STRINGSTRING
Ssed_2298 Ssed_2298 Ssed_0173 Ssed_0173 recG recG Ssed_0463 Ssed_0463 Ssed_0562 Ssed_0562 Ssed_0647 Ssed_0647 rnr rnr priB priB rsgA rsgA lysS lysS recO recO Ssed_1257 Ssed_1257 rlmD rlmD ligA ligA Ssed_1806 Ssed_1806 Ssed_1884 Ssed_1884 infA infA pnp pnp rpsL rpsL rplB rplB rpsQ rpsQ ccmE ccmE rho rho Ssed_4025 Ssed_4025 nusA nusA aspS aspS ruvA ruvA efp efp asnS asnS pheT pheT Ssed_2610 Ssed_2610 Ssed_2614 Ssed_2614 rne rne Ssed_2639 Ssed_2639 metG metG Ssed_2658 Ssed_2658 Ssed_3146 Ssed_3146 Ssed_3278 Ssed_3278
Nodes:
Network nodes represent proteins
splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.
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colored nodes:
query proteins and first shell of interactors
white nodes:
second shell of interactors
Node Content
empty nodes:
proteins of unknown 3D structure
filled nodes:
a 3D structure is known or predicted
Edges:
Edges represent protein-protein associations
associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding to each other.
Known Interactions
from curated databases
experimentally determined
Predicted Interactions
gene neighborhood
gene fusions
gene co-occurrence
Others
textmining
co-expression
protein homology
Your Input:
Ssed_2298Ribosomal protein S1; Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence. (555 aa)
Ssed_0173KEGG: slo:Shew_3634 RNA binding S1 domain protein. (804 aa)
recGATP-dependent DNA helicase RecG; Critical role in recombination and DNA repair. Helps process Holliday junction intermediates to mature products by catalyzing branch migration. Has a DNA unwinding activity characteristic of a DNA helicase with a 3'- to 5'- polarity. Unwinds branched duplex DNA (Y- DNA); Belongs to the helicase family. RecG subfamily. (691 aa)
Ssed_0463KEGG: shw:Sputw3181_3627 protein of unknown function DUF107. (157 aa)
Ssed_0562KEGG: slo:Shew_0407 ribonuclease, Rne/Rng family. (500 aa)
Ssed_0647KEGG: sfr:Sfri_3647 cold-shock DNA-binding domain protein. (217 aa)
rnrExoribonuclease II; 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs. (833 aa)
priBSingle-strand binding protein/primosomal replication protein N; Binds single-stranded DNA at the primosome assembly site (PAS); Belongs to the PriB family. (101 aa)
rsgARibosome small subunit-dependent GTPase A; One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Helps release RbfA from mature subunits. May play a role in the assembly of ribosomal proteins into the subunit. Circularly permuted GTPase that catalyzes slow GTP hydrolysis, GTPase activity is stimulated by the 30S ribosomal subunit; Belongs to the TRAFAC class YlqF/YawG GTPase family. RsgA subfamily. (352 aa)
lysSKEGG: slo:Shew_0812 lysyl-tRNA synthetase; Belongs to the class-II aminoacyl-tRNA synthetase family. (500 aa)
recODNA repair protein RecO; Involved in DNA repair and RecF pathway recombination. (226 aa)
Ssed_1257KEGG: ppr:PBPRB0036 putative Cold shock-like protein. (70 aa)
rlmDRNA methyltransferase, TrmA family; Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA; Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily. (442 aa)
ligADNA ligase (NAD(+)); DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double- stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. (670 aa)
Ssed_1806KEGG: pin:Ping_1470 elongation factor P-like protein YeiP. (191 aa)
Ssed_1884KEGG: slo:Shew_1564 cold-shock DNA-binding domain protein. (68 aa)
infATranslation initiation factor IF-1; One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. (72 aa)
pnpPolyribonucleotide nucleotidyltransferase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction. (704 aa)
rpsLRibosomal protein S12; With S4 and S5 plays an important role in translational accuracy. (124 aa)
rplBRibosomal protein L2; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. (275 aa)
rpsQRibosomal protein S17; One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. (82 aa)
ccmECcmE/CycJ protein; Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH. Belongs to the CcmE/CycJ family. (161 aa)
rhoTranscription termination factor Rho; Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA- dependent ATPase activity, and release of the mRNA from the DNA template. (421 aa)
Ssed_4025Single-strand binding protein; Plays an important role in DNA replication, recombination and repair. Binds to ssDNA and to an array of partner proteins to recruit them to their sites of action during DNA metabolism. (231 aa)
nusANusA antitermination factor; Participates in both transcription termination and antitermination. (499 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. (595 aa)
ruvAHolliday junction DNA helicase RuvA; The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. (205 aa)
efpTranslation elongation factor P; Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. (186 aa)
asnSKEGG: slo:Shew_1900 asparaginyl-tRNA synthetase. (466 aa)
pheTPhenylalanine--tRNA ligase; KEGG: slo:Shew_2215 phenylalanyl-tRNA synthetase, beta subunit. (795 aa)
Ssed_2610KEGG: slo:Shew_1618 hypothetical protein; Belongs to the CvfB family. (277 aa)
Ssed_2614KEGG: slo:Shew_1614 cold-shock DNA-binding domain protein. (68 aa)
rneRibonuclease, Rne/Rng family; Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs. Belongs to the RNase E/G family. RNase E subfamily. (1201 aa)
Ssed_2639KEGG: slo:Shew_1587 ATP dependent DNA ligase. (281 aa)
metGMethionine--tRNA ligase; Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. (692 aa)
Ssed_2658KEGG: sdn:Sden_2190 protein of unknown function DUF107. (501 aa)
Ssed_3146KEGG: slo:Shew_2620 DNA polymerase III, alpha subunit. (1157 aa)
Ssed_3278KEGG: sfr:Sfri_0868 hypothetical protein. (274 aa)
Your Current Organism:
Shewanella sediminis
NCBI taxonomy Id: 425104
Other names: S. sediminis HAW-EB3, Shewanella sediminis HAW-EB3, Shewanella sediminis str. HAW-EB3, Shewanella sediminis strain HAW-EB3
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