GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Paraburkholderia bryophila 376MFSha3.1

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate H281DRAFT_02680 H281DRAFT_02680 succinate semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__Burk376:H281DRAFT_02680
          Length = 492

 Score =  554 bits (1427), Expect = e-162
 Identities = 276/480 (57%), Positives = 363/480 (75%), Gaps = 6/480 (1%)

Query: 46  LLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103
           LLR  +++ G+W       TF V DPA+G K+  V      E R A+ A   A   W+++
Sbjct: 17  LLRTLAYIDGQWCGADDARTFAVDDPATGEKIADVPLMTGAETRRAIEAGEHAQRGWRKL 76

Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163
           +  +RS++L++W+ LMI N D+LA I++AE GKPL EA+GEI Y+A F+EWF+E+A+RV 
Sbjct: 77  TAAQRSTILKRWHALMIANTDDLAIIMSAEQGKPLAEAKGEIGYAASFIEWFAEQAKRVD 136

Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223
           GD++ + A DKR LV K+P+GV + ITPWNFP+AMITRKV  ALAAGC +++KPAE TP 
Sbjct: 137 GDVLASPAADKRMLVTKEPIGVCAAITPWNFPAAMITRKVAPALAAGCAMILKPAEATPL 196

Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283
           SALALA+LA++AG+P GV++V+       + +G  + ++P+V K+SFTGST  G++L+  
Sbjct: 197 SALALAELAHRAGVPAGVFSVVVGD---PRSIGAEMTSNPIVRKLSFTGSTPVGRMLMSQ 253

Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343
            A +VK++S+ELGG APFIVFD A++D AV GA+ASK+RNAGQTCVC+NR  VQ G++D+
Sbjct: 254 CAPTVKKLSLELGGNAPFIVFDDADLDAAVEGALASKYRNAGQTCVCTNRVYVQDGVYDA 313

Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403
           F  KFA A+ + ++VGNGFE G TQGPLINE AVEKVE H+ DAVA GA V+TGGKRH +
Sbjct: 314 FAEKFAAAVGR-IKVGNGFESGVTQGPLINEAAVEKVEAHIADAVAHGARVLTGGKRHAA 372

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
           G  FFEPT++ +VT  M   TEETFGPVAP+ +F  E EA+A ANA + GLA YFYS+D 
Sbjct: 373 GKLFFEPTVVGDVTARMRFATEETFGPVAPLFRFTNEREAIAAANATEFGLAAYFYSRDI 432

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523
            +IWRVAE LE GMVG+N GLIS+   PFGGVKQSGLGREGSKYGI++YLE+KY+C GGL
Sbjct: 433 GRIWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSKYGIEDYLEIKYLCMGGL 492


Lambda     K      H
   0.318    0.135    0.400 

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: 660
Number of extensions: 19
Number of successful extensions: 3
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: 523
Length of database: 492
Length adjustment: 34
Effective length of query: 489
Effective length of database: 458
Effective search space:   223962
Effective search space used:   223962
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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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