GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artM in Collimonas arenae Ter10

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate WP_061534023.1 CAter10_RS14915 amino acid ABC transporter permease

Query= TCDB::Q9HU29
         (230 letters)



>NCBI__GCF_001584165.1:WP_061534023.1
          Length = 219

 Score =  124 bits (312), Expect = 1e-33
 Identities = 70/218 (32%), Positives = 123/218 (56%), Gaps = 9/218 (4%)

Query: 5   ELILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGT 64
           +L+L+  P + +G   TL     +++ GL L  PL IAR     + +    AY+   RGT
Sbjct: 5   DLLLQAAPILFKGVGYTLVFAVASMLGGLLLGFPLAIARIVPSRWAQWPATAYVSLMRGT 64

Query: 65  PLLLQLFIVYYGLAQFEEVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVPV 124
           PLL+Q+F++YYGL                 P    +L ++L+  AY++E LRGAI  V  
Sbjct: 65  PLLVQIFVIYYGLPSIG---------ISFSPLTAGILALSLNAGAYLSESLRGAILGVHN 115

Query: 125 GEVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMAR 184
           G+  A+ +LG++  Q L +I++P+A+RI +P+ SN +I ++K +++V  +T+ ++M   +
Sbjct: 116 GQWSASYSLGLNYGQTLRYIVIPQAIRIAVPSMSNTLISLIKDTSLVSVITVTELMLATK 175

Query: 185 TIIARTYESMLFFCLAGALYLVITIVLTRIFRLIERWL 222
            +IA T+  +  +  A A+Y  ++I   R+   +ER L
Sbjct: 176 EVIAVTFRPLPLYLAAAAVYWCLSICFERLQIRLERKL 213


Lambda     K      H
   0.332    0.142    0.443 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 129
Number of extensions: 5
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 230
Length of database: 219
Length adjustment: 22
Effective length of query: 208
Effective length of database: 197
Effective search space:    40976
Effective search space used:    40976
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 46 (22.3 bits)

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