GapMind for catabolism of small carbon sources

 

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

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Ac3H11_493 toluenesulfonate zinc-independent alcohol dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_493
          Length = 253

 Score =  143 bits (361), Expect = 3e-39
 Identities = 89/253 (35%), Positives = 139/253 (54%), Gaps = 3/253 (1%)

Query: 18  RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77
           R+ NK +++TGA  GIGE I    A++  +++++DI     + V A     G      KA
Sbjct: 2   RVSNKSIIVTGAGNGIGEGIAKRLAAEGGKVIVNDINEAGGQRVVAEITAAGGTAAFFKA 61

Query: 78  DVSNQQDLHAMARHAVERHGRIDVLVNCAG-VNVFRDPLEMTEEDWRRCFAIDLDGAWYG 136
           DV+N   + AM   AV  +GR+DV+VN AG  +  R  LE++EE++ + +AI++   +  
Sbjct: 62  DVTNSAQVKAMVDEAVRLYGRLDVVVNNAGWTHRNRPMLEVSEEEFDKVYAINMKSIYLS 121

Query: 137 CKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196
               +P + + G GSIINIAST      PG   Y  +K  ++  ++++  E  P  +RVN
Sbjct: 122 AIHAVPALRQAGGGSIINIASTAGLRPRPGLTWYNGSKGAVIITSKSMAAELGPDNIRVN 181

Query: 197 AIAPGY-IETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFI 255
            I P +  +T L  ++  G  D  A R + L   P  R    ++VA  A++LAS+EA FI
Sbjct: 182 CINPVFNPDTGLAAEFAGGPVDD-ARRAKFLATIPLGRFSTALDVANAALYLASEEASFI 240

Query: 256 NASCITIDGGRSV 268
           +  CI +DGGR V
Sbjct: 241 SGVCIEVDGGRCV 253


Lambda     K      H
   0.321    0.137    0.419 

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: 130
Number of extensions: 5
Number of successful extensions: 3
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: 272
Length of database: 253
Length adjustment: 25
Effective length of query: 247
Effective length of database: 228
Effective search space:    56316
Effective search space used:    56316
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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