GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17600 in Acidovorax sp. GW101-3H11

Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate Ac3H11_4901 amino acid ABC transporter, permease protein

Query= uniprot:A0A1N7U128
         (237 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4901
          Length = 224

 Score = 86.7 bits (213), Expect = 4e-22
 Identities = 61/197 (30%), Positives = 97/197 (49%), Gaps = 14/197 (7%)

Query: 22  GVAMTLWLFIISVVLGFFLSIPLALARVSE----HVWLRWPVEVYTYLFRGTPLYIQLLI 77
           GV  T+ L I+   LG  L    A AR          LRW V  Y  L R TP  +QL  
Sbjct: 20  GVVWTIGLTIVGTGLGLLLGTACAWARARNLGHRPTALRWAVASYVELVRNTPFIVQLFF 79

Query: 78  CYTGLYSLEIVQDNALLNQFFRNALNCTLLAFVLNTCAYTVEIFAGAIRNIPHGEIEAAR 137
            + GL +L +     L  +F       ++LA V+N  AY+ EI    I   P G+IEAA 
Sbjct: 80  LFFGLPALGL----KLSPEF------ASVLAMVINLGAYSAEIIRAGIEATPRGQIEAAH 129

Query: 138 AYGLHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATVADILKVARDANAETF 197
           +  L   +    VV+P AL++  PA  +++I+++  +++    +  ++   A   ++ TF
Sbjct: 130 SLALTPGQTFRRVVLPPALQKVWPAMVSQIIIVMLGSAVCGQISTPELSYAANLISSNTF 189

Query: 198 LTFQAFGIAALLYMLLS 214
             F+AF +A  +Y++LS
Sbjct: 190 RAFEAFILATAVYLVLS 206


Lambda     K      H
   0.332    0.143    0.443 

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: 136
Number of extensions: 17
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: 237
Length of database: 224
Length adjustment: 23
Effective length of query: 214
Effective length of database: 201
Effective search space:    43014
Effective search space used:    43014
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 (22.0 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