StarFunc result for job id P34897

User Input

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

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:P34897	1.000	1.000	6.295E-98	504	1.000	1.000	P34897.pdb.gz	GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial OS=Homo sapiens OX=9606 GN=SHMT2 PE=1 SV=3
2	AFDB:A9LDD9	0.926	0.948	6.707E-85	492	0.762	0.780	A9LDD9.pdb.gz	A9LDD9_DANRE glycine hydroxymethyltransferase OS=Danio rerio OX=7955 GN=shmt2 PE=1 SV=1
3	PDB:7byiA	0.912	0.993	1.394E-81	463	0.915	0.996	7byiA.pdb.gz	Structure of SHMT2 with CBX
4	PDB:5x3vB	0.865	0.985	1.042E-76	442	0.873	0.995	5x3vB.pdb.gz
5	PDB:6dk3A	0.828	0.985	5.444E-74	423	0.833	0.993	6dk3A.pdb.gz
6	AFDB:Q6TXG7	0.906	0.671	6.655E-73	681	0.591	0.438	Q6TXG7.pdb.gz	Q6TXG7_RAT Serine hydroxymethyltransferase OS=Rattus norvegicus OX=10116 GN=Shmt1 PE=1 SV=1
7	AFDB:Q2TL58	0.909	0.952	4.167E-72	481	0.595	0.624	Q2TL58.pdb.gz
8	AFDB:Q9SZJ5	0.908	0.885	4.641E-72	517	0.577	0.563	Q9SZJ5.pdb.gz	GLYM1_ARATH Serine hydroxymethyltransferase 1, mitochondrial OS=Arabidopsis thaliana OX=3702 GN=SHM1 PE=1 SV=1
9	AFDB:Q9W457	0.910	0.854	5.261E-71	537	0.567	0.533	Q9W457.pdb.gz	Q9W457_DROME Serine hydroxymethyltransferase OS=Drosophila melanogaster OX=7227 GN=Shmt PE=1 SV=1
10	AFDB:Q2F5L3	0.904	0.979	1.005E-70	465	0.552	0.598	Q2F5L3.pdb.gz	GLYC_BOMMO Serine hydroxymethyltransferase OS=Bombyx mori OX=7091 GN=692975 PE=1 SV=1
11	AFDB:Q94C74	0.912	0.889	2.515E-70	517	0.565	0.551	Q94C74.pdb.gz	GLYM2_ARATH Serine hydroxymethyltransferase 2, mitochondrial OS=Arabidopsis thaliana OX=3702 GN=SHM2 PE=1 SV=2
12	AFDB:Q60V73	0.916	0.903	1.492E-69	511	0.548	0.540	Q60V73.pdb.gz	GLYC_CAEBR Serine hydroxymethyltransferase OS=Caenorhabditis briggsae OX=6238 GN=mel-32 PE=3 SV=3
13	AFDB:Q94JQ3	0.869	0.828	2.850E-69	529	0.548	0.522	Q94JQ3.pdb.gz	GLYP3_ARATH Serine hydroxymethyltransferase 3, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=SHM3 PE=1 SV=2
14	PDB:6smnD	0.898	0.942	3.522E-68	480	0.550	0.577	6smnD.pdb.gz	Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models.
15	PDB:1ejiA	0.899	0.947	7.912E-68	478	0.591	0.623	1ejiA.pdb.gz	Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers.
16	PDB:6smrA	0.886	0.944	2.933E-63	473	0.536	0.571	6smrA.pdb.gz	Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models.
17	PDB:4o6zA	0.858	0.963	7.700E-54	448	0.413	0.464	4o6zA.pdb.gz	The structure of Plasmodium falciparum serine hydroxymethyltransferase reveals a novel redox switch that regulates its activities.
18	PDB:3h7fB	0.769	0.902	4.237E-48	428	0.407	0.479	3h7fB.pdb.gz
19	PDB:1dfoB	0.790	0.951	2.026E-47	417	0.389	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.
20	PDB:2hufA	0.542	0.689	3.929E-15	385	0.111	0.145	2hufA.pdb.gz	Crystal Structures of Aedes aegypti Alanine Glyoxylate Aminotransferase.

(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	615	478	0.595	0.628	A0A8I5ZKU9_RAT Serine hydroxymethyltransferase OS=Rattus norvegicus OX=10116 GN=Shmt1 PE=1 SV=1
2	A0A8I6GI43	931	496	0.903	0.917	A0A8I6GI43_RAT Serine hydroxymethyltransferase OS=Rattus norvegicus OX=10116 GN=Shmt2 PE=1 SV=1
3	A9LDD9	805	492	0.762	0.780	A9LDD9_DANRE glycine hydroxymethyltransferase OS=Danio rerio OX=7955 GN=shmt2 PE=1 SV=1
4	B7Z0X1	595	467	0.548	0.591	B7Z0X1_DROME Serine hydroxymethyltransferase OS=Drosophila melanogaster OX=7227 GN=Shmt PE=1 SV=1
5	O23254	550	471	0.548	0.586	GLYC4_ARATH Serine hydroxymethyltransferase 4 OS=Arabidopsis thaliana OX=3702 GN=SHM4 PE=1 SV=1
6	P34896	617	483	0.603	0.629	GLYC_HUMAN Serine hydroxymethyltransferase, cytosolic OS=Homo sapiens OX=9606 GN=SHMT1 PE=1 SV=1
7	P34897	1045	504	1.000	1.000	GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial OS=Homo sapiens OX=9606 GN=SHMT2 PE=1 SV=3
8	P37291	548	469	0.502	0.539	GLYC_YEAST Serine hydroxymethyltransferase, cytosolic OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=SHM2 PE=1 SV=2
9	P37292	527	490	0.490	0.504	GLYM_YEAST Serine hydroxymethyltransferase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=SHM1 PE=1 SV=2
10	P50431	618	478	0.597	0.630	GLYC_MOUSE Serine hydroxymethyltransferase, cytosolic OS=Mus musculus OX=10090 GN=Shmt1 PE=1 SV=3
11	P50432	581	507	0.554	0.550	GLYC_CAEEL Serine hydroxymethyltransferase OS=Caenorhabditis elegans OX=6239 GN=mel-32 PE=1 SV=2
12	Q10104	560	488	0.540	0.557	GLYM_SCHPO Serine hydroxymethyltransferase, mitochondrial OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=shm2 PE=3 SV=2
13	Q2F5L3	598	465	0.554	0.600	GLYC_BOMMO Serine hydroxymethyltransferase OS=Bombyx mori OX=7091 GN=692975 PE=1 SV=1
14	Q4Q828	530	474	0.534	0.568	Q4Q828_LEIMA Serine hydroxymethyltransferase OS=Leishmania major OX=5664 GN=SHMT-L PE=3 SV=1
15	Q54Z26	565	457	0.548	0.604	GLYC1_DICDI Serine hydroxymethyltransferase 1 OS=Dictyostelium discoideum OX=44689 GN=shmt1 PE=1 SV=1
16	Q5U3Z7	978	504	0.938	0.938	Q5U3Z7_RAT Serine hydroxymethyltransferase OS=Rattus norvegicus OX=10116 GN=Shmt2 PE=1 SV=1
17	Q60V73	581	511	0.552	0.544	GLYC_CAEBR Serine hydroxymethyltransferase OS=Caenorhabditis briggsae OX=6238 GN=mel-32 PE=3 SV=3
18	Q6FUP6	559	469	0.516	0.554	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	613	681	0.591	0.438	Q6TXG7_RAT Serine hydroxymethyltransferase OS=Rattus norvegicus OX=10116 GN=Shmt1 PE=1 SV=1
20	Q7SXN1	638	481	0.593	0.622	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	PF00464 SHMT	2.3e-210	709.8	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.ENSP00000333667

Rank	PPI partner	STRING score	Description
1	9606.ENSP00000298492	0.998	BRISC complex subunit Abraxas 2
2	9606.ENSP00000352408	0.998	BRISC and BRCA1-A complex member 1
3	9606.ENSP00000358474	0.998	Lys-63-specific deubiquitinase BRCC36
4	9606.ENSP00000371253	0.998	Trifunctional purine biosynthetic protein adenosine-3
5	9606.ENSP00000343412	0.997	BRISC and BRCA1-A complex member 2
6	9606.ENSP00000273588	0.996	Aminomethyltransferase, mitochondrial
7	9606.ENSP00000236959	0.995	Bifunctional purine biosynthesis protein PURH
8	9606.ENSP00000216605	0.993	C-1-tetrahydrofolate synthase, cytoplasmic
9	9606.ENSP00000377617	0.993	Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
10	9606.ENSP00000478253	0.992	Monofunctional C1-tetrahydrofolate synthase, mitochondrial
11	9606.ENSP00000370737	0.991	Glycine dehydrogenase (decarboxylating), mitochondrial
12	9606.ENSP00000379108	0.989	Probable bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase 2
13	9606.ENSP00000378854	0.986	Phosphoserine phosphatase
14	9606.ENSP00000315644	0.985	Thymidylate synthase
15	9606.ENSP00000360938	0.983	Sarcosine dehydrogenase, mitochondrial
16	9606.ENSP00000365777	0.983	Methylenetetrahydrofolate reductase
17	9606.ENSP00000396308	0.981	Dihydrofolate reductase
18	9606.ENSP00000319531	0.979	Glycine cleavage system H protein, mitochondrial
19	9606.ENSP00000302620	0.973	Alanine-glyoxylate aminotransferase
20	9606.ENSP00000355536	0.972	Methionine synthase

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:0004372	1.000	glycine hydroxymethyltransferase activity
GO:0030170	1.000	pyridoxal phosphate binding
GO:0005515	0.996	protein binding
GO:0042802	0.656	identical protein 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:0044237	0.998	cellular metabolic process
GO:0044238	0.995	primary metabolic process
GO:1901564	0.995	organonitrogen compound metabolic process
GO:0044281	0.991	small molecule metabolic process
GO:0009069	0.955	serine family amino acid metabolic process
GO:0065007	0.945	biological regulation
GO:0006544	0.935	glycine metabolic process
GO:0050789	0.929	regulation of biological process
GO:0050794	0.917	regulation of cellular process
GO:1901360	0.825	organic cyclic compound metabolic process
GO:0006725	0.797	cellular aromatic compound metabolic process
GO:0046483	0.796	heterocycle metabolic process
GO:0006563	0.687	L-serine metabolic process
GO:0006575	0.647	cellular modified amino acid metabolic process
GO:0042558	0.620	pteridine-containing compound metabolic process
GO:0006760	0.507	folic acid-containing compound metabolic process
GO:1901576	0.448	organic substance biosynthetic process
GO:0044249	0.441	cellular biosynthetic process
GO:0046653	0.433	tetrahydrofolate metabolic process
GO:1901566	0.420	organonitrogen compound biosynthetic 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:0005739	0.999	mitochondrion
GO:0016020	0.961	membrane
GO:0043233	0.869	organelle lumen
GO:0070013	0.859	intracellular organelle lumen
GO:0005634	0.731	nucleus
GO:0005759	0.669	mitochondrial matrix
GO:0043232	0.569	intracellular non-membrane-bounded organelle
GO:0005856	0.358	cytoskeleton
GO:0031090	0.335	organelle membrane
GO:0015630	0.306	microtubule cytoskeleton

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	1.000	(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine
EC:2.1.2.1	1.000	glycine hydroxymethyltransferase.

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