GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctO in Azospirillum thiophilum BV-S

Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate WP_082109398.1 AL072_RS27445 alpha-hydroxy-acid oxidizing protein

Query= BRENDA::Q8Z0C8
         (365 letters)



>NCBI__GCF_001305595.1:WP_082109398.1
          Length = 415

 Score =  243 bits (621), Expect = 5e-69
 Identities = 142/369 (38%), Positives = 206/369 (55%), Gaps = 26/369 (7%)

Query: 16  LAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQPLQL 75
           LA+  + +M +DY   G+  E T + N A    ++ R R+ + ++     + +LG+ + +
Sbjct: 17  LARRRVPRMFYDYVDCGSWTESTYRANTADLAALQFRQRIGMSIAGRTTESRILGESVAM 76

Query: 76  PLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVA-EVGSKFSPSLQWF 134
           P+ +AP     + H +GE+  A AA   G    LST+S  S+E+VA   G  F     WF
Sbjct: 77  PVALAPTGLTGMQHADGEILAARAAERFGVPFTLSTVSICSIEDVAANTGKPF-----WF 131

Query: 135 QLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANLTTI 194
           QLY+ +DR     L+ RA AA   AL LT+D  + GQR +D +N    PP   L NL  +
Sbjct: 132 QLYVMRDRAFVERLIARAKAANCSALVLTLDLQIQGQRHKDLKNGLSTPPKPTLRNLVDL 191

Query: 195 S-----------------GLNIPHAPGES---GLFTYFAQQLNPALTWDDLEWLQSLSPL 234
           +                 G  + H  G S    L  + +QQ +P LTW+D+ W++ L   
Sbjct: 192 ATKPGWCLGMLRTKRRTFGNIVGHVSGVSDVSSLAAWVSQQFDPTLTWEDVRWIKKLWGG 251

Query: 235 PLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVLLD 294
            L++KG+L  +DA  AVE GA AIVVSNHGGRQLDGA +S+  LP I  AV  + EVL D
Sbjct: 252 KLIVKGVLDVEDARLAVENGADAIVVSNHGGRQLDGAPSSIAMLPAIAEAVGQQTEVLFD 311

Query: 295 GGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGCSQ 354
            GIR G DI+KA A+GA+ V++GR  L+GL   G+AGV+  + +LQ+EL++ M L G + 
Sbjct: 312 SGIRSGQDILKAAALGAKGVMVGRAFLYGLGAMGEAGVTRCLEILQRELDLTMGLCGLTD 371

Query: 355 LQDIDTSFL 363
           +   D S L
Sbjct: 372 IGAADPSIL 380


Lambda     K      H
   0.320    0.136    0.391 

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: 341
Number of extensions: 15
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: 365
Length of database: 415
Length adjustment: 30
Effective length of query: 335
Effective length of database: 385
Effective search space:   128975
Effective search space used:   128975
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: 50 (23.9 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