GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate Ac3H11_2554 Amino acid ABC transporter, permease protein

Query= reanno::pseudo3_N2E3:AO353_16280
         (223 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2554
          Length = 222

 Score =  108 bits (269), Expect = 1e-28
 Identities = 65/221 (29%), Positives = 122/221 (55%), Gaps = 8/221 (3%)

Query: 1   MDLDFSGVVQAVPGMWNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSK-LLSNIAGAYV 59
           M+LDFS V   VP +  G ++T+++T   ++ G ++G L+ + RL+  + ++  +  AYV
Sbjct: 1   MELDFSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYV 60

Query: 60  NYFRSIPLLLVITWFYLAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQ 119
              R  PLL+ +   +  +P            + AF   ++   ++  AY  E+VR  +Q
Sbjct: 61  AAIRGTPLLVQLFILFFGLPQF-------GILLPAFVCGVIGLGIYSGAYVSEVVRGAIQ 113

Query: 120 SIPKGQMGAAKALGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFL 179
           SI KGQM AA+++GM  G  MR ++LPQA  +M P L  + I L ++++LV  + + D +
Sbjct: 114 SIDKGQMEAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLM 173

Query: 180 NATRASGDIIGRANEFLIIAGLVYFTISFAASRLVKRLQKR 220
           +  +    +  R+ E  +   +VYF ++ A + +++R++ R
Sbjct: 174 HEGQKIISVSYRSLEVYLAIAVVYFILTGATTLVLRRIELR 214


Lambda     K      H
   0.331    0.143    0.425 

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: 118
Number of extensions: 7
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: 223
Length of database: 222
Length adjustment: 22
Effective length of query: 201
Effective length of database: 200
Effective search space:    40200
Effective search space used:    40200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 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