Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 16751 b2661 succinate-semialdehyde dehydrogenase I, NADP-dependent (NCBI)
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__Keio:16751 Length = 482 Score = 538 bits (1385), Expect = e-157 Identities = 262/480 (54%), Positives = 356/480 (74%), Gaps = 6/480 (1%) Query: 44 ADLLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWK 101 ++L R + + G WL V +PA+G KLG+V G E RAA+ AA A +W+ Sbjct: 6 SNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALPAWR 65 Query: 102 EISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARR 161 ++ KER+++LR W++LM++++D+LA+++T E GKPL EA+GEI Y+A F+EWF+EE +R Sbjct: 66 ALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKR 125 Query: 162 VYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDT 221 +YGD I DKR +V+KQP+GV + ITPWNFP+AMITRK G ALAAGCT+V+KPA T Sbjct: 126 IYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQT 185 Query: 222 PYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILL 281 P+SALALA+LA +AG+P GV+NV+ S A VG L ++PLV K+SFTGST G+ L+ Sbjct: 186 PFSALALAELAIRAGVPAGVFNVVTGS---AGAVGNELTSNPLVRKLSFTGSTEIGRQLM 242 Query: 282 HHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIH 341 A +K+VS+ELGG APFIVFD A++D+AV GA+ASKFRNAGQTCVC+NR VQ G++ Sbjct: 243 EQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVY 302 Query: 342 DSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRH 401 D F K +A+ K L +G+G + G T GPLI+EKAV KVE+H+ DA+ KGA VV GGK H Sbjct: 303 DRFAEKLQQAVSK-LHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAH 361 Query: 402 QSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQ 461 + GGNFF+PT+L +V + EETFGP+AP+ +F E + +A AN + GLA YFY++ Sbjct: 362 ERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYAR 421 Query: 462 DPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521 D ++++RV E LE G+VG+N G+IS+ PFGG+K SGLGREGSKYGI++YLE+KY+C G Sbjct: 422 DLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481 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: 626 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: 482 Length adjustment: 34 Effective length of query: 489 Effective length of database: 448 Effective search space: 219072 Effective search space used: 219072 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