTMTRCSHQQSPYQLLF
GEPYIFEELLSLKIRISPDAFFQINTAGAEMLYRTVGELTGVNSDTILLDICCGTGVIGL
SLAQHTSRVLGIELLEQAVEDARWTAAFNGITNSEFHTGQAEKILPGLLKSKEDGQSIVA
VVNPARAGLHYKVIQAIRNFRAIHTLVFVSCKLHGESTRNVIELCCPPDPAKKLLGEPFV
LQQAVPVDLFPHTPHCELVLLFTR

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	Q96GJ1-D1	1-153,305-504	353		MAGLKRRVPLHSLRYFISMVGLFSKPGLLPWYARNPPGWSQLFLGTVCKGDFTRVIATKCQKGQKSQKKPSHLGPLDGSWQERLADVVTPLWRLSYEEQLKVKFAAQKKILQRLESYIQMLNGVSVTTAVPKSERLSCLLHPIIPSPVINGYRIFEELLSLKIRISPDAFFQINTAGAEMLYRTVGELTGVNSDTILLDICCGTGVIGLSLAQHTSRVLGIELLEQAVEDARWTAAFNGITNSEFHTGQAEKILPGLLKSKEDGQSIVAVVNPARAGLHYKVIQAIRNFRAIHTLVFVSCKLHGESTRNVIELCCPPDPAKKLLGEPFVLQQAVPVDLFPHTPHCELVLLFTR
2	Q96GJ1-D2	154-304	151		NKSTFSVNRGPDGNPKTVGFYLGTWRDGNVVCVQSNHLKNIPEKHSQVAQYYEVFLRQSPLEPCLVFHEGGYWRELTVRTNSQGHTMAIITFHPQKLSQEELHVQKEIVKEFFIRGPGAACGLTSLYFQESTMTRCSHQQSPYQLLFGEPY

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.84

(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	5xj1A	0.79	2.94	0.233	0.863	model1_5xj1A.pdb.gz
2	1uwvA	0.70	3.22	0.185	0.784	model1_1uwvA.pdb.gz
3	2vs1A	0.69	2.98	0.226	0.760	model1_2vs1A.pdb.gz
4	3bt7A	0.64	2.78	0.194	0.704	model1_3bt7A.pdb.gz
5	3vseA	0.48	4.92	0.091	0.601	model1_3vseA.pdb.gz
6	2b78A	0.47	4.89	0.055	0.589	model1_2b78A.pdb.gz
7	2cwwB	0.47	5.08	0.103	0.591	model1_2cwwB.pdb.gz
8	4dmgA	0.46	4.97	0.113	0.579	model1_4dmgA.pdb.gz
9	2as0A	0.46	5.12	0.127	0.583	model1_2as0A.pdb.gz
10	3c0kA	0.46	5.39	0.104	0.597	model1_3c0kA.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:1901363	0.81	heterocyclic compound binding
GO:0097159	0.81	organic cyclic compound binding
GO:0003676	0.74	nucleic acid binding
GO:0003824	0.67	catalytic activity
GO:0016740	0.63	transferase activity
GO:0008168	0.62	methyltransferase activity
GO:0008757	0.58	S-adenosylmethionine-dependent methyltransferase activity
GO:0003723	0.56	RNA binding
GO:0008173	0.55	RNA methyltransferase activity
GO:0044822	0.50	poly(A) RNA 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	1.00	metabolic process
GO:0016070	0.99	RNA metabolic process
GO:0009451	0.98	RNA modification
GO:0034660	0.96	ncRNA metabolic process
GO:0006396	0.96	RNA processing
GO:0034470	0.95	ncRNA processing
GO:0032259	0.81	methylation
GO:0001510	0.78	RNA methylation
GO:0016072	0.68	rRNA metabolic process
GO:0006399	0.63	tRNA metabolic process
GO:0008033	0.62	tRNA processing
GO:0006400	0.60	tRNA modification
GO:0006364	0.54	rRNA processing

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:0044424	1.00	intracellular part
GO:0044444	0.88	cytoplasmic part
GO:0043229	0.85	intracellular organelle
GO:0043231	0.77	intracellular membrane-bounded organelle
GO:0005739	0.72	mitochondrion

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	0.414	3bt7A	0.641	2.78	0.194	0.704	2.1.1.35	325
2	0.128	3bt7B	0.641	2.78	0.189	0.704	2.1.1.35	NA
3	0.060	2ip2A	0.375	4.60	0.067	0.460	2.1.1.-	359
4	0.060	2jkbA	0.376	7.44	0.040	0.615	3.2.1.18 4.2.2.15	NA
5	0.060	1yr2A	0.366	7.25	0.031	0.581	3.4.21.26	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	0.03	2bh2A	0.726	3.22	0.188	0.806	0.17	SF4	complex1.pdb.gz	86,88,89,185
2	0.03	3bt7A	0.641	2.78	0.194	0.704	0.33	RQA	complex2.pdb.gz	155,157,159,173,174,176,191,227,246,319,495
3	0.01	2bf4A	0.405	6.28	0.039	0.585	0.16	FMN	complex3.pdb.gz	25,26,27,84,85,86
4	0.01	2bf4A	0.405	6.28	0.039	0.585	0.15	NAP	complex4.pdb.gz	428,455,456
5	0.01	3eq8A	0.387	6.99	0.045	0.591	0.12	X98	complex5.pdb.gz	7,455,456,460
6	0.01	2bn4A	0.404	6.20	0.044	0.583	0.11	NAP	complex6.pdb.gz	425,426,458,459,460

	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.