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_3326 Amino acid ABC transporter, permease protein

Query= TCDB::Q52813
         (400 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3326
          Length = 260

 Score = 97.4 bits (241), Expect = 4e-25
 Identities = 87/247 (35%), Positives = 125/247 (50%), Gaps = 27/247 (10%)

Query: 145 LLVIFFWYLG-VLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVA 203
           L+V+    LG +LS LP+P  S    FS           +      +I+  + LV+   A
Sbjct: 26  LMVLALALLGQLLSFLPEPIGSNAQAFS--------DGARTTLWLTLISGSVGLVLGTGA 77

Query: 204 SII-IARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGG 262
           ++   ARWA  R AA+      +W    +I G PLLV ++  +   F +PV     L  G
Sbjct: 78  ALARTARWAVVRWAAS----FYIW----VIRGTPLLVQILFVY---FALPV-----LVPG 121

Query: 263 SVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQA 322
             + P+F +  LAL     ++ AE +R G+  VP+GQ+EAA ALGL    V   VV PQA
Sbjct: 122 LNL-PDFAAAVLALGLNVGAYNAEAIRAGLLAVPRGQTEAAKALGLGRMHVFFDVVFPQA 180

Query: 323 LRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSI 382
            +I +PPL S ++ L K+SSLA AIG  +L  VG  I + + Q I  +    I YL L+ 
Sbjct: 181 FKISLPPLVSNFVALLKDSSLAYAIGVVELTNVGNRIQSATFQPIATLSTVAITYLLLTT 240

Query: 383 LTSLFMN 389
           L +   N
Sbjct: 241 LVTQISN 247


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: 263
Number of extensions: 17
Number of successful extensions: 1
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: 400
Length of database: 260
Length adjustment: 28
Effective length of query: 372
Effective length of database: 232
Effective search space:    86304
Effective search space used:    86304
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