Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate AZOBR_RS19635 AZOBR_RS19635 succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__azobra:AZOBR_RS19635 Length = 485 Score = 570 bits (1468), Expect = e-167 Identities = 276/478 (57%), Positives = 370/478 (77%), Gaps = 5/478 (1%) Query: 46 LLRGDSFVGGRWLP--TPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 LLR ++V G W + TF V +PA+G +L VAD G E R A+ AA A +W+ Sbjct: 8 LLRTQAYVNGVWRDAFSGKTFAVTNPATGEELAQVADVGAEETRQAINAADAALPAWRAK 67 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + KER+++LR+W++L++ +++LA ++T E GKPL EA+GE+ Y A F+EWF+EE +RVY Sbjct: 68 TAKERAAILRRWFELIMAAQEDLAVLMTLEQGKPLAEARGEVAYGASFIEWFAEEGKRVY 127 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 GD+I + A +KR +VLK+P+GV + ITPWNFP+AMITRKVG ALAAGCT+VVKPAEDTP Sbjct: 128 GDVIPSFAGNKRIVVLKEPIGVVAAITPWNFPNAMITRKVGPALAAGCTIVVKPAEDTPL 187 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 SALALA+LA +AG+P GV+N++ S A +G L P+V K+SFTGST GKIL+ Sbjct: 188 SALALAELAERAGVPAGVFNIVTGSDPVA--IGGELTASPIVRKLSFTGSTEVGKILMRQ 245 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 +A++VK+VS+ELGG APFIVFD A++D+AV GA+ASK+RN+GQTCVC+NR LVQ G++D+ Sbjct: 246 SADTVKKVSLELGGNAPFIVFDDADLDEAVKGALASKYRNSGQTCVCANRLLVQAGVYDA 305 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F K AEA+K+ +RVGNG E G TQGP+IN +AVEKVE+ + DA+AKGA V GGKRH Sbjct: 306 FAAKLAEAVKQ-IRVGNGMEAGVTQGPMINGQAVEKVEELMGDALAKGAKVALGGKRHGL 364 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 GG FFEPT+L+ VT +M EE FGPVAP+ KF+ E +A+ +AN + GLA YFYS+D Sbjct: 365 GGTFFEPTILTGVTTEMRVAREEIFGPVAPLFKFETEADAIRMANDTEFGLAAYFYSRDI 424 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521 ++WRVAEQLE GMVG+NEG++S+ PFGG+KQSG+GREGSKYG++++LE+KY+C G Sbjct: 425 GRVWRVAEQLEYGMVGINEGILSTEVAPFGGIKQSGIGREGSKYGVEDFLEIKYLCVG 482 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: 688 Number of extensions: 26 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: 485 Length adjustment: 34 Effective length of query: 489 Effective length of database: 451 Effective search space: 220539 Effective search space used: 220539 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 Apr 09 2024. 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