Align Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized)
to candidate WP_013554530.1 NITSA_RS08060 aldehyde dehydrogenase
Query= curated2:A6UVT6 (465 letters) >NCBI__GCF_000186245.1:WP_013554530.1 Length = 484 Score = 310 bits (793), Expect = 9e-89 Identities = 169/457 (36%), Positives = 268/457 (58%), Gaps = 11/457 (2%) Query: 13 IEVKNPYNNEIIGYIPSLSRNETKEAIKIAEEHKSTMKNLSPTIRYNILMKIASELSKNK 72 IE KNPY +++ P S + K A+++A+ R L +A+++ +N+ Sbjct: 31 IERKNPYTGKVVSRYPVCSPEDAKRALEVAKVAAKAAAKAPLHQRIAWLEDVAAKIRENQ 90 Query: 73 RELAKLITIDVGKPIKQSIIEVDRTITTFKFSAFYSRELRGETIPFD------DGMVITK 126 + A+LI ++ KPI + IEV R T + +A GETIP D + + Sbjct: 91 EDFARLIVDEIAKPIHFARIEVQRCAETIELTAKELVHFVGETIPTDVAPSGREATAYWR 150 Query: 127 REPVGLVGAITPFNFPLNLFAHKIAPAIAMGNSIVAHPSSKAPMITIELTKIIEKVLKSK 186 R P G+ ITPFNFPLNL AHKIAPA+ GN++V P+ +AP+ +L K+ ++S+ Sbjct: 151 RIPAGVAVCITPFNFPLNLIAHKIAPALGAGNAVVLKPTPEAPLTAYKLAKLF---IESE 207 Query: 187 KIPLGVFNLLTGEGHIVGDEIVKNNKINKLSFTGSVEVGESITKKAGFKKITLELGGNNP 246 +L+ G+ VG +VK+ +SFTGSV VG+ I+ +AG KK++LELGGN Sbjct: 208 HAVPDALSLVYGDAE-VGSALVKSPIPRVISFTGSVPVGKIISSEAGIKKVSLELGGNAA 266 Query: 247 MIILKDANINKAVESCMSGKFLNSGQVCISVGRVLIEQEVADEFINKIVEKVKKLKIGNP 306 I K+AN+ A C G F NSGQVCIS+ R+ + + V +EF + ++ K LK+G+P Sbjct: 267 TYIDKEANLADAAAKCAFGSFYNSGQVCISLQRIYVHEAVYEEFAELMAKETKLLKVGSP 326 Query: 307 LDEDTNISSLISLDSAERVEKLINKSIGQGGKLICGGKRENSIIYPTIL-EITADNILAN 365 +E+T + LI D+ R + + + +G ++ GG+ + I PT++ ++T + + Sbjct: 327 YEEETFMGPLIDEDARHRAKSWVASARDEGATILVGGEEVDGIFPPTVVTDVTDEMKIVC 386 Query: 366 IEIFAPVLPIIRVNDMNEALNQANNSNYGLHSGVFTQDINKALYFADNLEYGGVLINNSP 425 E+FAPV+ ++ V DM AL + N+S YGL +FT I A F D E GGV++N+ P Sbjct: 387 EEVFAPVVSLVSVPDMETALEKINSSPYGLQYSIFTDSIRAAKAFIDAAEAGGVVVNDIP 446 Query: 426 TFRIDNMPFGGIKHSGLGREGIKYAIDEMSEIKTIIV 462 T R D P+GG+K SG+GREG ++A++E +EI+++++ Sbjct: 447 TVRFDVQPYGGVKLSGVGREGPRFALEEFTEIQSVVI 483 Lambda K H 0.316 0.136 0.377 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: 520 Number of extensions: 22 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: 465 Length of database: 484 Length adjustment: 33 Effective length of query: 432 Effective length of database: 451 Effective search space: 194832 Effective search space used: 194832 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 (21.6 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