GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Sinorhizobium meliloti 1021

Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate SMa0503 SMa0503 ABC transporter permease

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__Smeli:SMa0503
          Length = 218

 Score =  102 bits (255), Expect = 8e-27
 Identities = 65/197 (32%), Positives = 112/197 (56%), Gaps = 11/197 (5%)

Query: 180 VLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLP 239
           VL+FVG  +   +GI+LAL R +R+     +   +++VI+G+PL+ +LF+      LF  
Sbjct: 24  VLAFVGGGI---MGIVLALLRIARIRAFSAITTFYMQVIQGLPLLVLLFLCYYAPSLF-- 78

Query: 240 TGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQ 299
            G  +  L  A I ++I +SA++  +    L+AIPK Q+E AD+L L  ++  R +I PQ
Sbjct: 79  -GIEIAALTAAAIALTINSSAFLGAIWESALRAIPKAQWESADALALTPYKTLRFVIAPQ 137

Query: 300 AIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFI 359
           AI+L +PS V   +   K TSL +IIG  ++    +L  S+A +     P+   +    +
Sbjct: 138 AIRLALPSTVGFLVQIIKQTSLASIIGFIEITRAGQL-VSNATF----EPLKAFLSVAAL 192

Query: 360 FWLFCFGMSRYSGFMER 376
           ++  CF +++ S ++ER
Sbjct: 193 YFAVCFPLTQLSLWLER 209


Lambda     K      H
   0.330    0.145    0.469 

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: 224
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 384
Length of database: 218
Length adjustment: 26
Effective length of query: 358
Effective length of database: 192
Effective search space:    68736
Effective search space used:    68736
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

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:

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