GapMind for catabolism of small carbon sources

 

Protein GFF3781 in Marinobacter adhaerens HP15

Annotation: HP15_3723 PTS system, glucose-specific EIIA/HPr/phosphoenolpyruvate-protein phosphotransferase components

Length: 978 amino acids

Source: Marino in FitnessBrowser

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism fruI hi Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized) 50% 100% 870.9 trehalose-specific PTS system, I, HPr, and IIA components 43% 490.7
sucrose catabolism fruI hi Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized) 50% 100% 870.9 trehalose-specific PTS system, I, HPr, and IIA components 43% 490.7
trehalose catabolism treEIIA med trehalose-specific PTS system, I, HPr, and IIA components (characterized) 43% 83% 490.7 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 50% 870.9
N-acetyl-D-glucosamine catabolism nagF med N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 41% 85% 464.5 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 50% 870.9
D-glucosamine (chitosamine) catabolism nagF med N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 41% 85% 464.5 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 50% 870.9
D-fructose catabolism fruB med Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr (characterized) 41% 99% 253.8 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 50% 870.9
sucrose catabolism fruB med Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr (characterized) 41% 99% 253.8 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 50% 870.9
glycerol catabolism dhaM lo PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized) 30% 76% 143.3 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 50% 870.9
D-mannitol catabolism cmtB lo Mannitol-specific phosphotransferase enzyme IIA component, component of The mannitol porter (MtlA) (mannitol-1-P forming), MtlAF (characterized) 35% 99% 98.2 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 50% 870.9

Sequence Analysis Tools

View GFF3781 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MISDHICFTIDFKHADTIQQTKTDTQYQNKKRGNLMLTLTANDVRLGATASDWQDALQQA
ARDLERAGRTSPEYLAGMNAREQQSSTVLGNGIAIPHGTPESRDAVLETGVRILQFPEGV
SWHDGARVHVLVAIAAQSDEHLDILRHLTRVLDKPGLAEKLGHATDATELVALLSKAPAV
AKCDSETLCLGIDASTPNELALIAAARLQSLRCVDTDFLASIVGQPPVDLGQGFWLTHHT
VGARRPTLSLATPKRATAELRGVFCLAGPGDECHDLLERIDTFLAGDEPIQGLSAEALLA
RLSGEAADAVTAKVTLLNTHGLHARPAKQLVQEARRHNASIRLRLLEGEGAAVSATSLTR
VIGLGARRGQTLLLSATGDDASQAIQSLTSAIEGGLGEKVSPLRSADPQTKVPEAEQAPA
LTDDQPVKAVAASPGLALAPAFVMRQPTLEYPQFAEDSEQQIQRLNQAVDSADGQLRTLI
RQAEGGEAAPILSVHVEMLQDEDLYQATLEAINEGASAEAGWWKAIDTAARGQEALADRL
LAERAADLRDVGRRVLSNLCGVAMPTPPDTPYILVADDLGPSDVARLDTTRVRGLVTARG
GATSHSAILARALGLPAVVGTGERILTILNGSDLVVDGERGCLVPNPGAERCEKIRRRLQ
QLDALQAEAHENRNQPATTVDGHTIEVCANLGNTAHTPDAVERGADGVGLLRTEFIFMAH
PEAPDLATQVTEYQHAFDALNGLPLVARTLDVGGDKPLDYWPLPQEDNPFLGMRGIRLSL
TRPDILETQVRALLTAAGDRPLRIMFPMVKDLEEFRAARAIVTKVQSEVSASNVQVGVMI
EVPSCALLASTLAPEVDFFSIGTNDLTQYTLAIDRGHGQLSAESDGLHPSVLRLIRMTVE
AAHAHNRWVGVCGELASDPQAIPVLVGLDVDELSVTSRRVPLVKACIRGLNLENARQQAE
KALSLATASEVRDALEAW

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory