Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_012469747.1 GLOV_RS08400 succinate-semialdehyde dehydrogenase I
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000020385.1:WP_012469747.1 Length = 484 Score = 553 bits (1424), Expect = e-162 Identities = 268/480 (55%), Positives = 364/480 (75%), Gaps = 6/480 (1%) Query: 46 LLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 LLR ++ G+WL + T V +PA+G LGT+ G E R A+ AA A+ +W+ Sbjct: 8 LLRQSCYLNGQWLAADSGKTIDVTNPATGEVLGTIPKMGTAETRRAIEAANAAWPAWRVK 67 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + KER+++LR+W++LM++N+++LA I+TAE GKPL E++GEI Y+A F+EWF+EE +R+Y Sbjct: 68 TAKERATILRRWFELMLENQEDLAIIMTAEQGKPLAESRGEISYAASFIEWFAEEGKRLY 127 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 GD I +DKR +V+K+P+GV + ITPWNFPSAMITRK G ALAAGCT+VVKPA TP+ Sbjct: 128 GDTIPAHGRDKRIVVIKEPIGVCAAITPWNFPSAMITRKAGPALAAGCTMVVKPATATPF 187 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 SALALA+L +AGIP GV++VI S + E+G + ++P+V K++FTGST GK L Sbjct: 188 SALALAELGERAGIPAGVFSVITGS---SSEIGTEMTSNPIVRKLTFTGSTEIGKQLTAQ 244 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 A ++K+VSMELGG APFIVFD A++D AV GA+ASK+RN GQTCVC+NR LVQ G++D Sbjct: 245 CAATMKKVSMELGGNAPFIVFDDADLDAAVEGAIASKYRNTGQTCVCTNRLLVQAGVYDL 304 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F K A A+ K +RVG+G ++ QGPLI+E +V+KVE+H++DAV+KGA + GGKRH+ Sbjct: 305 FAEKLATAVAK-MRVGDGLKDDVQQGPLIDEASVQKVEEHIHDAVSKGARIALGGKRHEL 363 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 GG FF+PT+L +VT ML EETFGPVAP+ KF + EA+ +AN + GLA YFY++D Sbjct: 364 GGTFFQPTILCDVTPQMLVAREETFGPVAPIFKFTTDAEAIKMANDTEFGLASYFYTRDI 423 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 ++WRVAE LE GMVG+N GL+S+ PFGGVK+SG+GREGSKYGI+E+ EVKY+C GG+ Sbjct: 424 GRVWRVAEALEYGMVGINTGLVSTEIAPFGGVKESGIGREGSKYGIEEFCEVKYLCMGGI 483 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: 676 Number of extensions: 23 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