GapMind for catabolism of small carbon sources

 

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

Align Arginine ABC transporter permease protein ArtQ (characterized)
to candidate Ac3H11_3200 Amino acid ABC transporter permease protein

Query= SwissProt::P0AE34
         (238 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3200
          Length = 604

 Score = 83.6 bits (205), Expect = 8e-21
 Identities = 71/225 (31%), Positives = 110/225 (48%), Gaps = 12/225 (5%)

Query: 6   PLASAAGMTVGLAVCALIVGLALAMFFAVWESAKWRPVAWAGSALVTILRGLPEILVVLF 65
           P+    G T+ L     + G  L    A+   ++   +A      + I R +P ++V+L 
Sbjct: 81  PVLVGLGRTLLLTALGALFGFTLGTALALARVSRSPLLAGLSWTFIWIFRSIP-VIVLLL 139

Query: 66  IYFGSSQLLLTLSDG--FTINLGFVQIPVQMDIENFDVSPFLCGVIALSLLYAAYASQTL 123
           I      L  T+S G  FT    F     Q+      +SPF+  +I L+L  AA+AS+ +
Sbjct: 140 IINNLGYLYETVSVGLPFTDWTFFSYPTTQL------ISPFVAALIGLTLNQAAFASEIV 193

Query: 124 RGALKAVPVGQWESGQALGLSKSAIFFRLVMPQMWRHALPGLGNQWLVLLKDTALVSLIS 183
           RG + +V  GQ E+  ALGL +    FR+V+PQ  R  LP   N  + L K T+ V +++
Sbjct: 194 RGGILSVDQGQLEAAAALGLPRRRQAFRIVLPQAMRSILPAGFNDIIGLAKGTSNVYILA 253

Query: 184 VNDLMLQTKSIATRTQEPFTWYIVAAAIYLVI-TLLS--QYILKR 225
           + +L    + I  R  E     +VA   YLVI T+LS  QY ++R
Sbjct: 254 LPELFYTIQIIYRRNLEVIPLLMVATVWYLVILTVLSLLQYYIER 298


Lambda     K      H
   0.328    0.139    0.423 

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: 342
Number of extensions: 13
Number of successful extensions: 1
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: 238
Length of database: 604
Length adjustment: 30
Effective length of query: 208
Effective length of database: 574
Effective search space:   119392
Effective search space used:   119392
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 (21.8 bits)
S2: 50 (23.9 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