Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate WP_012383189.1 BIND_RS00880 alcohol dehydrogenase
Query= SwissProt::P0A9S1 (382 letters) >NCBI__GCF_000019845.1:WP_012383189.1 Length = 387 Score = 217 bits (552), Expect = 5e-61 Identities = 135/388 (34%), Positives = 200/388 (51%), Gaps = 9/388 (2%) Query: 1 MANRMILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLA 60 M + + L G GA L ++ G + IVTD L + G + ++A+GL Sbjct: 1 MTSTIALPRLLRIGAGASRELASVLQSLGLSRPFIVTDAYLQESGRADGLVQGLEASGLT 60 Query: 61 WAIYDGVVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRS 120 A++ VP+PT+ V L F+ D +I GGGSP DT KA+ +++ + + Sbjct: 61 AAVFSHTVPDPTVRSVDAALEAFRQGDHDCIIGFGGGSPIDTAKAVAVLAVHG--GPMSQ 118 Query: 121 LEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADM 180 + + P VPI+AIPTTAGT +EVT +ITDE K +C +P A +D ++ Sbjct: 119 YKAPHAQDLPGVPIIAIPTTAGTGSEVTRFTIITDESNDEKMLCAGLAYLPVAALVDYEL 178 Query: 181 MDGMPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAG--DKDA 238 P L A TG+DALTHAIE Y+++ A + + A+ IA LR A D+ A Sbjct: 179 TLTKPKRLTADTGIDALTHAIEAYVSKKANPFSSTFALAAMRAIAPNLRRVFANPDDRPA 238 Query: 239 GEEMALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEK 298 E M LG AG+ FSN + LVHGM+ P+GA ++ PHG++NA+LLP + ++A Sbjct: 239 REAMMLGATQAGIAFSNSSVALVHGMSRPIGAHFHVPHGLSNAMLLPAITAFSAPVALPL 298 Query: 299 YRDIARVMGVKVEGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKED----IPALAQ 354 Y D AR MGV E + + ++ + LN D+ +P R G+ + +P +A+ Sbjct: 299 YADCARAMGVAREEEGDQASVARLIDELRQLNADLQVPGP-RAYGIEETRWNSLLPLMAE 357 Query: 355 AALDDVCTGGNPREATLEDIVELYHTAW 382 AL G NP T + I LY AW Sbjct: 358 QALASGSPGNNPIVPTSDQIQTLYRQAW 385 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: 391 Number of extensions: 14 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: 382 Length of database: 387 Length adjustment: 30 Effective length of query: 352 Effective length of database: 357 Effective search space: 125664 Effective search space used: 125664 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 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