Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000009985.1:WP_011383730.1 Length = 485 Score = 553 bits (1425), Expect = e-162 Identities = 279/480 (58%), Positives = 358/480 (74%), Gaps = 5/480 (1%) Query: 46 LLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 LLR +++ G W+ + V +PA G+ + V G E R A+ AA A+ WK Sbjct: 9 LLRDHAYINGSWVAAQSGERLAVTNPADGSLIIRVPAMGAAETRQAIEAADRAWGPWKAK 68 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + KERS++LR+W++L++ +++LAK++TAE GKPL EA+GE+ Y A F+EWF+EEA+RVY Sbjct: 69 TAKERSAVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAKGEVAYGASFVEWFAEEAKRVY 128 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 GD I +R +V+K+P+GV + ITPWNFP AMITRK ALAAGC VVVKPAEDTP Sbjct: 129 GDTIPEHMPGRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVKPAEDTPL 188 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 SALALA+LA +AG PPGV+NVI KA VG L +P V K+SFTGST GK+L+ Sbjct: 189 SALALAELAERAGFPPGVFNVITAGDPKA--VGFELTANPKVRKLSFTGSTEVGKLLMAQ 246 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 A +VK++S+ELGG APF+VFD A++D AVAGAMASK+RN GQTCVC+NR LVQ GI+D+ Sbjct: 247 CAATVKKLSLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGIYDA 306 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F + AEA+ +L+VG G E QGPLINE+AV KVE+H+ DAVAKGA VV GGKRH Sbjct: 307 FTARLAEAVA-ALKVGPGLEGDFQQGPLINEEAVRKVERHIADAVAKGARVVMGGKRHAR 365 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 GG FFEPT+L++VT DM EETFGPVAP+ +F EEEAV +AN + GLA YFYS+D Sbjct: 366 GGTFFEPTILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAYFYSRDV 425 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 ++WRV+ LE G+VG+NEGLIS+ PFGGVK+SGLGREGSKYGI+++LEVKY+C GG+ Sbjct: 426 GRVWRVSRALEYGIVGINEGLISTEVAPFGGVKESGLGREGSKYGIEDFLEVKYLCMGGI 485 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: 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: 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 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