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_RS22315 AZOBR_RS22315 aldehyde dehydrogenase

Query= BRENDA::Q402C7
         (499 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS22315 AZOBR_RS22315 aldehyde
           dehydrogenase
          Length = 497

 Score =  387 bits (993), Expect = e-112
 Identities = 205/476 (43%), Positives = 291/476 (61%), Gaps = 5/476 (1%)

Query: 20  HFIGGEWVSGDSGKTIDLINPATGAVLTKIQAGNAKDIQRAVAAAKAAFPKWSESSPAER 79
           HF GGE+    SGK   ++NPATG  + +   G A D+  AVAAA AA  +W++    ER
Sbjct: 22  HFFGGEFRPASSGKGFPVVNPATGETVAEAAFGEAADVDAAVAAAVAAQKEWAKRPVRER 81

Query: 80  QEILIEVARRLKARHQHYATLETLNNGKPIRESMYFDMPQAISQFEVFAGAAYGLHGQTL 139
            +++ E  R L A  +  A L  L  GK +R     +       F  F G A  L G+T+
Sbjct: 82  GKLVAECGRVLDAHKEEIAKLIALETGKALRTESRVEAGVLSDAFVFFGGLAPELKGETI 141

Query: 140 DY-PDAIGIVHREPLGVCAQIIPWNVPILMMACKIAPALASGNTVVLKPAETVCLSVIEF 198
            + P  + +  REP+GV   IIPWNVP+L+MA KIAPA+ +GN VV+K AE   L+V+  
Sbjct: 142 PFNPSMLTMTVREPVGVVGAIIPWNVPLLLMALKIAPAMVAGNAVVVKSAEEAPLAVLRV 201

Query: 199 FVEMADLLPPGVINVVTGYGADVGEALVTHEDVRKVAFTGSVATARRIIQYASSNIIPQT 258
              +  ++P GV+N+++GYG + G  LV H+DV+KV FTGSV T + + + A+  +IP T
Sbjct: 202 VQLINTVIPAGVVNILSGYGPECGAPLVAHKDVKKVTFTGSVETGKIVYKTAAEKLIPVT 261

Query: 259 LELGGKSAHIVCADADIDAAVESATMSTVFNK-GEVCLAGSRLFLHQSIQDEFLAKFKVA 317
           LELGGKS  IVC DAD+D A+  A     F + G+ C A SR+F+H SI D F+ K K  
Sbjct: 262 LELGGKSPMIVCGDADLDQAIAGAIAGMRFTRQGQSCTASSRIFVHDSIHDAFVEKLKEK 321

Query: 318 LEGIRQGDPLDFATQLGAQASQMQMDKVQSYLQLATEEGAT--VLTGGSRNESLADGHFI 375
           +  ++ GDPLD +T +G   S  Q+D+VQSY+ +  E GAT  V +    +  L  G ++
Sbjct: 322 VNAMKMGDPLDESTDIGTIVSPQQLDRVQSYIAIGKEGGATPHVCSAMPSDPKLTKGLYV 381

Query: 376 KPTVFTNVSNSMRIAREEIFGPVTSVLTWNDEDDMMALANDTTYGLAGGVWTRDISRAHR 435
           +P +FT V NS RIA+EEIFGPV  V+ W D ++++A ANDT YGLA  +WTRD+  A  
Sbjct: 382 QPHIFTGVKNSDRIAQEEIFGPVCCVIRWTDYEEVIAQANDTEYGLAATIWTRDLKVAMD 441

Query: 436 IARKLETGTVWVNRYYNLKPNMPLGGYKQSGFGREFSHE-VLHHYTQTKSVVINLQ 490
              +LE G V VN+   ++PN+  GG K SG G+E S E +L H+T  K+++IN++
Sbjct: 442 AVHRLEAGFVQVNQNLVVQPNLSYGGVKSSGLGKEASLEAMLEHFTHKKTIIINMK 497


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: 558
Number of extensions: 19
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: 497
Length adjustment: 34
Effective length of query: 465
Effective length of database: 463
Effective search space:   215295
Effective search space used:   215295
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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