Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_013074434.1 BTUS_RS01875 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000092905.1:WP_013074434.1 Length = 482 Score = 331 bits (849), Expect = 3e-95 Identities = 174/478 (36%), Positives = 281/478 (58%), Gaps = 7/478 (1%) Query: 6 QHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPA 65 ++ +Y+DGQ+ +V NPAT V+ + D ED +A+DAA RA P+W A A Sbjct: 3 RYGLYVDGQWTPAGSGKTFEVYNPATGDVVGEVADASKEDVLRAVDAAHRAFPDWAAKTA 62 Query: 66 IERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGE 125 ER+ LR+ + E++ ++ E GK A+ E+ + AD++ + +E A+R GE Sbjct: 63 KERSEILRRAYDLMVANLDELAVIMTTEQGKPLAEAKGEIQYAADFVLWYSEEAKRVYGE 122 Query: 126 IIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNA 185 I + P + IL+ ++ +GV I PWNFP +I RK+APAL G T+++KP++ TP A Sbjct: 123 TIPASFPHKRILVLRQPVGVVAAITPWNFPAAMITRKIAPALAAGCTVIVKPAKQTPLTA 182 Query: 186 IAFAKIVDEIGLPRGVFNLVLG-RGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKN 244 +I +E G+P GV NL+ G R + + + +V ++ TGS G+++M AA Sbjct: 183 CRLVEIFEEAGMPPGVVNLITGSRAAEIADTMLADERVRKITFTGSTEVGKQLMRKAADT 242 Query: 245 ITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNR 304 + + LELGG AP +V +DAD++ A + + S+ N+GQ C C RVYV + I + F Sbjct: 243 VKHISLELGGHAPFLVFEDADIDAAAREVAASKFRNAGQTCVCTNRVYVHESIAEPFAAA 302 Query: 305 LGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGG-----KAVE 359 L + ++ GN E + +GPLI+ A E+VE+ V AV++GARV GG + Sbjct: 303 LAKRAAEMKVGNGLEEG-VVIGPLIDRQAAEKVEEHVRDAVQKGARVVTGGHRLSRTGTK 361 Query: 360 GKGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQN 419 G+ +++ PT+LLDV +M +++EETFGPV PV F E+A+ AND+ YGL + ++T++ Sbjct: 362 GEVHFFEPTVLLDVSDDMLVLYEETFGPVAPVQTFRDDEEAVRKANDTRYGLAAYLFTRD 421 Query: 420 LNVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 L+ A++ + L++G IN Q G+++SG+G G+HG+ E+L+ + V L Sbjct: 422 LSRAVRVAESLEYGIVGINDGLPSVAQAPFGGFKESGLGREGGRHGIEEFLEIKYVSL 479 Lambda K H 0.318 0.135 0.392 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: 503 Number of extensions: 15 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: 479 Length of database: 482 Length adjustment: 34 Effective length of query: 445 Effective length of database: 448 Effective search space: 199360 Effective search space used: 199360 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: 51 (24.3 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