GapMind for catabolism of small carbon sources

 

Protein PP_1484 in Pseudomonas putida KT2440

Annotation: PP_1484 predicted polyamine ABC transporter, ATP-binding protein

Length: 343 amino acids

Source: Putida in FitnessBrowser

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 44% 96% 272.7 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 44% 92% 247.3 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-cellobiose catabolism msiK med MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 45% 82% 240.4 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 84% 234.2 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 84% 234.2 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 43% 87% 234.2 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-maltose catabolism malK1 med 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) 41% 93% 228.4 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-cellobiose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 77% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-glucose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 77% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
lactose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 77% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-maltose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 77% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
sucrose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 77% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
trehalose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 77% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 43% 72% 221.1 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 83% 220.7 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 53% 65% 246.9 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 50% 63% 231.5 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 40% 90% 228.8 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 90% 225.3 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 48% 65% 223.4 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 39% 92% 223.4 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 75% 188.7 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 75% 188.7 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 75% 188.7 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 75% 188.7 Uncharacterized ABC transporter ATP-binding protein YdcT 66% 424.1

Sequence Analysis Tools

View PP_1484 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

MPLAVQFTQVSRTFGEVKAVDQVSIDIIDGEFFSMLGPSGSGKTTCLRLIAGFEQPSSGS
IRIQGVEAAGLPPYQRDVNTVFQDYALFPHMNVLENIAYGLKVKGVGKAERHSRAEEALA
MVALAGYGARKPAQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKL
QRQLGITFIFVTHDQTEALSMSDRVAVFNRGRIEQVDTPRNLYMKPSTTFVAEFVGTSNV
VRGELAMQINGSPAPFSIRPELIRLGDPVVTSHEVQVSGVLHDVQYQGSATRYELQLDNG
QLLAVSQANDRWQKQMQAWQLGQRLQAHWPREAMTVLQETEGR

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