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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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