Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate AO356_10720 AO356_10720 succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_10720 Length = 480 Score = 537 bits (1383), Expect = e-157 Identities = 261/478 (54%), Positives = 359/478 (75%), Gaps = 8/478 (1%) Query: 46 LLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 L R +F+ G W+ T V +PA+G LGTV G E R A+ AA A +W+ + Sbjct: 8 LFRQQAFIDGAWVDADNGQTIKVTNPATGEVLGTVPKMGAAETRRAIEAADKALPAWRAL 67 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + KER++ LR+WY+L+I+N+D+L +++T E GKPL EA+GEI+Y+A F+EWF+EEA+R+Y Sbjct: 68 TAKERANKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIY 127 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 GD+I DKR +V+KQP+GV + ITPWNFP+AMITRK G ALAAGCT+V+KPA TP+ Sbjct: 128 GDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPF 187 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 SALAL +LA++AGIP GV +V+ S A ++G L ++P+V K+SFTGST G+ L+ Sbjct: 188 SALALVELAHRAGIPQGVLSVVTGS---AGDIGGELTSNPIVRKLSFTGSTEIGRQLMAE 244 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 A +K+VS+ELGG APFIVFD A++D+AV GA+ SK+RN GQTCVC+NR +Q ++D+ Sbjct: 245 CAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVYDA 304 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F K A+ K L++GNG ++GTT GPLI+ KAV KV++H+ DAV+KGATV++GGK + Sbjct: 305 FAEKLKVAVAK-LKIGNGLDDGTTTGPLIDGKAVAKVQEHIADAVSKGATVLSGGKAME- 362 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 GNFFEPT+L+NV ++ EETFGP+AP+ +F E E +A++N + GLA YFY++D Sbjct: 363 -GNFFEPTILTNVPKNAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDL 421 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521 +++RVAE LE GMVGVN GLIS+ PFGG+K SGLGREGSKYGI++YLE+KY+C G Sbjct: 422 GRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 479 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: 607 Number of extensions: 21 Number of successful extensions: 4 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: 480 Length adjustment: 34 Effective length of query: 489 Effective length of database: 446 Effective search space: 218094 Effective search space used: 218094 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