Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate AZOBR_RS09720 AZOBR_RS09720 succinate-semialdehyde dehdyrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__azobra:AZOBR_RS09720 Length = 497 Score = 351 bits (901), Expect = e-101 Identities = 182/462 (39%), Positives = 272/462 (58%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 ++DG+++ ++V NPA +V+ +P A++ R+AI+AAERA P W AL A ERA Sbjct: 25 FVDGRWIDADSGKTVEVTNPADGSVLGSVPMMGADETRRAIEAAERAWPAWRALTAKERA 84 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 LR + +I+ ++ E GK A EVA+ A +I++ AE +R G+ I Sbjct: 85 KTLRTWFDLMMANQEDIARIMTAEQGKPLAEARGEVAYAASFIEWFAEEGKRVYGDTIPQ 144 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 PG I++ K +GVT I PWNFP +I RK PAL G +VIKP+ TP A+A A Sbjct: 145 HLPGRRIVVTKEPIGVTAAITPWNFPAAMITRKAGPALAAGCPMVIKPATATPLTALAMA 204 Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249 + + G+P G+ ++V G +G E+ GNP V ++ TGS G+++MA A + KV Sbjct: 205 VLAERAGIPAGILSVVTGSARAIGGEMTGNPTVRKLTFTGSTEIGKELMAQCAGTVKKVS 264 Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309 LELGG AP +V +DADL+ AVK + S+ N+GQ C CA R+ VQ G+YD F +L EA+ Sbjct: 265 LELGGNAPFLVFNDADLDEAVKGAIASKYRNTGQTCVCANRLLVQSGVYDAFAAKLAEAV 324 Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369 +A++ G GPLI+ AA+E+VE + A E+GARV GGK E G ++ PT+ Sbjct: 325 KALKVGPGLTTEGAQQGPLIDMAAVEKVEDHIRDATEKGARVVLGGKRHELGGSFFEPTI 384 Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429 L DV M + EETFGPV P+ F+T E+A+ MAN +++GL + Y++++ + + Sbjct: 385 LADVTPAMKVAREETFGPVAPLFRFETEEEAVRMANATEFGLAAYFYSRDIGRVWRVAEA 444 Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQ 471 L++G IN G ++SGIG K+G+ +YL+ Sbjct: 445 LEYGIVGINEGIISTEVAPFGGMKESGIGREGSKYGIEDYLE 486 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: 593 Number of extensions: 24 Number of successful extensions: 1 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: 497 Length adjustment: 34 Effective length of query: 445 Effective length of database: 463 Effective search space: 206035 Effective search space used: 206035 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