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Shew_0016 Shew_0016 glyQ glyQ glyS glyS alaS alaS rlmN rlmN hisS hisS gltX gltX metG metG asnS asnS Shew_1966 Shew_1966 serS serS thrS thrS aspS aspS pth pth leuS leuS gluQ gluQ rph rph Shew_3489 Shew_3489 trmH trmH dtd dtd trmL trmL Shew_3586 Shew_3586 fmt fmt rnpA rnpA tyrS tyrS Shew_2099 Shew_2099 pheT pheT pheS pheS dusC dusC truA truA tgt tgt queA queA mnmC mnmC Shew_2412 Shew_2412 cysS cysS Shew_2514 Shew_2514 glnS glnS proS proS hemA hemA Shew_2722 Shew_2722 thiI thiI truB truB trmD trmD ileS ileS trmB trmB truD truD cca cca valS valS lysS lysS Shew_0768 Shew_0768 Shew_0707 Shew_0707 miaA miaA dusA dusA cmoM cmoM argS argS dusB dusB trpS trpS trmA trmA selU selU
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query proteins and first shell of interactors
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second shell of interactors
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proteins of unknown 3D structure
filled nodes:
a 3D structure is known or predicted
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experimentally determined
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Shew_0016TIGRFAM: ybaK/ebsC protein; PFAM: YbaK/prolyl-tRNA synthetase associated region; KEGG: vfi:VF1792 regulatory protein. (154 aa)
glyQGlycine--tRNA ligase; PFAM: glycyl-tRNA synthetase, alpha subunit; KEGG: shm:Shewmr7_0009 glycyl-tRNA synthetase, alpha subunit. (301 aa)
glySGlycine--tRNA ligase; KEGG: shm:Shewmr7_0008 glycyl-tRNA synthetase, beta subunit. (689 aa)
alaSalanyl-tRNA synthetase; Catalyzes the attachment of alanine to tRNA(Ala) in a two- step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain. (874 aa)
rlmNRadical SAM enzyme, Cfr family; Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity; Belongs to the radical SAM superfamily. RlmN family. (373 aa)
hisSKEGG: sfr:Sfri_1117 histidyl-tRNA synthetase; TIGRFAM: histidyl-tRNA synthetase; PFAM: tRNA synthetase, class II (G, H, P and S); Anticodon-binding domain protein. (423 aa)
gltXglutamyl-tRNA synthetase; Catalyzes the attachment of glutamate to tRNA(Glu) in a two- step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). (469 aa)
metGmethionyl-tRNA synthetase; Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. (673 aa)
asnSTIGRFAM: asparaginyl-tRNA synthetase; PFAM: tRNA synthetase, class II (D, K and N); nucleic acid binding, OB-fold, tRNA/helicase-type; KEGG: she:Shewmr4_2128 asparaginyl-tRNA synthetase. (466 aa)
Shew_1966PFAM: DTW domain containing protein; KEGG: sdn:Sden_1780 hypothetical protein. (249 aa)
serSseryl-tRNA synthetase; Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L- seryl-tRNA(Sec), which will be further converted into selenocysteinyl- tRNA(Sec). (428 aa)
thrSthreonyl-tRNA synthetase; Catalyzes the attachment of threonine to tRNA(Thr) in a two- step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). (642 aa)
aspSaspartyl-tRNA synthetase; Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp- AMP and then transferred to the acceptor end of tRNA(Asp). Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. (592 aa)
pthpeptidyl-tRNA hydrolase; The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. Belongs to the PTH family. (195 aa)
leuSTIGRFAM: leucyl-tRNA synthetase; KEGG: sdn:Sden_0797 leucyl-tRNA synthetase; Belongs to the class-I aminoacyl-tRNA synthetase family. (863 aa)
gluQGlutamate--tRNA ligase; Catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto a tRNA(Asp). Glutamate is transferred on the 2-amino-5-(4,5-dihydroxy-2- cyclopenten-1-yl) moiety of the queuosine in the wobble position of the QUC anticodon; Belongs to the class-I aminoacyl-tRNA synthetase family. GluQ subfamily. (319 aa)
rphRNAse PH; Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. (237 aa)
Shew_3489PFAM: YicC N-terminal domain protein; domain of unknown function DUF1732; KEGG: she:Shewmr4_3605 hypothetical protein. (287 aa)
trmHtRNA guanosine-2'-O-methyltransferase; Catalyzes the 2'-O methylation of guanosine at position 18 in tRNA; Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family. (234 aa)
dtdD-tyrosyl-tRNA(Tyr) deacylase; An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA- based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D- aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl- tRNA entities in vivo and helps enforce protein L-homochirality. Belongs to the DTD family. (145 aa)
trmLRNA methyltransferase, TrmH family, group 2; Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2'-OH of the wobble nucleotide. (154 aa)
Shew_3586PFAM: DTW domain containing protein; KEGG: sfr:Sfri_0299 DTW domain containing protein. (200 aa)
fmtmethionyl-tRNA formyltransferase; Attaches a formyl group to the free amino group of methionyl- tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus; Belongs to the Fmt family. (324 aa)
rnpARibonuclease P protein component; RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. (120 aa)
tyrStyrosyl-tRNA synthetase; Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two- step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr); Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 2 subfamily. (398 aa)
Shew_2099PFAM: DTW domain containing protein; KEGG: cps:CPS_2423 hypothetical protein. (189 aa)
pheTKEGG: she:Shewmr4_1809 phenylalanyl-tRNA synthetase, beta subunit; TIGRFAM: phenylalanyl-tRNA synthetase, beta subunit. (795 aa)
pheSKEGG: she:Shewmr4_1808 phenylalanyl-tRNA synthetase, alpha subunit; TIGRFAM: phenylalanyl-tRNA synthetase, alpha subunit; PFAM: phenylalanyl-tRNA synthetase, class IIc; aminoacyl tRNA synthetase, class II domain protein; Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. (336 aa)
dusCDihydrouridine synthase, DuS; Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. Specifically modifies U16 in tRNAs. Belongs to the Dus family. DusC subfamily. (309 aa)
truAtRNA pseudouridine synthase A; Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. (261 aa)
tgtQueuine tRNA-ribosyltransferase; Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming PreQ1, allowing a nucleophilic attack on the C1' of the ribose to form th [...] (374 aa)
queAS-adenosylmethionine--tRNA-ribosyltransferase- isomerase; Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). (345 aa)
mnmCFAD dependent oxidoreductase; Catalyzes the last two steps in the biosynthesis of 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34; In the N-terminal section; belongs to the methyltransferase superfamily. tRNA (mnm(5)s(2)U34)-methyltransferase family. (686 aa)
Shew_2412PFAM: tRNA/rRNA methyltransferase (SpoU); KEGG: sdn:Sden_1541 tRNA/rRNA methyltransferase (SpoU). (174 aa)
cysSKEGG: sfr:Sfri_2599 cysteinyl-tRNA synthetase; TIGRFAM: cysteinyl-tRNA synthetase; PFAM: cysteinyl-tRNA synthetase, class Ia; Belongs to the class-I aminoacyl-tRNA synthetase family. (459 aa)
Shew_2514PFAM: tRNA--hydroxylase; KEGG: shm:Shewmr7_2569 tRNA hydroxylase. (256 aa)
glnSKEGG: shm:Shewmr7_2571 glutaminyl-tRNA synthetase; TIGRFAM: glutaminyl-tRNA synthetase; PFAM: glutamyl-tRNA synthetase, class Ic. (556 aa)
proSprolyl-tRNA synthetase; Catalyzes the attachment of proline to tRNA(Pro) in a two- step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves dea [...] (569 aa)
hemAglutamyl-tRNA reductase; Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (416 aa)
Shew_2722KEGG: sdn:Sden_2403 hypothetical protein. (235 aa)
thiIThiamine biosynthesis/tRNA modification protein ThiI; Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS. (485 aa)
truBtRNA pseudouridine synthase B; Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs; Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. (315 aa)
trmDtRNA (Guanine37-N(1)-) methyltransferase; Specifically methylates guanosine-37 in various tRNAs. Belongs to the RNA methyltransferase TrmD family. (248 aa)
ileSIsoleucyl-tRNA synthetase; Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily. (940 aa)
trmBtRNA (guanine-N(7)-)-methyltransferase; Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. (238 aa)
truDPseudouridylate synthase; Responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs; Belongs to the pseudouridine synthase TruD family. (355 aa)
ccaMetal dependent phosphohydrolase; Catalyzes the addition and repair of the essential 3'- terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. Also shows phosphatase, 2'-nucleotidase and 2',3'-cyclic phosphodiesterase activities. These phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases. (413 aa)
valSvalyl-tRNA synthetase; Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a 'posttransfer' editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA- dependent manner; Belongs to the class-I aminoacyl-tRNA synthetase family. ValS type 1 subfamily. (959 aa)
lysSTIGRFAM: lysyl-tRNA synthetase; PFAM: tRNA synthetase, class II (D, K and N); nucleic acid binding, OB-fold, tRNA/helicase-type; KEGG: sdn:Sden_3127 lysyl-tRNA synthetase; Belongs to the class-II aminoacyl-tRNA synthetase family. (500 aa)
Shew_0768Methyltransferase small; Specifically methylates the adenine in position 37 of tRNA(1)(Val) (anticodon cmo5UAC). (243 aa)
Shew_0707PFAM: YbaK/prolyl-tRNA synthetase associated region; KEGG: vpa:VPA0766 hypothetical protein. (159 aa)
miaAtRNA delta(2)-isopentenylpyrophosphate transferase; Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A); Belongs to the IPP transferase family. (308 aa)
dusATIM-barrel protein, yjbN family; Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. Specifically modifies U20 and U20a in tRNAs; Belongs to the Dus family. DusA subfamily. (329 aa)
cmoMMethyltransferase type 12; Catalyzes the methylation of 5-carboxymethoxyuridine (cmo5U) to form 5-methoxycarbonylmethoxyuridine (mcmo5U) at position 34 in tRNAs; Belongs to the class I-like SAM-binding methyltransferase superfamily. CmoM family. (284 aa)
argSKEGG: shm:Shewmr7_0456 arginyl-tRNA synthetase; TIGRFAM: arginyl-tRNA synthetase. (581 aa)
dusBPutative TIM-barrel protein, nifR3 family; Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines; Belongs to the Dus family. DusB subfamily. (322 aa)
trpStryptophanyl-tRNA synthetase; Catalyzes the attachment of tryptophan to tRNA(Trp). Belongs to the class-I aminoacyl-tRNA synthetase family. (332 aa)
trmAtRNA (uracil-5-)-methyltransferase; Dual-specificity methyltransferase that catalyzes the formation of 5-methyluridine at position 54 (m5U54) in all tRNAs, and that of position 341 (m5U341) in tmRNA (transfer-mRNA). (365 aa)
selUtRNA 2-selenouridine synthase; Involved in the post-transcriptional modification of the uridine at the wobble position (U34) of tRNA(Lys), tRNA(Glu) and tRNA(Gln). Catalyzes the conversion of 2-thiouridine (S2U-RNA) to 2- selenouridine (Se2U-RNA). Acts in a two-step process involving geranylation of 2-thiouridine (S2U) to S-geranyl-2-thiouridine (geS2U) and subsequent selenation of the latter derivative to 2-selenouridine (Se2U) in the tRNA chain. (372 aa)
Your Current Organism:
Shewanella loihica
NCBI taxonomy Id: 323850
Other names: S. loihica PV-4, Shewanella loihica PV-4, Shewanella loihica str. PV-4, Shewanella loihica strain PV-4, Shewanella sp. PV-4
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