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.
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:
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