GapMind for catabolism of small carbon sources

 

Alignments 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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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