GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctO in Acidovorax sp. GW101-3H11

Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate Ac3H11_1623 L-lactate dehydrogenase (EC 1.1.2.3)

Query= BRENDA::Q8Z0C8
         (365 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1623
          Length = 390

 Score =  256 bits (654), Expect = 7e-73
 Identities = 148/371 (39%), Positives = 219/371 (59%), Gaps = 26/371 (7%)

Query: 16  LAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQPLQL 75
           +A+  + +M +DY  SG+  E T + N + F+RIKLR R+ V++   +  T+++GQ + +
Sbjct: 16  IAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRTTMVGQDVAM 75

Query: 76  PLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSLQWFQ 135
           P+ IAP     + H +GE+  A AA + G    LST+S  S+E++AE   +      WFQ
Sbjct: 76  PVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGRHP---FWFQ 132

Query: 136 LYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANLTTIS 195
           +Y+ +DR     L++RA AA   AL LT+D  +LGQR +D +N    PP   +ANL  ++
Sbjct: 133 VYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIANLINLA 192

Query: 196 -----------------GLNIPHAPGE---SGLFTYFAQQLNPALTWDDLEWLQSLSPLP 235
                            G  + HA G    S L ++ A+Q +P L W D+EW++      
Sbjct: 193 TKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWGDVEWIKKRWGGK 252

Query: 236 LVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEI---VAAVNGKAEVL 292
           L+LKGI+  +DA  AV  GA A++VSNHGGRQLDGA +S+ ALP I   VA + G  EV 
Sbjct: 253 LILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVAQMGGGIEVW 312

Query: 293 LDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGC 352
           +DGGIR G D++KA A+GAQ  LIGR  L+GL   G+AGV+  + ++QKEL++ MA  G 
Sbjct: 313 MDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKELDITMAFCGH 372

Query: 353 SQLQDIDTSFL 363
           + +  +D S L
Sbjct: 373 TNINTVDRSIL 383


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: 321
Number of extensions: 19
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: 390
Length adjustment: 30
Effective length of query: 335
Effective length of database: 360
Effective search space:   120600
Effective search space used:   120600
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