GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctO in Dechlorosoma suillum PS

Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate Dsui_1668 Dsui_1668 alpha-hydroxyacid dehydrogenase, FMN-dependent L-lactate dehydrogenase

Query= BRENDA::Q8Z0C8
         (365 letters)



>FitnessBrowser__PS:Dsui_1668
          Length = 374

 Score =  301 bits (771), Expect = 2e-86
 Identities = 163/353 (46%), Positives = 227/353 (64%), Gaps = 8/353 (2%)

Query: 12  EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71
           +YE  A+  L   A+ Y  SG+ DE+T + N+  F+R++L  R+L DV   +    + GQ
Sbjct: 20  DYEPYARRRLDDNAWTYLHSGSADELTFRWNKEAFDRLRLNGRVLADVRGGHTRLELFGQ 79

Query: 72  PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131
             + PL +AP+A Q L H EGELAT + A +   GMV+STL++  LE++A        + 
Sbjct: 80  RYEHPLFLAPVAHQKLFHPEGELATVLGAGALQAGMVVSTLASTPLEDIAAQAE----AP 135

Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANL 191
            WFQLY   DR  TR LV+RA AAGY+AL +TVD P+ G R R++R  F LP G+  ANL
Sbjct: 136 LWFQLYFQPDRDFTRQLVQRAEAAGYQALVVTVDVPIFGLRNREQRIGFHLPAGIDPANL 195

Query: 192 TTISGLNIPHA-PGESGLFTYFAQQLNPALTWDDLEWLQSLSPLPLVLKGILRGDDAARA 250
             ++    P   PG+S +F      +  A TW+D+ W++SL+ LPL+LKGI    DA +A
Sbjct: 196 RGMAAPAQPALHPGQSIVFDGI---MAAAPTWEDIAWVRSLTRLPLILKGITHPGDARQA 252

Query: 251 VEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVLLDGGIRRGTDIIKALAIG 310
            + G   ++VSNHGGR LD   AS++ALP +V AV G+  VLLDGGIRRG+D++KALA+G
Sbjct: 253 ADLGVDGLIVSNHGGRSLDTLPASIEALPAVVQAVAGRLPVLLDGGIRRGSDVVKALALG 312

Query: 311 AQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGCSQLQDIDTSFL 363
           A AVL+GRP ++GLA  G  GV+H + LL++EL V MA+ GC+ L DI+   L
Sbjct: 313 AAAVLLGRPWVYGLAAAGPLGVAHTLKLLREELEVTMAMAGCTTLADINADLL 365


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: 326
Number of extensions: 12
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: 365
Length of database: 374
Length adjustment: 30
Effective length of query: 335
Effective length of database: 344
Effective search space:   115240
Effective search space used:   115240
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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