GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Desulfovibrio vulgaris Hildenborough

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 207828 DVU2341 amino acid ABC transproter, permease protein, His/Glu/Gln/Arg/opine family

Query= TCDB::Q52813
         (400 letters)



>MicrobesOnline__882:207828
          Length = 233

 Score = 98.2 bits (243), Expect = 2e-25
 Identities = 53/125 (42%), Positives = 77/125 (61%)

Query: 268 EFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIII 327
           EF +  ++L+ YTA+FIAE +R GI  +P+ Q EA+ A GL        VV+PQA RII+
Sbjct: 100 EFAAGVISLTVYTAAFIAEEIRSGIFSIPRTQLEASRACGLSFMQAMSYVVLPQAFRIIV 159

Query: 328 PPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSLF 387
           PPL SQ LNL KNSSL + IG  +L  +   I + +    E   +  ++YL +S++ SL 
Sbjct: 160 PPLISQALNLFKNSSLCMTIGVMELTYMARQIESYTFHGFEAFTVSTLIYLCISLMVSLL 219

Query: 388 MNWFN 392
           +N +N
Sbjct: 220 INLYN 224



 Score = 46.6 bits (109), Expect = 7e-10
 Identities = 24/69 (34%), Positives = 37/69 (53%)

Query: 92  LLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFW 151
           ++ G++ T  ++   +  A ++G LI + RLS           + E FRN P L+ IFFW
Sbjct: 19  IVQGVITTCQLSGLSLVLAMLLGTLIAVMRLSGVRPFVWFSVAFTEFFRNTPLLVQIFFW 78

Query: 152 YLGVLSVLP 160
           Y G  +VLP
Sbjct: 79  YFGSDAVLP 87


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: 232
Number of extensions: 11
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: 233
Length adjustment: 27
Effective length of query: 373
Effective length of database: 206
Effective search space:    76838
Effective search space used:    76838
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