Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_061535023.1 CAter10_RS21305 NADP-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_001584165.1:WP_061535023.1 Length = 484 Score = 549 bits (1414), Expect = e-160 Identities = 269/480 (56%), Positives = 361/480 (75%), Gaps = 6/480 (1%) Query: 46 LLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 L R +++ G W + T V +PA+G +G+V G E + A+ AA DA+ W+ Sbjct: 9 LFRQQAYINGEWCNADSGKTHAVTNPATGETIGSVPLMGAAETKRAISAANDAWRQWRRK 68 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + KERS +LRKW DLM+ N D+L I+T E GKPL EA+GEI Y+A F+EWF+EE +R Sbjct: 69 TAKERSIILRKWNDLMLANVDDLGLIMTVEQGKPLAEAKGEIAYAASFIEWFAEEGKRAG 128 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 GD I + + + R +V+K+ +GV + ITPWNFP+AMITRK G ALAAGC++V+KPAE TP+ Sbjct: 129 GDTIPSPSPNSRIVVIKESIGVCAAITPWNFPAAMITRKAGPALAAGCSMVLKPAESTPF 188 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 SALALA LA +AGIP GV++V+ S A+E+G + ++P+V K++FTGST G++L+ Sbjct: 189 SALALAVLAERAGIPAGVFSVVTGS---AREIGAEMTSNPIVRKLTFTGSTGVGRLLMEQ 245 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 A ++K++S+ELGG APFIVFD A++D AV GAMASK+RNAGQTCVC+NR VQ GI+D+ Sbjct: 246 CAPTIKKLSLELGGNAPFIVFDDADLDAAVEGAMASKYRNAGQTCVCANRLYVQDGIYDA 305 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F K A+ K L+VGNG +EG TQGPLI++KAV KVE+H+ DAV+KGA ++ GGKRH Sbjct: 306 FAAKLVAAVAK-LKVGNGQQEGVTQGPLIDDKAVAKVEQHIADAVSKGARILVGGKRHAL 364 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 G +FFEPT+L++VT DML EETFGP+AP+ +F ++EA+A+AN + GLA YFYS+D Sbjct: 365 GHSFFEPTVLADVTSDMLVAREETFGPMAPLFRFKTDDEAIALANDTEFGLASYFYSRDI 424 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 +IWRVAE LE GMVG+N GLIS+ PFGGVKQSGLGREGSKYGI++Y +KY+C GG+ Sbjct: 425 GRIWRVAEGLESGMVGINTGLISNEVAPFGGVKQSGLGREGSKYGIEDYQVIKYLCMGGI 484 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: 636 Number of extensions: 28 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: 484 Length adjustment: 34 Effective length of query: 489 Effective length of database: 450 Effective search space: 220050 Effective search space used: 220050 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 24 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