StarFunc result for job id P34896

User Input

>input (483 residues)
MTMPVNGAHKDADLWSSHDKMLAQPLKDSDVEVYNIIKKESNRQRVGLELIASENFASRA
VLEALGSCLNNKYSEGYPGQRYYGGTEFIDELETLCQKRALQAYKLDPQCWGVNVQPYSG
SPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMPYKVNPDTGY
INYDQLEENARLFHPKLIIAGTSCYSRNLEYARLRKIADENGAYLMADMAHISGLVAAGV
VPSPFEHCHVVTTTTHKTLRGCRAGMIFYRKGVKSVDPKTGKEILYNLESLINSAVFPGL
QGGPHNHAIAGVAVALKQAMTLEFKVYQHQVVANCRALSEALTELGYKIVTGGSDNHLIL
VDLRSKGTDGGRAEKVLEACSIACNKNTCPGDRSALRPSGLRLGTPALTSRGLLEKDFQK
VAHFIHRGIELTLQIQSDTGVRATLKEFKERLAGDKYQAAVQALREEVESFASLFPLPGL
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Proteins with similar structure

Top structural analogs (as identified by Foldseek and TM-align)

Rank	Structure template	TM-score1	TM-score2	Foldseek E-value	Length	ID1	ID2	Download	Description
1	AFDB:Q6TXG7	0.979	0.695	4.116E-92	681	0.899	0.637	Q6TXG7.pdb.gz	Q6TXG7_RAT Serine hydroxymethyltransferase OS=Rattus norvegicus OX=10116 GN=Shmt1 PE=1 SV=1
2	AFDB:Q2TL58	0.988	0.992	8.991E-88	481	0.787	0.790	Q2TL58.pdb.gz
3	PDB:1ejiA	0.972	0.982	2.913E-86	478	0.899	0.908	1ejiA.pdb.gz	Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers.
4	AFDB:P34897	0.947	0.908	2.622E-76	504	0.631	0.605	P34897.pdb.gz	GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial OS=Homo sapiens OX=9606 GN=SHMT2 PE=1 SV=3
5	AFDB:Q2F5L3	0.953	0.990	6.882E-76	465	0.615	0.639	Q2F5L3.pdb.gz	GLYC_BOMMO Serine hydroxymethyltransferase OS=Bombyx mori OX=7091 GN=692975 PE=1 SV=1
6	AFDB:A9LDD9	0.951	0.934	3.571E-75	492	0.615	0.604	A9LDD9.pdb.gz	A9LDD9_DANRE glycine hydroxymethyltransferase OS=Danio rerio OX=7955 GN=shmt2 PE=1 SV=1
7	AFDB:Q9W457	0.957	0.862	7.235E-74	537	0.582	0.523	Q9W457.pdb.gz	Q9W457_DROME Serine hydroxymethyltransferase OS=Drosophila melanogaster OX=7227 GN=Shmt PE=1 SV=1
8	AFDB:Q60V73	0.947	0.895	8.105E-74	511	0.605	0.571	Q60V73.pdb.gz	GLYC_CAEBR Serine hydroxymethyltransferase OS=Caenorhabditis briggsae OX=6238 GN=mel-32 PE=3 SV=3
9	AFDB:Q9SZJ5	0.955	0.893	1.168E-72	517	0.571	0.534	Q9SZJ5.pdb.gz	GLYM1_ARATH Serine hydroxymethyltransferase 1, mitochondrial OS=Arabidopsis thaliana OX=3702 GN=SHM1 PE=1 SV=1
10	AFDB:Q94C74	0.952	0.890	4.312E-72	517	0.573	0.536	Q94C74.pdb.gz	GLYM2_ARATH Serine hydroxymethyltransferase 2, mitochondrial OS=Arabidopsis thaliana OX=3702 GN=SHM2 PE=1 SV=2
11	AFDB:Q94JQ3	0.917	0.838	1.727E-70	529	0.582	0.531	Q94JQ3.pdb.gz	GLYP3_ARATH Serine hydroxymethyltransferase 3, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=SHM3 PE=1 SV=2
12	PDB:6smnD	0.956	0.962	1.141E-69	480	0.571	0.575	6smnD.pdb.gz	Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models.
13	PDB:7byiA	0.933	0.973	5.558E-67	463	0.625	0.652	7byiA.pdb.gz	Structure of SHMT2 with CBX
14	PDB:6smrA	0.930	0.950	5.698E-66	473	0.565	0.577	6smrA.pdb.gz	Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models.
15	PDB:5x3vB	0.887	0.968	2.211E-63	442	0.592	0.647	5x3vB.pdb.gz
16	PDB:6dk3A	0.847	0.966	1.552E-59	423	0.545	0.622	6dk3A.pdb.gz
17	PDB:4o6zA	0.888	0.957	5.980E-55	448	0.431	0.464	4o6zA.pdb.gz	The structure of Plasmodium falciparum serine hydroxymethyltransferase reveals a novel redox switch that regulates its activities.
18	PDB:1dfoB	0.806	0.931	1.266E-49	417	0.406	0.470	1dfoB.pdb.gz	Crystal structure at 2.4 A resolution of E. coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate.
19	PDB:3h7fB	0.803	0.904	5.069E-48	428	0.404	0.456	3h7fB.pdb.gz
20	PDB:6pk3B	0.522	0.616	3.039E-14	400	0.133	0.160	6pk3B.pdb.gz	Crystal Structure Of Photorespiratory Alanine:Glyoxylate Aminotransferase 1 (AGT1) FromArabidopsis thaliana.

(a)	The query structure is shown in cartoon, while the structural analog is displayed using a backbone trace.
(b)	Ranking of proteins is based on E-value of Foldseek alignment.
(c)	TM-score1 and ID1 are TM-score and sequence identity normalized by query sequence length.
(d)	TM-score2 and ID2 are TM-score and sequence identity normalized by template sequence length.

Proteins with similar sequence

Top sequence homologs in UniProt

Rank	Template	Bit-score	Length	ID1	ID2	Description
1	A0A8I5ZKU9	886	478	0.899	0.908	A0A8I5ZKU9_RAT Serine hydroxymethyltransferase OS=Rattus norvegicus OX=10116 GN=Shmt1 PE=1 SV=1
2	A0A8I6GI43	597	496	0.598	0.583	A0A8I6GI43_RAT Serine hydroxymethyltransferase OS=Rattus norvegicus OX=10116 GN=Shmt2 PE=1 SV=1
3	A9LDD9	617	492	0.611	0.600	A9LDD9_DANRE glycine hydroxymethyltransferase OS=Danio rerio OX=7955 GN=shmt2 PE=1 SV=1
4	B7Z0X1	583	467	0.578	0.597	B7Z0X1_DROME Serine hydroxymethyltransferase OS=Drosophila melanogaster OX=7227 GN=Shmt PE=1 SV=1
5	O23254	539	471	0.565	0.580	GLYC4_ARATH Serine hydroxymethyltransferase 4 OS=Arabidopsis thaliana OX=3702 GN=SHM4 PE=1 SV=1
6	P34896	1007	483	1.000	1.000	GLYC_HUMAN Serine hydroxymethyltransferase, cytosolic OS=Homo sapiens OX=9606 GN=SHMT1 PE=1 SV=1
7	P34897	638	504	0.629	0.603	GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial OS=Homo sapiens OX=9606 GN=SHMT2 PE=1 SV=3
8	P37291	555	469	0.534	0.550	GLYC_YEAST Serine hydroxymethyltransferase, cytosolic OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=SHM2 PE=1 SV=2
9	P37292	525	490	0.532	0.524	GLYM_YEAST Serine hydroxymethyltransferase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=SHM1 PE=1 SV=2
10	P50431	886	478	0.903	0.912	GLYC_MOUSE Serine hydroxymethyltransferase, cytosolic OS=Mus musculus OX=10090 GN=Shmt1 PE=1 SV=3
11	P50432	602	507	0.596	0.568	GLYC_CAEEL Serine hydroxymethyltransferase OS=Caenorhabditis elegans OX=6239 GN=mel-32 PE=1 SV=2
12	Q10104	534	488	0.534	0.529	GLYM_SCHPO Serine hydroxymethyltransferase, mitochondrial OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=shm2 PE=3 SV=2
13	Q2F5L3	619	465	0.615	0.639	GLYC_BOMMO Serine hydroxymethyltransferase OS=Bombyx mori OX=7091 GN=692975 PE=1 SV=1
14	Q4KLG7	555	352	0.578	0.793	Q4KLG7_RAT glycine hydroxymethyltransferase (Fragment) OS=Rattus norvegicus OX=10116 GN=Shmt1 PE=2 SV=1
15	Q54Z26	550	457	0.576	0.608	GLYC1_DICDI Serine hydroxymethyltransferase 1 OS=Dictyostelium discoideum OX=44689 GN=shmt1 PE=1 SV=1
16	Q5U3Z7	627	504	0.617	0.591	Q5U3Z7_RAT Serine hydroxymethyltransferase OS=Rattus norvegicus OX=10116 GN=Shmt2 PE=1 SV=1
17	Q60V73	608	511	0.602	0.569	GLYC_CAEBR Serine hydroxymethyltransferase OS=Caenorhabditis briggsae OX=6238 GN=mel-32 PE=3 SV=3
18	Q6FUP6	546	469	0.536	0.552	GLYC_CANGA Serine hydroxymethyltransferase, cytosolic OS=Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138) OX=284593 GN=SHM2 PE=3 SV=1
19	Q6TXG7	887	681	0.899	0.637	Q6TXG7_RAT Serine hydroxymethyltransferase OS=Rattus norvegicus OX=10116 GN=Shmt1 PE=1 SV=1
20	Q7SXN1	801	481	0.781	0.784	Q7SXN1_DANRE Serine hydroxymethyltransferase OS=Danio rerio OX=7955 GN=zgc:77524 PE=1 SV=1

(a)	Ranking of proteins is based on the E-value of a BLASTp alignment.
(b)	ID1 and ID2 are sequence identities normalized by the query and template sequence lengths, respectively.

Pfam families

Top Pfam family matches

Rank	Pfam family	E-value	Score	Description
1	PF00155 Aminotran_1_2	0.53	21.0	Aminotransferase class I and II
2	PF00464 SHMT	6.5e-213	718.2	Serine hydroxymethyltransferase

(a)	Ranking of Pfam families is based on the E-value provided by HMMsearch.

Protein-protein interaction (PPI) partners

Top PPI partners to 9606.ENSP00000318868

Rank	PPI partner	STRING score	Description
1	9606.ENSP00000371253	0.999	Trifunctional purine biosynthetic protein adenosine-3
2	9606.ENSP00000216605	0.996	C-1-tetrahydrofolate synthase, cytoplasmic
3	9606.ENSP00000236959	0.996	Bifunctional purine biosynthesis protein PURH
4	9606.ENSP00000273588	0.996	Aminomethyltransferase, mitochondrial
5	9606.ENSP00000315644	0.991	Thymidylate synthase
6	9606.ENSP00000370737	0.991	Glycine dehydrogenase (decarboxylating), mitochondrial
7	9606.ENSP00000377617	0.991	Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
8	9606.ENSP00000478253	0.991	Monofunctional C1-tetrahydrofolate synthase, mitochondrial
9	9606.ENSP00000379108	0.990	Probable bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase 2
10	9606.ENSP00000365777	0.989	Methylenetetrahydrofolate reductase
11	9606.ENSP00000378854	0.984	Phosphoserine phosphatase
12	9606.ENSP00000396308	0.984	Dihydrofolate reductase
13	9606.ENSP00000355536	0.983	Methionine synthase
14	9606.ENSP00000360938	0.982	Sarcosine dehydrogenase, mitochondrial
15	9606.ENSP00000319531	0.981	Glycine cleavage system H protein, mitochondrial
16	9606.ENSP00000258494	0.977	Mitochondrial 10-formyltetrahydrofolate dehydrogenase
17	9606.ENSP00000273450	0.976	Cytosolic 10-formyltetrahydrofolate dehydrogenase
18	9606.ENSP00000302620	0.974	Alanine-glyoxylate aminotransferase
19	9606.ENSP00000377768	0.969	Dihydrofolate reductase 2, mitochondrial
20	9606.ENSP00000381231	0.967	Hydro-lyase catalyzing the first step of the transsulfuration pathway, where the hydroxyl group of L-serine is displaced by L- homocysteine in a beta-replacement reaction to form L-cystathionine, the precursor of L-cysteine. This catabolic route allows the elimination of L-methionine and the toxic metabolite L-homocysteine. Also involved in the production of hydrogen sulfide, a gasotransmitter with signaling and cytoprotective effects on neurons.

A higher STRING score indicates a greater likelihood of interaction.
The query and PPI partners are shown as grey oval and white rectangles, respectively.
Interactions between query and PPI partners are shown by solid black lines. Interactions among PPI partners are by dashed grey lines.
Values in the rectangles are the STRING scores between query and each corresponding PPI partner

Predicted Gene Ontology (GO) Terms

GO term	C-score	Name
GO:0043168	0.999	anion binding
GO:0004372	0.999	glycine hydroxymethyltransferase activity
GO:0097159	0.998	organic cyclic compound binding
GO:1901363	0.997	heterocyclic compound binding
GO:0019842	0.997	vitamin binding
GO:0005515	0.993	protein binding
GO:0030170	0.992	pyridoxal phosphate binding
GO:0042802	0.913	identical protein binding
GO:0043177	0.418	organic acid binding
GO:0031406	0.408	carboxylic acid binding

C-score is the confidence score of a predicted GO term. Its value ranges from (0,1], where a higher value indicates a higher confidence prediction.
If a child GO term and its parent term have the same C-score, only the child term is shown in this table.

The graph shows the predicted terms for the Molecular Function (MF) GO aspect. GO terms shown in the table are colored by C-score in the graph:

[0.3,0.4)

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

GO term	C-score	Name
GO:0071704	0.995	organic substance metabolic process
GO:0044238	0.994	primary metabolic process
GO:0044237	0.994	cellular metabolic process
GO:0044281	0.991	small molecule metabolic process
GO:0009058	0.980	biosynthetic process
GO:0006807	0.979	nitrogen compound metabolic process
GO:0006520	0.973	amino acid metabolic process
GO:1901605	0.936	alpha-amino acid metabolic process
GO:0009069	0.884	serine family amino acid metabolic process
GO:0044249	0.846	cellular biosynthetic process
GO:0006544	0.813	glycine metabolic process
GO:1901576	0.735	organic substance biosynthetic process
GO:1901566	0.716	organonitrogen compound biosynthetic process
GO:0006563	0.641	L-serine metabolic process
GO:1901360	0.493	organic cyclic compound metabolic process
GO:0046483	0.476	heterocycle metabolic process
GO:0006725	0.474	cellular aromatic compound metabolic process
GO:0065007	0.354	biological regulation
GO:1901607	0.315	alpha-amino acid biosynthetic process
GO:0034641	0.307	cellular nitrogen compound metabolic process

C-score is the confidence score of a predicted GO term. Its value ranges from (0,1], where a higher value indicates a higher confidence prediction.
If a child GO term and its parent term have the same C-score, only the child term is shown in this table.

The graph shows the predicted terms for the Biological Process (BP) GO aspect. GO terms shown in the table are colored by C-score in the graph:

[0.3,0.4)

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

GO term	C-score	Name
GO:0043231	0.999	intracellular membrane-bounded organelle
GO:0005829	0.998	cytosol
GO:0005634	0.986	nucleus
GO:0043233	0.915	organelle lumen
GO:0070013	0.914	intracellular organelle lumen
GO:0005739	0.887	mitochondrion

C-score is the confidence score of a predicted GO term. Its value ranges from (0,1], where a higher value indicates a higher confidence prediction.
If a child GO term and its parent term have the same C-score, only the child term is shown in this table.

The graph shows the predicted terms for the Cellular Component (CC) GO aspect. GO terms shown in the table are colored by C-score in the graph:

[0.3,0.4)

[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 reactions (EC numbers and Rhea reactions)

Reaction	C-score	Name
RHEA:15481	0.999	(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine
EC:2.1.2.1	0.999	glycine hydroxymethyltransferase.

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