GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Gallaecimonas xiamenensis 3-C-1

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_035481637.1 B3C1_RS09380 acetoacetyl-CoA reductase

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



>NCBI__GCF_000299915.1:WP_035481637.1
          Length = 246

 Score =  135 bits (339), Expect = 1e-36
 Identities = 85/247 (34%), Positives = 129/247 (52%), Gaps = 6/247 (2%)

Query: 20  KNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKADV 79
           K  V L+TGA  GIG AI  A A +  ++        + E      + +G + H + AD+
Sbjct: 3   KGNVALVTGANGGIGTAICRALAKEGYQVAALCRCPSRAEPWLEQEKAQGYNPHLVIADI 62

Query: 80  SNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCKA 139
            +Q  + +         G I+++VN AG+   +    M E+DW      +L GA++ C+A
Sbjct: 63  KDQDGIFSAVSVVEAELGAINLVVNNAGITRDKTLKRMQEDDWLEVIQTNLTGAYHLCRA 122

Query: 140 VLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIA 199
           V+P M+E+  G I+NI+S +      G   Y  AK GL GLT +L  E A KG+ VN I+
Sbjct: 123 VVPLMLERQYGRIVNISSINGEKGQMGQTNYAAAKAGLHGLTMSLAQEVASKGITVNTIS 182

Query: 200 PGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINASC 259
           PGYI T + +      A P   RQ  ++  P  R+G+P E+A    FLAS +A FI  S 
Sbjct: 183 PGYIATDMVM------AVPEEIRQSIINQIPVGRLGEPSEIARIVTFLASPDAGFITGSN 236

Query: 260 ITIDGGR 266
           ++ +GG+
Sbjct: 237 LSANGGQ 243


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: 136
Number of extensions: 6
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: 246
Length adjustment: 24
Effective length of query: 248
Effective length of database: 222
Effective search space:    55056
Effective search space used:    55056
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 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