GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Haloglycomyces albus DSM 45210

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_025272362.1 HALAL_RS0101795 3-oxoacyl-ACP reductase FabG

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



>NCBI__GCF_000527155.1:WP_025272362.1
          Length = 236

 Score =  113 bits (283), Expect = 3e-30
 Identities = 78/243 (32%), Positives = 123/243 (50%), Gaps = 14/243 (5%)

Query: 23  VVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQADVSKQ 82
           VVL+TG  +GIG A     A+Q+ +    D     V + +    E   DVH  Q DVS  
Sbjct: 5   VVLITGGTRGIGRA-----AAQRLK---DDGFTVAVASRSIPDAENRLDVHHYQVDVSDG 56

Query: 83  QDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCKAVLP 142
              + +     +  G IDVL+N AG+      L MT +DW      +LDG +  C+++  
Sbjct: 57  NACKDLITTVEDEVGDIDVLINSAGIVRDSPLLTMTGDDWNDVIRTNLDGTYNMCRSMAF 116

Query: 143 QMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAPGY 202
            M+++  GSIIN++SV      P    Y  +K G++G ++AL  E     +RVN +APG+
Sbjct: 117 SMMKRKNGSIINLSSVAGIQGNPTQSNYSASKAGIIGFSKALSKELGRFNIRVNVVAPGF 176

Query: 203 IETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFINASCITI 262
           IET +  D         + +++A++  P  R+G   +VA    FLAS  A ++  + + +
Sbjct: 177 IETDMTADL------AESVKKKAVENIPLGRMGSVDDVAHLVGFLASPRATYMTGAVVPV 230

Query: 263 DGG 265
           DGG
Sbjct: 231 DGG 233


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: 144
Number of extensions: 7
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: 236
Length adjustment: 24
Effective length of query: 248
Effective length of database: 212
Effective search space:    52576
Effective search space used:    52576
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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