Aligments for a candidate for adh in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Aligments for a candidate for adh in Azospirillum brasilense Sp245

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate AZOBR_RS26825 AZOBR_RS26825 aldehyde dehydrogenase

Query= BRENDA::Q402C7
         (499 letters)



>FitnessBrowser__azobra:AZOBR_RS26825
          Length = 494

 Score =  373 bits (957), Expect = e-108
 Identities = 204/474 (43%), Positives = 282/474 (59%), Gaps = 6/474 (1%)

Query: 22  IGGEWVSGDSGKTIDLINPATGAVLTKIQAGNAKDIQRAVAAAKAAFPKWSESSPAERQE 81
           IGGE     +GKT D++NPATG V+     G  +D+  AV AA AA   W+  S  ER  
Sbjct: 20  IGGELRPAATGKTFDVVNPATGDVIATAADGGERDVDAAVRAAVAAQGAWARLSARERGR 79

Query: 82  ILIEVARRLKARHQHYATLETLNNGKPIRESMYFDMPQAISQFEVFAGAAYGLHGQTLDY 141
           +L+E  RRL    +    L  L  GK IR     +          + G A  L G+T+ +
Sbjct: 80  LLVECGRRLVGHAEEIGRLLALETGKAIRTESRVEASLVADTLTFYGGLASELKGETVPF 139

Query: 142 -PDAIGIVHREPLGVCAQIIPWNVPILMMACKIAPALASGNTVVLKPAETVCLSVIEFFV 200
            P  +    REP+GV   IIPWNVP+ +MA KIAPAL +GN V++K AE   L+ +    
Sbjct: 140 HPKMLTFTQREPIGVVGAIIPWNVPLYLMALKIAPALVAGNAVIVKSAEEAPLAALRVIQ 199

Query: 201 EMADLLPPGVINVVTGYGADVGEALVTHEDVRKVAFTGSVATARRIIQYASSNIIPQTLE 260
            M  LLPPGV+N+++G G   G  LVTH  V KV FTGSV T + I   A+  +IP TLE
Sbjct: 200 VMNQLLPPGVLNILSGDGPGCGAPLVTHPGVGKVTFTGSVETGKIISHLAADKLIPVTLE 259

Query: 261 LGGKSAHIVCADADIDAAVESATMSTVFNK-GEVCLAGSRLFLHQSIQDEFLAKFKVALE 319
           LGGKS  IV  DAD+D A++ A     F + G+ C A SR+F+H+S+ D F+ K K  ++
Sbjct: 260 LGGKSPMIVMGDADLDKAIDGAVAGMRFTRQGQSCTASSRIFVHESLHDAFIDKLKAKVD 319

Query: 320 GIRQGDPLDFATQLGAQASQMQMDKVQSYLQLA-TEEGATV--LTGGSRNESLADGHFIK 376
            +  GDPLD AT +G   S  Q ++VQSY+ L  T  GA     +    +E LA G F++
Sbjct: 320 AMTMGDPLDEATDIGTIISPQQFERVQSYIALGETTAGAIAHRCSALPTDERLARGLFVQ 379

Query: 377 PTVFTNVSNSMRIAREEIFGPVTSVLTWNDEDDMMALANDTTYGLAGGVWTRDISRAHRI 436
           P +FT ++N  R+AREEIFGPVT V+ + D +D +A+AND+ +GLA  +WTRD+  A   
Sbjct: 380 PVLFTGLANDHRLAREEIFGPVTCVIAFRDYEDALAMANDSDFGLAATIWTRDLRTALDA 439

Query: 437 ARKLETGTVWVNRYYNLKPNMPLGGYKQSGFGREFSHE-VLHHYTQTKSVVINL 489
            R+L+ G V VN+   ++P +  GG+KQSG G+E S E +L H+T  K+V+IN+
Sbjct: 440 TRRLQAGFVQVNQNLVVQPGLSYGGFKQSGLGKEASLEAMLDHFTHKKTVIINM 493


Lambda     K      H
   0.318    0.133    0.390 

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: 555
Number of extensions: 21
Number of successful extensions: 5
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: 499
Length of database: 494
Length adjustment: 34
Effective length of query: 465
Effective length of database: 460
Effective search space:   213900
Effective search space used:   213900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources