GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Pandoraea thiooxydans ATSB16

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_047214213.1 PATSB16_RS11230 glucose 1-dehydrogenase

Query= reanno::pseudo5_N2C3_1:AO356_20240
         (272 letters)



>NCBI__GCF_001931675.1:WP_047214213.1
          Length = 255

 Score =  141 bits (356), Expect = 1e-38
 Identities = 92/250 (36%), Positives = 134/250 (53%), Gaps = 6/250 (2%)

Query: 18  RLKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQ-AQKVEAVAAHWRERGADVHALQ 76
           R+ D V L+TG+AQGIG AI    A + A++V+ D Q A   E   A  R  G+D   + 
Sbjct: 2   RMNDTVALVTGSAQGIGRAIAVRLAQEGAKIVVEDRQDADAAEQTLAQVRAAGSDGCVIA 61

Query: 77  ADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYG 136
            +V    D + +   AV   GRIDVLVN AGV      LE++E D+     ++L GA++ 
Sbjct: 62  GNVGSVHDARGVVDAAVAKLGRIDVLVNNAGVERNAPFLEVSEADYDLVLDVNLKGAFFM 121

Query: 137 CKAVLPQMIEQGVGS-IINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRV 195
            +AV+  + +   G  I+NI+SVH     P    Y  +K G+  + R L IE AP G+ V
Sbjct: 122 TQAVVRHLRDSHRGGRIVNISSVHEELPFPHFTSYCASKGGMKMMVRNLAIELAPLGITV 181

Query: 196 NAIAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFI 255
           N +APG + T +N    N      AE    L   P +R+G+  +VA   +FLASDEA ++
Sbjct: 182 NNVAPGAVGTAIN----NKLLHDPAELSALLANIPLKRLGKVEDVANAVLFLASDEASYV 237

Query: 256 NASCITIDGG 265
             + + +DGG
Sbjct: 238 TGTTVYVDGG 247


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: 156
Number of extensions: 5
Number of successful extensions: 4
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: 255
Length adjustment: 25
Effective length of query: 247
Effective length of database: 230
Effective search space:    56810
Effective search space used:    56810
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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