GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctO in Azospirillum brasilense Sp245

Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate AZOBR_RS27055 AZOBR_RS27055 L-lactate dehydrogenase

Query= BRENDA::Q8Z0C8
         (365 letters)



>FitnessBrowser__azobra:AZOBR_RS27055
          Length = 384

 Score =  213 bits (541), Expect = 9e-60
 Identities = 137/380 (36%), Positives = 201/380 (52%), Gaps = 29/380 (7%)

Query: 3   AISSPINLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQI 62
           A+++ +N+ E  Q A+  L +  F+Y   GA DE  +  ++   + +  +PR+LVDVS+ 
Sbjct: 2   AVTASLNIAEARQRARARLPRGLFEYIDRGAEDETGIATSKTALDSLVFKPRVLVDVSKR 61

Query: 63  NLTTSVLGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVA- 121
           + TT + G    +PL++AP A   L   +GE+  A AAA+ G    +ST S  S+E +A 
Sbjct: 62  DATTRLFGVDQPMPLVVAPTAVAGLVWYDGEVELAKAAAAVGIPFCVSTQSITSVERIAG 121

Query: 122 EVGSKFSPSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFV 181
           E G++      WFQLY+ + R  TR LV RA  AG +AL LTVD  V   RE + RN F 
Sbjct: 122 ESGARL-----WFQLYVWRSRERTRELVRRAERAGAEALVLTVDTAVTPNREYNVRNGFG 176

Query: 182 LP--PGLH-----LANLTTISGLNIPH-APGESGLFTYFAQQLNPAL------------- 220
           +P  P +      LA+    +G+   +   G    + ++  +   AL             
Sbjct: 177 IPIKPSVRAGLDCLAHPRWFAGVFAKYLRNGGVPTYAHYPDEFRTALGRVAVGDEIGLAQ 236

Query: 221 --TWDDLEWLQSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDAL 278
              W D+  L+      L+LKG+LR DDA +A E G   IVVSNHG R LD AI  +  L
Sbjct: 237 DVGWGDVRSLRDAWKGKLILKGVLRADDAEKAAELGVDGIVVSNHGARNLDHAIHPVRCL 296

Query: 279 PEIVAAVNGKAEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISL 338
            +I   V  +  VL D G+RRG+ +   L +GAQ VL+GR VL+GLA  G AG   V+ +
Sbjct: 297 TDIAERVGDRVTVLADSGVRRGSHVAGYLGLGAQGVLLGRAVLYGLATDGAAGAQAVLEM 356

Query: 339 LQKELNVAMALIGCSQLQDI 358
           +++EL   M  +G   + DI
Sbjct: 357 IRRELLTTMGFLGAPTVADI 376


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: 312
Number of extensions: 15
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 365
Length of database: 384
Length adjustment: 30
Effective length of query: 335
Effective length of database: 354
Effective search space:   118590
Effective search space used:   118590
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 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