Alignments for a candidate for ald-dh-CoA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Burkholderia phytofirmans PsJN

Align alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71); acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate BPHYT_RS21770 BPHYT_RS21770 aldehyde dehydrogenase

Query= BRENDA::A0A0H3W5U9
         (873 letters)



>FitnessBrowser__BFirm:BPHYT_RS21770
          Length = 481

 Score =  236 bits (603), Expect = 2e-66
 Identities = 149/434 (34%), Positives = 226/434 (52%), Gaps = 9/434 (2%)

Query: 23  RLREAQSVYATYTQEQVDKIFFEAAMAANK--MRIPLAKMAVEETGMGVVEDKVIKNHYA 80
           + R AQ  +    Q+ +D     AA A  +      LA+ AV +TG+G  +DK  KN+  
Sbjct: 29  KARAAQRAFEQAGQQALDTAADAAAWAIMEPERNRQLAERAVHDTGLGNADDKFRKNYRK 88

Query: 81  SEYIYNAYKNTKTCGVIEEDPAFGIKKIAEPLGVIAAVIPTTNPTSTAIFKTLIALKTRN 140
           +  +       KT GVI ED A G+ +IA  +GV+AA+ P+TNP +T   K + ALK  N
Sbjct: 89  TLGLLRDLHEQKTTGVIAEDKASGLVEIARAVGVVAAITPSTNPAATPANKIINALKCGN 148

Query: 141 AIIISPHPRAKNSTIEAAKIVLEAAVKAGAPEGIIGWIDVP-SLELTNLVMREADVILAT 199
           A+I++P P+  +S     + +     KAG    ++  +  P S   T  +MR+ D+++AT
Sbjct: 149 AVIVAPSPKGYSSCALLIEFIHAQFAKAGIDPDLVQMLPAPISKAATAALMRQCDLVVAT 208

Query: 200 GGPGLVKAAYSSGKPAIGVGAGNTPAIIDDSADIVLAVNSIIHSKTFDNGMICASEQSVI 259
           G    V+ AY+SG PA GVGAGN  +I+  SAD+  A   I+ SKTFDN   C+SE S++
Sbjct: 209 GSQANVRMAYASGTPAFGVGAGNVASIVTASADLHDAARKILRSKTFDNATSCSSENSIV 268

Query: 260 VLDGVYKEVKKEFEKRGCYFLNEDETEKVRKTIIINGALNAKIVGQKAHTIANLAGFE-- 317
           + + VY+ +  E    G   L+  +  K++  + +NG L+ +   + A  IA +AG E  
Sbjct: 269 IEEAVYQPMLAELTSCGGVLLDAAQKAKLQTAMWVNGKLSEQCTAKSAEVIARVAGLEEV 328

Query: 318 VPETTKILIGEVTSVDISEEFAHEKLCPVLAMYRAKDFDDALDKAERLVADGGFGHTSSL 377
                  L+ E +       F+ EKL PVL +YRA  FD A +    + A  G GH+  L
Sbjct: 329 AARHPAFLMVEESGAGSDYPFSGEKLAPVLTVYRAAGFDAAAEVVRSIYAYMGAGHSVGL 388

Query: 378 YIDTVTQKEKLQKFSERMKTCRILVNTPSSQGGIGDLYNFKLAPSLTLGCGSWGGNSVSD 437
           +     Q  +L      +   R++VN        G+  N  L  SL++GCG+WG N+ S 
Sbjct: 389 HSSDAAQAVQL---GVTLPVARVIVNQAHCLATGGNFDN-GLPFSLSMGCGTWGRNNFSG 444

Query: 438 NVGVKHLLNIKTVA 451
           N+G +H LN   VA
Sbjct: 445 NLGFRHYLNTTRVA 458


Lambda     K      H
   0.318    0.134    0.382 

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: 885
Number of extensions: 42
Number of successful extensions: 4
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: 873
Length of database: 481
Length adjustment: 38
Effective length of query: 835
Effective length of database: 443
Effective search space:   369905
Effective search space used:   369905
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: 54 (25.4 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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