GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_03644
          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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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