Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate WP_028487567.1 Q394_RS0100600 iron-containing alcohol dehydrogenase
Query= SwissProt::P0A9S1 (382 letters) >NCBI__GCF_000621325.1:WP_028487567.1 Length = 403 Score = 135 bits (340), Expect = 2e-36 Identities = 117/386 (30%), Positives = 171/386 (44%), Gaps = 28/386 (7%) Query: 13 FGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVPNPT 72 FG G + L + G + +I + + + + AAG W I V P+ Sbjct: 20 FGAGVLRKLPAIAAQYGKRLLIITGTSSFTASDAGKTLFNALQAAGFTWEIRR-VTHEPS 78 Query: 73 ITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAI-GIISNNPEFADVRSLEGLSPT---N 128 V E + Q D +I IGGGSP D KA+ G++ D LEG+ P Sbjct: 79 PHWVDETVAGLQGDSFDAVIGIGGGSPLDAAKAVAGLLKPGNSVMD--HLEGVGPELPYQ 136 Query: 129 KPSVPILAIPTTAGTAAEVTINYV--ITDEEKRRKFVCVDPHDIPQVAFIDADMMDGMPP 186 S P +A+PTTAGT +E T N V ++ E +K D + + A ID D++ PP Sbjct: 137 GSSTPFIAVPTTAGTGSEATKNAVLSVSGEHGFKKSFRADKL-VAEYAIIDPDLLASCPP 195 Query: 187 ALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKD--AGEEMAL 244 A AA G+DA T +E Y++ + LTDAL + +E + +L D A +MA Sbjct: 196 AQIAANGMDAFTQLMEAYVSTRSNPLTDALALAGMEAVRDSLLAFYRDPADSVARGKMAY 255 Query: 245 GQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIAR 304 ++G+ + GLG VHG+ PLGAF+ HGV +L+ R N D + D Sbjct: 256 ASLLSGICLAQTGLGSVHGVVAPLGAFHPIGHGVGCGMLVTEATRLNIDLLEARDADSPA 315 Query: 305 VMGVKVEGMSLEEARNA------------AVEAVFALNRDVGIPPHLRDVGVRKEDIPAL 352 + V G EE + + + + + + P L D GV + DIP L Sbjct: 316 LAKYVVIGKLFEETPPSLPLSGEEQEVAPLIHTLETWAKQLHL-PRLSDFGVTEADIPKL 374 Query: 353 -AQAALDDVCTGGNPREATLEDIVEL 377 A + + T NP E T DI L Sbjct: 375 VANSRGSSMKT--NPVELTDSDIANL 398 Lambda K H 0.319 0.136 0.404 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: 424 Number of extensions: 28 Number of successful extensions: 5 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: 382 Length of database: 403 Length adjustment: 31 Effective length of query: 351 Effective length of database: 372 Effective search space: 130572 Effective search space used: 130572 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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