GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Streptacidiphilus oryzae TH49

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_037569935.1 BS73_RS04585 SDR family oxidoreductase

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



>NCBI__GCF_000744815.1:WP_037569935.1
          Length = 258

 Score =  146 bits (369), Expect = 4e-40
 Identities = 91/244 (37%), Positives = 130/244 (53%), Gaps = 7/244 (2%)

Query: 25  LLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQADVSKQQD 84
           L+TG A GIG A+ A  A+  A + I+D   +     AA     G    AL+ DV+  + 
Sbjct: 19  LVTGGASGIGLAVAARLAAGGAAVAIADYNEEAAHKAAADLAAGGVRATALRMDVTDPES 78

Query: 85  LQAMARRAVELHGRIDVLVNCAGVNVFRDPL-EMTEEDWRRCFAIDLDGAWYGCKAVLPQ 143
           ++A    A E  G + + VN AG++    P  E   E WRR  A +LDG +Y  +  LP 
Sbjct: 79  VRAGTEAAAEALGGLHLAVNNAGISGEAAPTGEYPVEVWRRVLATNLDGVFYSLRYELPL 138

Query: 144 MIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAPGYI 203
           ++  G G+++N+AS+  ++   G   Y  AKHG++GLT+   +EYA +GVR+NA  PG+I
Sbjct: 139 ILAAGGGAVVNMASILGTNGFAGAPAYVAAKHGVVGLTKTAALEYAGQGVRINAAGPGFI 198

Query: 204 ETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFINASCITID 263
           +T L     +G     A     + LHP  R+G+  EVA    FL S  A FIN S   ID
Sbjct: 199 DTPL----LSGM--DRAAHDALVTLHPQGRLGRAEEVAELTAFLLSHRASFINGSYHLID 252

Query: 264 GGRS 267
           GG S
Sbjct: 253 GGYS 256


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: 145
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: 258
Length adjustment: 25
Effective length of query: 247
Effective length of database: 233
Effective search space:    57551
Effective search space used:    57551
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