GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_03349 H281DRAFT_03349 amino acid ABC transporter membrane protein, PAAT family

Query= TCDB::Q52813
         (400 letters)



>FitnessBrowser__Burk376:H281DRAFT_03349
          Length = 222

 Score = 92.4 bits (228), Expect = 1e-23
 Identities = 63/194 (32%), Positives = 105/194 (54%), Gaps = 15/194 (7%)

Query: 192 AVGIALVIAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDV 251
           A  +AL   +   I I R   +R+   G  F T +  +    G PLLV +   F L F +
Sbjct: 27  AASLALSCVLGLLIGIGRLTPQRRIVYG--FCTAY--LTFFRGTPLLVQL---FLLFFGL 79

Query: 252 PVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPS 311
           P  G        ++ P F+   L L  Y+A++++EIVRG I+ V +GQ EAA ++G+   
Sbjct: 80  PQFG--------ILLPAFLCGMLGLGLYSAAYVSEIVRGAIQSVDRGQMEAARSIGMSSG 131

Query: 312 SVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVC 371
              R +++PQA+  +IPPL ++++ L KNS+L   +   DL+  G  I++ S +++E+  
Sbjct: 132 QAMRAIILPQAIVRMIPPLGNEFIALIKNSALVSLLTIDDLMHEGQKIISVSYRSLEVYL 191

Query: 372 IWGIVYLSLSILTS 385
              +VYL L+  T+
Sbjct: 192 AIALVYLVLTQATN 205



 Score = 41.6 bits (96), Expect = 2e-08
 Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 92  LLVGILNTLLVAVTGIFTATIIGFLIGIGRLS-RNWLIAKLCTVYVEVFRNIPPLLVIFF 150
           ++ G + T+ V    +  + ++G LIGIGRL+ +  ++   CT Y+  FR  P L+ +F 
Sbjct: 15  IMHGAIVTVEVTAASLALSCVLGLLIGIGRLTPQRRIVYGFCTAYLTFFRGTPLLVQLFL 74

Query: 151 WYLGV 155
            + G+
Sbjct: 75  LFFGL 79


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: 250
Number of extensions: 17
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