GapMind for catabolism of small carbon sources

 

Protein WP_011382978.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein

Length: 553 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 46% 89% 208.8 ABC transporter for nitrate, ATPase component 74% 796.2
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 81% 166.8 ABC transporter for nitrate, ATPase component 74% 796.2
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 81% 166.8 ABC transporter for nitrate, ATPase component 74% 796.2
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 86% 171 ABC transporter for nitrate, ATPase component 74% 796.2
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 86% 171 ABC transporter for nitrate, ATPase component 74% 796.2
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 86% 171 ABC transporter for nitrate, ATPase component 74% 796.2
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 86% 171 ABC transporter for nitrate, ATPase component 74% 796.2
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 86% 171 ABC transporter for nitrate, ATPase component 74% 796.2
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 86% 171 ABC transporter for nitrate, ATPase component 74% 796.2
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 39% 72% 161 ABC transporter for nitrate, ATPase component 74% 796.2
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 42% 57% 160.6 ABC transporter for nitrate, ATPase component 74% 796.2
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 35% 77% 156.4 ABC transporter for nitrate, ATPase component 74% 796.2
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 68% 152.5 ABC transporter for nitrate, ATPase component 74% 796.2
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 42% 64% 149.1 ABC transporter for nitrate, ATPase component 74% 796.2
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 36% 60% 144.1 ABC transporter for nitrate, ATPase component 74% 796.2
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 36% 60% 144.1 ABC transporter for nitrate, ATPase component 74% 796.2
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 36% 59% 143.3 ABC transporter for nitrate, ATPase component 74% 796.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 36% 59% 143.3 ABC transporter for nitrate, ATPase component 74% 796.2
trehalose catabolism thuK lo Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 31% 90% 142.5 ABC transporter for nitrate, ATPase component 74% 796.2
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 37% 61% 140.2 ABC transporter for nitrate, ATPase component 74% 796.2
D-maltose catabolism malK1 lo MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 36% 58% 139.8 ABC transporter for nitrate, ATPase component 74% 796.2
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 88% 130.6 ABC transporter for nitrate, ATPase component 74% 796.2
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 88% 130.6 ABC transporter for nitrate, ATPase component 74% 796.2
L-glutamate catabolism gltL lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 88% 130.6 ABC transporter for nitrate, ATPase component 74% 796.2
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 36% 68% 129.4 ABC transporter for nitrate, ATPase component 74% 796.2

Sequence Analysis Tools

View WP_011382978.1 at NCBI

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

MPILELKGVAKSYGASSVLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGEV
LLRGKPVDGPGADRGVVFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKYIGMV
GLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIEAIWE
QEKKTVILITNDVDEALLLADRIIPLNPGPGATFGPSFKVNLPRPRDRAAVNSDPDFKRL
RAEVTEYLMAVGVERGGESGETRILPNVAPISFGGPPKAYREAGQVNNPDRYVEFSRVKK
IYPTPKGPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGGVILDGREV
SEAGPDRAVVFQAPSLFPWLTALQNVALGVDRVYPHASPAERLDIVSYYLERVGLGDSMD
KKASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVLMEVWTRTRVTAI
CVTHDVDEAILLADKVVMMTNGPNARIGKVLNVDIPRPRTRRALLEHPRYYEYRAEVLNF
LDEYETGAHAKAS

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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