GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Cupriavidus basilensis 4G11

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 RR42_RS27120 RR42_RS27120 amino acid ABC transporter permease

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__Cup4G11:RR42_RS27120
          Length = 218

 Score =  126 bits (316), Expect = 6e-34
 Identities = 77/208 (37%), Positives = 116/208 (55%), Gaps = 12/208 (5%)

Query: 178 TLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLF 237
           T+VLS V  A    +G+L+ L R SR    R     FIEV +G PL+  LF+A   L LF
Sbjct: 20  TVVLSLVAFAGGAVIGLLVLLMRISRRAPARRAAWAFIEVFQGTPLLMQLFLAFFGLALF 79

Query: 238 LPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIM 297
              G  +   L A + +S+++ AY+AE+ RG ++AIPKGQ+E A  L LG+ Q+ R +I+
Sbjct: 80  ---GVEIPAWLAAGLALSLWSGAYLAEIWRGCVEAIPKGQWEAAGCLSLGHLQQMRYVIL 136

Query: 298 PQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDL--LGIVKLNFSDANWASAVTPITGLIF 355
           PQA+++ I   V   +   K T+L +IIG  +L   G V  N       +  +P T    
Sbjct: 137 PQALRIAIAPTVGFVVQIIKGTALASIIGFVELSKAGTVITN-------ATFSPFTVYAL 189

Query: 356 AGFIFWLFCFGMSRYSGFMERHLDTGHK 383
              I++  C+ +SRYS ++ER L+  H+
Sbjct: 190 VALIYFALCWPLSRYSRYLERKLNVAHR 217


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: 249
Number of extensions: 17
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: 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