GapMind for catabolism of small carbon sources

 

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

Align Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate Ac3H11_2554 Amino acid ABC transporter, permease protein

Query= TCDB::Q9HU30
         (231 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2554
          Length = 222

 Score =  116 bits (290), Expect = 4e-31
 Identities = 70/216 (32%), Positives = 117/216 (54%), Gaps = 12/216 (5%)

Query: 11  QLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTS-KYAALRFLGGTYTTIVRGVPETLWVL 69
           QLLAG  +T++++ A++ +G ++GLL  I + + K   +  L   Y   +RG P  + + 
Sbjct: 14  QLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLF 73

Query: 70  MIYFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHREA 129
           +++FG           FG   + L  F  G + LG+  GAY +EV RGA+ SI +G  EA
Sbjct: 74  ILFFGLPQ--------FG---ILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEA 122

Query: 130 GQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVASNA 189
            +++G+S G     +VLPQ     +P LGN ++ L+K++ALVSL+T+ ++M + Q   + 
Sbjct: 123 ARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISV 182

Query: 190 TKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRG 225
           +      Y+  A +Y  LT    + L  +E R   G
Sbjct: 183 SYRSLEVYLAIAVVYFILTGATTLVLRRIELRLRAG 218


Lambda     K      H
   0.327    0.143    0.431 

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: 107
Number of extensions: 3
Number of successful extensions: 2
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: 231
Length of database: 222
Length adjustment: 22
Effective length of query: 209
Effective length of database: 200
Effective search space:    41800
Effective search space used:    41800
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: 46 (22.3 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