Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_084610126.1 A3GO_RS0115130 succinate-semialdehyde dehydrogenase I
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000428045.1:WP_084610126.1 Length = 486 Score = 567 bits (1460), Expect = e-166 Identities = 274/482 (56%), Positives = 366/482 (75%), Gaps = 6/482 (1%) Query: 44 ADLLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWK 101 + L R F+ G+W T V +PASG +GTV G E R A+ AA A +W+ Sbjct: 6 SSLFRQQCFIDGQWCDADRGETITVTNPASGTAIGTVPKMGRDETRNAIYAAERAQVAWR 65 Query: 102 EISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARR 161 I+ K+R+ +LR+WY+L+++N+++LA ++T+E GKPL E++GEI Y A ++EWF+EEA+R Sbjct: 66 SITAKQRAVILRRWYELILENQEDLAVLMTSEQGKPLSESRGEIAYGASYIEWFAEEAKR 125 Query: 162 VYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDT 221 VYGD I A DKR +V+KQPVGV + ITPWNFP+AMI RK G ALAAGC++VVKPA T Sbjct: 126 VYGDTIPAPASDKRIVVVKQPVGVVAAITPWNFPNAMIARKCGPALAAGCSIVVKPASMT 185 Query: 222 PYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILL 281 PYSALALA+L +AGIP GV NV+ S A +GE L ++P++ K++FTGST GK+L+ Sbjct: 186 PYSALALAELGKRAGIPNGVLNVVTGS---ASAIGEELTSNPIIRKLTFTGSTDIGKVLI 242 Query: 282 HHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIH 341 A++VK+VSMELGG APFIVF+ A++DQAV GA+ASK+RN GQTCVC NR LVQ GIH Sbjct: 243 RQCADTVKKVSMELGGNAPFIVFNDADIDQAVQGAIASKYRNTGQTCVCVNRILVQEGIH 302 Query: 342 DSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRH 401 D FVTK +A+ L+V +GFEEG+ QGPLI+ AVEKVE+H+ DA KGA++ GG+RH Sbjct: 303 DEFVTKLVKAVSL-LKVADGFEEGSQQGPLIDISAVEKVEEHIADAKKKGASIAFGGERH 361 Query: 402 QSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQ 461 GG FF+PT+L+ VT DM C EETFGP+AP+ KF E++A+ +ANA + GLA YFYS+ Sbjct: 362 ALGGTFFQPTVLTGVTADMDCAREETFGPLAPIFKFANEDDAIQMANATEFGLASYFYSR 421 Query: 462 DPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521 D +++WRVAE LE G+VG+NEG+IS+ PFGG+K+SG GREGSKYG+D+Y+E+KY+C G Sbjct: 422 DISRVWRVAEALEYGIVGINEGIISTEVAPFGGIKESGNGREGSKYGLDDYMEIKYLCMG 481 Query: 522 GL 523 G+ Sbjct: 482 GI 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: 628 Number of extensions: 17 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: 486 Length adjustment: 34 Effective length of query: 489 Effective length of database: 452 Effective search space: 221028 Effective search space used: 221028 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