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_RS19085 AZOBR_RS19085 glycolate oxidase

Query= BRENDA::Q8Z0C8
         (365 letters)



>FitnessBrowser__azobra:AZOBR_RS19085
          Length = 362

 Score =  288 bits (737), Expect = 2e-82
 Identities = 171/365 (46%), Positives = 226/365 (61%), Gaps = 11/365 (3%)

Query: 1   MTAISSPINLFEYEQLAKTHLSQMAFDYYISGAG-DEITLQENRAVFERIKLRPRMLVDV 59
           M+  +  ++L++YE+     +   A   YI+G G D IT Q NR  ++R++L PR L D+
Sbjct: 1   MSVPADTVSLYDYERHFTARVDA-ATRAYIAGTGADGITRQANRDAYDRMRLMPRALRDL 59

Query: 60  SQINLTTSVLGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEE 119
           S  +  TS+ GQ +  P+LIAPMAF  L H +GE ATA AA   GT M +ST S+ +LEE
Sbjct: 60  SGASAATSLFGQAMPYPILIAPMAFHRLVHRDGERATAQAAGLTGTWMTVSTQSSVTLEE 119

Query: 120 VAEVGSKFSPSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNE 179
           VA           WFQ+Y       T ALV RA AAGY+AL LTVDAPV G R  ++R  
Sbjct: 120 VAAAAG----GPLWFQIYTQPRPEDTLALVRRAEAAGYRALVLTVDAPVSGLRNIEQRAG 175

Query: 180 FVLPPGLHLANLTTISGLNI-PHAPGESGLFTYFAQQLNPALTWDDLEWLQSLSPLPLVL 238
           F LP G+   NL  ++  +  P  PG       F   L+ A +WD + WL + + LP++L
Sbjct: 176 FRLPDGIAPVNLAGLAPDSFTPTRPGSP----VFQGMLHAAASWDTVRWLCAETRLPVLL 231

Query: 239 KGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVLLDGGIR 298
           KGI+  DD   AVE GA  I+VSNHGGR LD   A  + LP +     G+  +L DGGIR
Sbjct: 232 KGIMNPDDVDLAVEAGAAGIIVSNHGGRTLDTLPAVAEVLPLVATRAAGRLPILADGGIR 291

Query: 299 RGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGCSQLQDI 358
           RGTDI+KALA+GA AVL+G+PVL  LAVGG AGV+H++++LQ EL VAMAL G ++L DI
Sbjct: 292 RGTDILKALALGADAVLVGQPVLHALAVGGMAGVAHMLTILQTELEVAMALSGRARLADI 351

Query: 359 DTSFL 363
           D S +
Sbjct: 352 DRSVI 356


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: 335
Number of extensions: 18
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: 362
Length adjustment: 29
Effective length of query: 336
Effective length of database: 333
Effective search space:   111888
Effective search space used:   111888
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