GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Herbaspirillum seropedicae SmR1

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 HSERO_RS07530 HSERO_RS07530 amino acid ABC transporter permease

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__HerbieS:HSERO_RS07530
          Length = 216

 Score =  115 bits (288), Expect = 1e-30
 Identities = 67/211 (31%), Positives = 124/211 (58%), Gaps = 13/211 (6%)

Query: 166 VVETPLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLIT 225
           ++E   W  L+  L     GIA     G ++AL R S +  +R+L   +I++I+G P++ 
Sbjct: 13  LLEAARWTLLLSALAFLGGGIA-----GFIVALMRTSHLAPLRLLSAVYIQIIQGTPVLI 67

Query: 226 VLFMASVMLPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLG 285
           +LF++   L +F   G+ +  ++ A I ++I++SAY+ E+ RG ++A+P  Q+E + +L 
Sbjct: 68  LLFLSFYGLAIF---GYKLPPMVAATIAMTIYSSAYLGEIWRGCIEAVPVPQWEASTALA 124

Query: 286 LGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWAS 345
           +  WQ+ R +I+PQA+++ +P  V   +   K+TS+ +IIG+ +L    KL  +      
Sbjct: 125 MTRWQQLRYVILPQAVRISLPPTVGFLVQIVKNTSIASIIGLVELAQAGKLVSNATFQPF 184

Query: 346 AVTPITGLIFAGFIFWLFCFGMSRYSGFMER 376
            V PI     AG I+++FC+ +SR++  +ER
Sbjct: 185 LVFPIV----AG-IYFVFCYPLSRFAFALER 210


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: 223
Number of extensions: 12
Number of successful extensions: 3
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: 384
Length of database: 216
Length adjustment: 26
Effective length of query: 358
Effective length of database: 190
Effective search space:    68020
Effective search space used:    68020
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: 47 (22.7 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