GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Paraburkholderia phymatum STM815

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 WP_012404402.1 BPHY_RS25820 ABC transporter permease subunit

Query= TCDB::Q52813
         (400 letters)



>NCBI__GCF_000020045.1:WP_012404402.1
          Length = 543

 Score = 77.0 bits (188), Expect = 1e-18
 Identities = 66/217 (30%), Positives = 108/217 (49%), Gaps = 27/217 (12%)

Query: 166 VGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVASIIIARWAHKRQAATGQPFHTV 225
           +GLP+ +    RG+ F   +   G+   G  +V  ++A++ ++R       A G   +TV
Sbjct: 8   LGLPYLL----RGIGFTIAVTALGL--AGGVVVGLVLAAMQLSRVGPLAALARG---YTV 58

Query: 226 WTAIALIVGLPLLVFVVSGFPLTFDVPVAG-KFNLTGGSVVGPEFMSLFLALSFYTASFI 284
                +  G PL++ +V  +     +P  G K + TG +          LAL+     FI
Sbjct: 59  -----IFRGTPLILQLVFAYDA---LPHIGLKLSATGAAA---------LALAANEGPFI 101

Query: 285 AEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLA 344
           AEI+R G+ GV +GQ  A  ALG+ PS + R V+ PQA+R I+P L ++ ++  KNSSLA
Sbjct: 102 AEILRAGVLGVERGQLLAGQALGMTPSVLMRRVIAPQAIRAIVPALGNESVSALKNSSLA 161

Query: 345 IAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLS 381
             I   +L      + + +     I    G++YL L+
Sbjct: 162 SVIAVDELTLRSTQLASSTFDFFSIFFASGLMYLILT 198



 Score = 35.4 bits (80), Expect = 4e-06
 Identities = 20/61 (32%), Positives = 31/61 (50%)

Query: 92  LLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFW 151
           LL GI  T+ V   G+    ++G ++   +LSR   +A L   Y  +FR  P +L + F 
Sbjct: 13  LLRGIGFTIAVTALGLAGGVVVGLVLAAMQLSRVGPLAALARGYTVIFRGTPLILQLVFA 72

Query: 152 Y 152
           Y
Sbjct: 73  Y 73


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: 479
Number of extensions: 31
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: 2
Length of query: 400
Length of database: 543
Length adjustment: 33
Effective length of query: 367
Effective length of database: 510
Effective search space:   187170
Effective search space used:   187170
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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