Alignments for a candidate for boxD in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for boxD in Burkholderia phytofirmans PsJN

Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate BPHYT_RS13360 BPHYT_RS13360 aldehyde dehydrogenase

Query= BRENDA::Q13WK4
         (531 letters)



>FitnessBrowser__BFirm:BPHYT_RS13360
          Length = 531

 Score =  960 bits (2482), Expect = 0.0
 Identities = 491/529 (92%), Positives = 506/529 (95%)

Query: 1   MTELLKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRAL 60
           MTELLKNHVAGQWIAG+G G+TLTDPVTGVALVRVSSEGLDLA AF FAR+ GGAALRAL
Sbjct: 1   MTELLKNHVAGQWIAGSGTGVTLTDPVTGVALVRVSSEGLDLAHAFGFARDTGGAALRAL 60

Query: 61  TYAQRAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGASLG 120
           TYAQRAARLADIVKLLQAKR DYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGASLG
Sbjct: 61  TYAQRAARLADIVKLLQAKRDDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGASLG 120

Query: 121 EVHALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVI 180
           +VHALRDG + SLSKD+SFS QHVL+PTRGVALFINAFNFPSWGLWEKAAPALLSGVPVI
Sbjct: 121 DVHALRDGESVSLSKDQSFSVQHVLTPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVI 180

Query: 181 VKPATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAAT 240
           VKPATATAWLTQRMVADVVDAGILPPGALS+ICGSSAGLLDQI+SFDVVSFTGSA TAAT
Sbjct: 181 VKPATATAWLTQRMVADVVDAGILPPGALSVICGSSAGLLDQIQSFDVVSFTGSAQTAAT 240

Query: 241 LRAHPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIR 300
           LRAHPAFVQRGARLNVEADSLNSAILCADA P TPAFDLFIKEVVREMTVKSGQKCTAIR
Sbjct: 241 LRAHPAFVQRGARLNVEADSLNSAILCADAAPGTPAFDLFIKEVVREMTVKSGQKCTAIR 300

Query: 301 RAFVPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVL 360
           RAFVPE ALE VLEAL AKLAKITVG+PRND VRMGSLVSREQYENVLAGIAALREEAVL
Sbjct: 301 RAFVPEGALEAVLEALNAKLAKITVGDPRNDTVRMGSLVSREQYENVLAGIAALREEAVL 360

Query: 361 AYDSSAVPLIDADANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNAL 420
           A+D SAVPLIDAD+NIAAC+APHLFVVNDPDNATLLHDVEVFGPVASVAPYRV TD   L
Sbjct: 361 AFDGSAVPLIDADSNIAACIAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVATDAATL 420

Query: 421 PEAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVM 480
           PEAHAVALARRGQGSLVASIYSND+AHLGRLALELADSHGRVHAISPSVQ SQTGHGNVM
Sbjct: 421 PEAHAVALARRGQGSLVASIYSNDEAHLGRLALELADSHGRVHAISPSVQQSQTGHGNVM 480

Query: 481 PMSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTLTQATHWP 529
           PMSLHGGPGRAGGGEELGGLRAL FYHRRSAIQAASAAIG+LTQATH P
Sbjct: 481 PMSLHGGPGRAGGGEELGGLRALGFYHRRSAIQAASAAIGSLTQATHLP 529


Lambda     K      H
   0.318    0.132    0.379 

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: 963
Number of extensions: 17
Number of successful extensions: 1
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: 531
Length of database: 531
Length adjustment: 35
Effective length of query: 496
Effective length of database: 496
Effective search space:   246016
Effective search space used:   246016
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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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