Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate BPHYT_RS09875 BPHYT_RS09875 aldehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__BFirm:BPHYT_RS09875 Length = 481 Score = 409 bits (1051), Expect = e-118 Identities = 212/476 (44%), Positives = 302/476 (63%), Gaps = 9/476 (1%) Query: 10 YIDGQFVTWRGDA----WIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPA 65 + +G+F+ D I V NPATEAVI+ + + A+DAA AQ W LP Sbjct: 7 FANGRFIEPAADTASRELIAVCNPATEAVIAHVTGATQAEVIAAVDAAAVAQKGWRKLPQ 66 Query: 66 IERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGE 125 ERA +L K++ + E A I A + E GK A E + + Y AEWARR EGE Sbjct: 67 AERAVYLHKLADALTECAPAIGAALALESGKSVADATNEAIYASQITRYHAEWARRIEGE 126 Query: 126 IIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNA 185 +I SD P EN++L + +GV ++P+N+P + RK+APAL+ GNT+V++PS TP +A Sbjct: 127 VIPSDAPDENLVLHREPIGVVACLIPFNYPVYTFMRKVAPALIAGNTVVVRPSNNTPTSA 186 Query: 186 IAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNI 245 AK V++ GLP GV N +L + L +PKV M+++TGSV AG K++ NI Sbjct: 187 FEIAKAVEKAGLPAGVVN-ILAMNHATAEVLCTHPKVGMITLTGSVGAGRKVLDYCKANI 245 Query: 246 TKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRL 305 K LELGGK PAI+ DADLE A + +V S+ + GQ+C ERVYVQ+ ++D+FV L Sbjct: 246 AKPSLELGGKTPAIIEADADLEKAARDLVASKTTHCGQLCTAIERVYVQESVHDRFVALL 305 Query: 306 GEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAV---EGKG 362 + M AV+ G+ +E+ + MGPL+N A+ + + V RAV GA + GGK +GKG Sbjct: 306 KKHMSAVESGDRSEQPSL-MGPLVNEASRQSIHAMVERAVAAGATLETGGKLPTPGQGKG 364 Query: 363 YYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNV 422 ++YP TLL + RQ+M I+ EETFGPV+PVV + TL++A+ MAND +GL+S +YT+N Sbjct: 365 FFYPATLLSNCRQDMEIIQEETFGPVMPVVKYRTLDEALEMANDHQFGLSSVLYTENYRG 424 Query: 423 AMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQ 478 AMK G++ GE Y+NR + QGFHAGW++SG+GG DGKHG+ E+ QT++V ++ Sbjct: 425 AMKVANGIEAGELYVNRTPADPYQGFHAGWKRSGLGGDDGKHGMLEFTQTRLVVMK 480 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: 558 Number of extensions: 20 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: 481 Length adjustment: 34 Effective length of query: 445 Effective length of database: 447 Effective search space: 198915 Effective search space used: 198915 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 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