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_RS22315 AZOBR_RS22315 aldehyde dehydrogenase

Query= BRENDA::Q402C7
         (499 letters)



>FitnessBrowser__azobra:AZOBR_RS22315
          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 (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