Aligments for a candidate for praB in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for praB in Paraburkholderia bryophila 376MFSha3.1

Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate H281DRAFT_03644 H281DRAFT_03644 betaine-aldehyde dehydrogenase

Query= metacyc::MONOMER-13361
         (500 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_03644 H281DRAFT_03644
           betaine-aldehyde dehydrogenase
          Length = 499

 Score =  333 bits (853), Expect = 1e-95
 Identities = 187/457 (40%), Positives = 263/457 (57%), Gaps = 8/457 (1%)

Query: 35  FANINPVNGKLISDVFEADAKQVNEAVVAAQNAL-KGPWGKLSVQDRAALIHKIADGIQA 93
           + ++ P +  +  ++  A+A    EAV AA  A  K  W  L    RA ++++IAD I A
Sbjct: 31  YKSLYPADQSVNMEISTANADDAREAVEAADIAWRKSDWSGLKPHQRALILYRIADLIMA 90

Query: 94  RFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMSTSDGSGALNY 153
           R E     +  D G+P+ + R L +  A   FR FA   +T    L E  T      L  
Sbjct: 91  RHEALAQLQRRDNGKPIGETRVL-VASAANTFRYFAACLET----LDEEVTPSRGDYLTM 145

Query: 154 TVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAGV 213
           +V +P+GVI  I+PWN P+     K+APALA GN VV KP+E +P  +  LA +  +AGV
Sbjct: 146 SVYEPIGVIAAITPWNSPIASDAQKLAPALAGGNAVVLKPAEVTPLVSLALARICEEAGV 205

Query: 214 PPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADGVKEVSFELGGKN 273
           P GV +++ G G    G+ L +HP +  ++FTG ++ G  I +  AD +  VS ELGGK+
Sbjct: 206 PKGVISVLPGKGS-VIGDVLVRHPLVKKVSFTGGTEVGRGIARIAADKLMPVSLELGGKS 264

Query: 274 AAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLVVGY 333
             VVF DADLD A+ GVL   F++SG+ C+   R++V RS++D F+  L   A +L VG 
Sbjct: 265 PTVVFDDADLDHAVNGVLYGIFSSSGEACIAGSRLFVQRSVYDAFMKRLVEGARKLRVGD 324

Query: 334 PDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDERDQGAYVQPTIWTG 393
           P +    MGPLI+  HR+ V  Y  L ++EG  ++ GG  P   D R+QG Y QPTI  G
Sbjct: 325 PSRVETQMGPLITQAHRETVERYVALGLEEGGRLLCGGERP-VGDGREQGTYFQPTILEG 383

Query: 394 LSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQIHV 453
           LS+ AR   EEIFGPV    PFDDE  ++   N+S +GLA  IWT +  RA+R +R +  
Sbjct: 384 LSNNARICQEEIFGPVLVAMPFDDEASLLKEANNSVFGLAAGIWTRDYKRAYRTARALEA 443

Query: 454 GLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFY 490
           G +W+NT+ L  + TPF G K SG+GRE GR  +  Y
Sbjct: 444 GTIWINTYKLFSISTPFSGWKESGMGREKGRLGIREY 480


Lambda     K      H
   0.318    0.135    0.405 

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: 547
Number of extensions: 24
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: 500
Length of database: 499
Length adjustment: 34
Effective length of query: 466
Effective length of database: 465
Effective search space:   216690
Effective search space used:   216690
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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