GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctO in Collimonas arenae Ter10

Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate WP_061533167.1 CAter10_RS09135 alpha-hydroxy-acid oxidizing protein

Query= BRENDA::Q8Z0C8
         (365 letters)



>NCBI__GCF_001584165.1:WP_061533167.1
          Length = 378

 Score =  259 bits (663), Expect = 6e-74
 Identities = 149/367 (40%), Positives = 217/367 (59%), Gaps = 23/367 (6%)

Query: 16  LAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQPLQL 75
           LA+  + +  +DY  SG+  E T + N      +KLR R+ ++V Q +  ++++GQ + +
Sbjct: 13  LAQKRVPKAFYDYADSGSYTESTYRANSDDLAALKLRQRVAINVDQRSTRSTMIGQDVTM 72

Query: 76  PLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSLQWFQ 135
           P+ IAP     +    GE+  A+AA   G    LST+S  S+E+VA V +K      WFQ
Sbjct: 73  PVAIAPTGLTGMQWANGEMLGAIAAEKFGIPFTLSTMSICSIEDVASVTTKPF----WFQ 128

Query: 136 LYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANLTTIS 195
           LY+ +DRG  ++L+ERA AA   AL LT+D  +LGQR +D +N   +PP + LANL  ++
Sbjct: 129 LYVMRDRGFIKSLIERAKAAKCSALVLTLDLQILGQRHKDLKNGMSVPPKMTLANLIDLA 188

Query: 196 ----------------GLNIPHAPGESGLFT---YFAQQLNPALTWDDLEWLQSLSPLPL 236
                           G    H  G  G+ T   + A Q +P L WDD+ W++      L
Sbjct: 189 SKPGWALRALGGRKSFGNLAGHVKGADGIMTLSKWTASQFDPTLCWDDIAWIKEQWGGKL 248

Query: 237 VLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVLLDGG 296
           +LKGIL  +DA  A   GA AIVVSNHGGRQLDGA++S+ ALP IV AV  + EV  DGG
Sbjct: 249 ILKGILDVEDAKIAATTGADAIVVSNHGGRQLDGAVSSISALPAIVDAVGDQIEVWFDGG 308

Query: 297 IRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGCSQLQ 356
           IR G D++KA+A+GA+  +IGR  L+ L   G+AGV+ ++ +LQ+EL+V+MAL G   ++
Sbjct: 309 IRSGQDVLKAVALGAKGTMIGRAFLYSLGAMGEAGVTRMLQILQQELDVSMALTGNKDIK 368

Query: 357 DIDTSFL 363
           D+    L
Sbjct: 369 DVGPHIL 375


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: 307
Number of extensions: 11
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: 378
Length adjustment: 30
Effective length of query: 335
Effective length of database: 348
Effective search space:   116580
Effective search space used:   116580
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 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