D-I-TASSER P34897

D-I-TASSER results for P34897

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

Summary of the Protein

Uniprot ID: P34897
Protein Name: Serine hydroxymethyltransferase, mitochondrial
Gene Name: SHMT2

Input Sequence in FASTA format

>P34897 (504 residues)
MLYFSLFWAARPLQRCGQLVRMAIRAQHSNAAQTQTGEANRGWTGQESLSDSDPEMWELL
QREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQ
RRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDV
KRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREV
CDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVD
PKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARA
MADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAIT
PGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQ
RLANLRQRVEQFARAFPMPGFDEH

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	P34897-D1	1-504	504		MLYFSLFWAARPLQRCGQLVRMAIRAQHSNAAQTQTGEANRGWTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGFDEH

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7399

(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	6smnA	0.92	0.77	0.593	0.927	model1_6smnA.pdb.gz
2	1bj4A	0.91	0.97	0.647	0.927	model1_1bj4A.pdb.gz
3	6smrA	0.90	1.43	0.579	0.925	model1_6smrA.pdb.gz
4	4o6zA	0.87	1.30	0.461	0.887	model1_4o6zA.pdb.gz
5	6cczA	0.86	1.11	0.599	0.871	model1_6cczA.pdb.gz
6	2a7vA	0.82	1.23	0.974	0.833	model1_2a7vA.pdb.gz
7	4j5uA	0.81	1.23	0.459	0.829	model1_4j5uA.pdb.gz
8	1eqbB	0.80	1.40	0.459	0.825	model1_1eqbB.pdb.gz
9	6ymdA	0.80	1.81	0.474	0.829	model1_6ymdA.pdb.gz
10	3h7fB	0.79	1.78	0.489	0.823	model1_3h7fB.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:0004372	0.98	glycine hydroxymethyltransferase activity
GO:0043167	0.67	ion binding
GO:0048037	0.65	cofactor binding
GO:0030170	0.64	pyridoxal phosphate 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	0.98	single-organism process
GO:0009987	0.95	cellular process
GO:0008152	0.95	metabolic process
GO:0044237	0.92	cellular metabolic process
GO:0044281	0.91	small molecule metabolic process
GO:0044763	0.90	single-organism cellular process
GO:0071704	0.88	organic substance metabolic process
GO:0006807	0.85	nitrogen compound metabolic process
GO:1901564	0.83	organonitrogen compound metabolic process
GO:0006082	0.81	organic acid metabolic process
GO:0044238	0.80	primary metabolic process
GO:0009069	0.77	serine family amino acid metabolic process
GO:0019752	0.73	carboxylic acid metabolic process
GO:0006520	0.72	cellular amino acid metabolic process
GO:0006544	0.68	glycine metabolic process
GO:0006563	0.62	L-serine metabolic process
GO:0016043	0.53	cellular component organization
GO:1901360	0.52	organic cyclic compound metabolic process
GO:0046483	0.52	heterocycle metabolic process
GO:0006725	0.52	cellular aromatic compound metabolic process
GO:0065003	0.50	macromolecular complex assembly

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	0.99	intracellular part
GO:0044444	0.97	cytoplasmic part
GO:0043229	0.83	intracellular organelle
GO:0043231	0.82	intracellular membrane-bounded organelle
GO:0005739	0.66	mitochondrion
GO:0044446	0.51	intracellular organelle part

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	0.456	2vmzA	0.787	1.20	0.473	0.802	2.1.2.1	76,142,172,253,255,280,286,425
2	0.432	1kkjA	0.786	1.25	0.473	0.802	2.1.2.1	98,251,254,277,280
3	0.391	3n0lA	0.744	1.50	0.469	0.764	2.1.2.1	227,255,280,383,406,408,410,426,431
4	0.363	1lc7A	0.568	3.18	0.120	0.641	4.1.1.81	368
5	0.262	1rv3B	0.905	1.11	0.631	0.919	2.1.2.1	104

	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	0.74	1ejiA	0.917	1.58	0.632	0.943	1.80	PLG	complex1.pdb.gz	76,142,143,144,171,225,226,251,253,254,277,280,425
	2	0.72	1rv4A	0.900	1.08	0.635	0.913	1.30	PO4	complex2.pdb.gz	76,254,280,425

	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.