Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000745975.1:WP_035239838.1 Length = 484 Score = 543 bits (1400), Expect = e-159 Identities = 264/474 (55%), Positives = 351/474 (74%), Gaps = 6/474 (1%) Query: 52 FVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKERS 109 F+ W+ + T V +PA+G LGTV CG E + A+ AA ++ +W+ + ERS Sbjct: 15 FIQDEWVAADSGKTVDVTNPATGQILGTVPFCGADETQRAINAANESLDAWRSKTAGERS 74 Query: 110 SLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIYT 169 ++LRKWYDL+++N+++LA I+TAE GKPL E++GEI Y+A F EWF+EEA+RVYGD+I Sbjct: 75 AILRKWYDLLMENQEDLAVIMTAEQGKPLAESRGEIAYAAAFFEWFAEEAKRVYGDVIPQ 134 Query: 170 SAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALALA 229 + +R +V+KQPVGV + ITPWNFPSAMITRK GAALAAGCT+V+KPA TP+SALA+A Sbjct: 135 TVASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVLKPATATPFSALAIA 194 Query: 230 QLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSVK 289 +L QAG+P GV+NV+ S + +G L +P+V K++FTGST GK L+ A ++K Sbjct: 195 KLGQQAGVPKGVFNVVTGS---SSAIGGELTANPIVRKLTFTGSTQVGKKLMRDCAGTMK 251 Query: 290 RVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKFA 349 R+SMELGG APFIVFD A++D AV GAMA K+RN+GQTCVC+NR VQ G++D F K Sbjct: 252 RLSMELGGNAPFIVFDDADIDAAVEGAMACKYRNSGQTCVCANRMYVQAGVYDEFCRKLT 311 Query: 350 EAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGGNFFE 409 A+++ L+VGNGF++G QGPLI+ AVE VE H+ DAV KG V+ GG RH G FF Sbjct: 312 AAVQE-LKVGNGFDDGVQQGPLIDMAAVETVESHIKDAVDKGGKVLAGGTRHALGRTFFA 370 Query: 410 PTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIWRV 469 PT++++VT DM EETFGP+APV KFD EEE V AN + GLA YFY++D A+ WR+ Sbjct: 371 PTIIADVTDDMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYTRDMARSWRI 430 Query: 470 AEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 E+LE G+VG+N G+IS+ PFGGVK+SG GREGSKYG+D+YLE+KY+C G+ Sbjct: 431 GEKLEYGLVGINSGIISNPVAPFGGVKESGNGREGSKYGLDDYLEIKYMCMAGI 484 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: 632 Number of extensions: 24 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: 484 Length adjustment: 34 Effective length of query: 489 Effective length of database: 450 Effective search space: 220050 Effective search space used: 220050 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