GapMind for catabolism of small carbon sources

 

Protein WP_009545045.1 in Crocosphaera subtropica ATCC 51142

Annotation: NCBI__GCF_000017845.1:WP_009545045.1

Length: 355 amino acids

Source: GCF_000017845.1 in NCBI

Candidate for 72 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 PotG aka B0855, component of Putrescine porter (characterized) 42% 87% 239.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 74% 218.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 74% 218.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 41% 77% 211.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-arabinose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 78% 208.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-fructose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 78% 208.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
sucrose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 78% 208.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
trehalose catabolism thuK med Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 40% 73% 208.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-xylose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 78% 208.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-cellobiose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 40% 77% 203.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-glucose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 40% 77% 203.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
lactose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 40% 77% 203.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-maltose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 40% 77% 203.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
sucrose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 40% 77% 203.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
trehalose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 40% 77% 203.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 75% 201.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 42% 79% 197.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 41% 75% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-proline catabolism opuBA med BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 40% 74% 172.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 85% 234.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 38% 94% 232.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
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) 39% 86% 218.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 97% 218.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 36% 98% 217.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 82% 216.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 82% 216.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 82% 216.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 82% 216.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 82% 216.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 82% 216.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 82% 216.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 82% 216.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 37% 88% 215.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-mannose catabolism TT_C0211 lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 43% 64% 213.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 38% 86% 212.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 36% 92% 210.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 93% 207.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 39% 76% 206.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 39% 82% 204.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
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) 33% 86% 203.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 34% 93% 203.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 39% 75% 202.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 70% 200.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 79% 200.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-cellobiose catabolism msiK lo 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) 43% 58% 198.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 41% 64% 192.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 77% 191.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 77% 191.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 77% 191.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 86% 190.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 86% 190.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 86% 190.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 86% 190.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 86% 190.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 86% 190.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 95% 185.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 80% 166.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 84% 159.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 82% 158.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 37% 96% 154.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 36% 84% 150.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 139 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 139 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 139 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 34% 84% 137.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 30% 96% 122.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 92% 114.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 92% 114.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 92% 114.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 96% 100.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 96% 100.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 96% 100.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 66% 456.4

Sequence Analysis Tools

View WP_009545045.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MENSIILQVNQLVKQFANHQIPAVDEVSFQLTQGDILGLLGPSGCGKTTLLRMIAGFEQP
SVGTIELGGNIIASTSQLLPPEQRNTGMVFQDYALFPHLNIADNIAFGLNKKKFSKKEIK
NRIGEVLTLVGLEGLEKRYPHQLSGGQQQRVALARALAPQPALILLDEPLSNLDVQVRIR
LRHEIRHILKATGITAIFVTHDQEEALAICDKIGVMSSGKIEQLGTPEAIYTRPASRFVA
EFVTQANFIPAKRQGTLWTTEIGQWELPSAHATVPEGELMVRQEDIMLKPDDTAKVVISD
RQFLGREYRYCLRTPSGGQIHARTTLQTQLPIGTKVHLAIASQSAQVFPVASSRG

This GapMind analysis is from Apr 09 2024. 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:

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