GapMind for catabolism of small carbon sources

 

Protein WP_058858789.1 in Kocuria flava HO-9041

Annotation: NCBI__GCF_001482365.1:WP_058858789.1

Length: 544 amino acids

Source: GCF_001482365.1 in NCBI

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism malF med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 35% 94% 278.1 MalF1; aka Maltose ABC transporter, permease 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 46% 275.8
D-maltose catabolism malF_Aa med Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 42% 80% 213 Maltose-transporting ATPase (EC 3.6.3.19) 35% 278.1
D-maltose catabolism malF1 lo MalF1; aka Maltose ABC transporter, permease 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) 46% 58% 275.8 Maltose-transporting ATPase (EC 3.6.3.19) 35% 278.1
trehalose catabolism malF1 lo MalF1; aka Maltose ABC transporter, permease 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) 46% 58% 275.8 Maltose-transporting ATPase (EC 3.6.3.19) 35% 278.1
D-maltose catabolism malF_Sm lo MalF, 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) 37% 56% 183.3 Maltose-transporting ATPase (EC 3.6.3.19) 35% 278.1
trehalose catabolism malF lo MalF, 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) 37% 56% 183.3 Maltose-transporting ATPase (EC 3.6.3.19) 35% 278.1
D-maltose catabolism thuF lo Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized) 36% 71% 149.8 Maltose-transporting ATPase (EC 3.6.3.19) 35% 278.1
D-glucosamine (chitosamine) catabolism SM_b21220 lo ABC transporter for D-Glucosamine, permease component 2 (characterized) 31% 85% 123.6 Maltose-transporting ATPase (EC 3.6.3.19) 35% 278.1
N-acetyl-D-glucosamine catabolism SMc02872 lo N-Acetyl-D-glucosamine ABC transport system, permease component 1 (characterized) 31% 79% 108.6 Maltose-transporting ATPase (EC 3.6.3.19) 35% 278.1
D-glucosamine (chitosamine) catabolism SMc02872 lo N-Acetyl-D-glucosamine ABC transport system, permease component 1 (characterized) 31% 79% 108.6 Maltose-transporting ATPase (EC 3.6.3.19) 35% 278.1
D-cellobiose catabolism msdC1 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 34% 66% 106.3 Maltose-transporting ATPase (EC 3.6.3.19) 35% 278.1

Sequence Analysis Tools

View WP_058858789.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MSTHITARGTTAAPGEAGGGAGLGAPLDLRNSHSRGFGLGFVVKLVLMALINAFGLYGIL
AAWAAGSWGILAFLALALIVADLVYFLPGRKILPAKYLYPGLIFLLIFQIFVVLYTAATA
FTNYGDGHNATKTAAISQLTTTYEQRVEGSQAYPVTVLEGDDGLALATVQDDQVLVGAAD
QPLAPLEDATVTDDRVVEAPGYEVLDYGGVVAAADELTDLRVPVSGQEADDAALRTDDGR
TAYVYESTLVHDEAADAMVADDGTVYANNGEGAFVGPEGEALRPGWRVFVGLDNFAAIFD
PAVLGGPFVSVTLWTFTFAIMSVVLTFFLGLLLAILFNDEKLRFRNVYRAIIFLPYAFPA
FLSILIWAGLLNTDYGFVNEILLGGAGVPWLDNPWLARISLLLVNLWLGFPYMFLVTTGA
LQSIPSEIYESSEMDGAGPVRQFGSITLPMLMVAVGPMLIASFAMNFNNFNVIYLLTGGG
PQDVESTTGVGATDILISFVYKIAFAGGTNDYGLASALSILIFIMVAVISALTFRRSKAL
EEIS

This GapMind analysis is from Sep 24 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:

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