GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Acidovorax sp. GW101-3H11

Align AapQ, 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 Ac3H11_2554 Amino acid ABC transporter, permease protein

Query= TCDB::Q52813
         (400 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2554
          Length = 222

 Score = 90.1 bits (222), Expect = 5e-23
 Identities = 54/160 (33%), Positives = 92/160 (57%), Gaps = 11/160 (6%)

Query: 229 IALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIV 288
           +A I G PLLV +   F L F +P  G        ++ P F+   + L  Y+ ++++E+V
Sbjct: 60  VAAIRGTPLLVQL---FILFFGLPQFG--------ILLPAFVCGVIGLGIYSGAYVSEVV 108

Query: 289 RGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIG 348
           RG I+ + KGQ EAA ++G+      R VV+PQA+  +IPPL ++++ L KNS+L   + 
Sbjct: 109 RGAIQSIDKGQMEAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLT 168

Query: 349 FSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSLFM 388
             DL+  G  I++ S +++E+     +VY  L+  T+L +
Sbjct: 169 IHDLMHEGQKIISVSYRSLEVYLAIAVVYFILTGATTLVL 208



 Score = 45.8 bits (107), Expect = 1e-09
 Identities = 33/105 (31%), Positives = 49/105 (46%), Gaps = 22/105 (20%)

Query: 92  LLVGILNTLLVAVTGIFTATIIGFLIGIGRLS-RNWLIAKLCTVYVEVFRNIPPLLVIFF 150
           LL G L T+ +    +    ++G L+GIGRL+ +  ++  LCT YV   R  P L+ +F 
Sbjct: 15  LLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLFI 74

Query: 151 WYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGI 195
            + G    LPQ        F + L         P F  G+I +GI
Sbjct: 75  LFFG----LPQ--------FGILL---------PAFVCGVIGLGI 98


Lambda     K      H
   0.327    0.141    0.432 

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: 248
Number of extensions: 12
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 400
Length of database: 222
Length adjustment: 26
Effective length of query: 374
Effective length of database: 196
Effective search space:    73304
Effective search space used:    73304
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 (21.7 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