Alignments for a candidate for pad-dh in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for pad-dh in Burkholderia phytofirmans PsJN

Align Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized)
to candidate BPHYT_RS09900 BPHYT_RS09900 aldehyde dehydrogenase

Query= SwissProt::O06837
         (502 letters)



>FitnessBrowser__BFirm:BPHYT_RS09900
          Length = 492

 Score =  631 bits (1627), Expect = 0.0
 Identities = 307/484 (63%), Positives = 369/484 (76%), Gaps = 1/484 (0%)

Query: 19  LPHQMLIGGQWVNAQSDKTLNVYNPATGDTLTDVPDGDVEDVNAAVESAAATLQSDAWRR 78
           LPH M I G+   + + KT  V+NPAT + +  +PD    D++ AV ++ A  +SDAWRR
Sbjct: 10  LPHTMFINGEKTGSAAGKTFPVFNPATAEEIAQIPDASEADIDHAVRTSKAAFESDAWRR 69

Query: 79  MPPSARERILLRLADLLEAHGDELARLETLNNGKLLIYSKMMEVGASAQWLRYMAGWATK 138
           MPP+ RE +LL+LADL+E H DELA LETLN GKL+ +SKM+EV  S QWLRYMAGWATK
Sbjct: 70  MPPAVREGLLLKLADLVERHSDELATLETLNQGKLIGFSKMLEVAGSVQWLRYMAGWATK 129

Query: 139 LTGSTLDLSLPLPPDVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLK 198
           + GST DLS+P PP  R  AST+RVP GVVAAI+PWNFPLLMAVWKIAPALACG TVVLK
Sbjct: 130 IEGSTFDLSIPFPPGTRYNASTKRVPAGVVAAIVPWNFPLLMAVWKIAPALACGCTVVLK 189

Query: 199 PAEETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRI 258
           PAEETPLTA+RLAELA EAG PAG  NVVTGRGETAG ALVRHP V KV FTGSTEVGRI
Sbjct: 190 PAEETPLTAIRLAELAHEAGFPAGVFNVVTGRGETAGAALVRHPLVKKVTFTGSTEVGRI 249

Query: 259 IGSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHES 318
           IG  C   LK  SLELGGKSPVIVL DCDP++A EGAA AIFFNHGQVCTAGSRLYV  S
Sbjct: 250 IGRQCADDLKRASLELGGKSPVIVLDDCDPRKAIEGAAGAIFFNHGQVCTAGSRLYVARS 309

Query: 319 IYEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTE 378
           IY++V+Q +A + + I +GSG +    MGPMVS +H + V   I  G ++G +++     
Sbjct: 310 IYDEVVQGIAAVADGITLGSGFDAATQMGPMVSARHRDKVAGMIAQGKDEGGEIVSRDAR 369

Query: 379 APCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASI 438
               +G+FV+PT+ ANR  K + ++ +EVFGPVLVA P+ D+ EV+ +AN S YGLGAS+
Sbjct: 370 VE-REGYFVRPTVIANRACKPLAVVKEEVFGPVLVAMPYDDLDEVLAQANASEYGLGASV 428

Query: 439 WTNDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRSL 498
           WTN L  ALR+ D +EAGTVWVNTHNMVDP +PFGGFK SG+GREHG + IE YT ++S+
Sbjct: 429 WTNQLDKALRLVDGIEAGTVWVNTHNMVDPAMPFGGFKASGIGREHGKSIIESYTESKSV 488

Query: 499 VIAY 502
            IAY
Sbjct: 489 CIAY 492


Lambda     K      H
   0.317    0.134    0.395 

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: 712
Number of extensions: 26
Number of successful extensions: 2
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: 502
Length of database: 492
Length adjustment: 34
Effective length of query: 468
Effective length of database: 458
Effective search space:   214344
Effective search space used:   214344
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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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
the source code
instructions for running GapMind on your computer

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