Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate RR42_RS24560 RR42_RS24560 alcohol dehydrogenase
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__Cup4G11:RR42_RS24560 Length = 389 Score = 199 bits (505), Expect = 1e-55 Identities = 120/317 (37%), Positives = 177/317 (55%), Gaps = 2/317 (0%) Query: 34 LIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTEELVQKGFAAYQSAECDYIIA 93 L+VTDG L K G+L+ ++L +FDEV +P E ++ + ++A D +I Sbjct: 40 LVVTDGGLHKAGVLEGAKASLAAAGFRVTVFDEVVADPPEAVLLRCVEHARAARVDLVIG 99 Query: 94 FGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVPLVAINTTAGTAAEMTSNAVIID 153 GGGS +D AK +L + P G+G VK A VPLV + TTAGT +E+T N I+ Sbjct: 100 LGGGSSMDIAKLAAVLVVSGQPLAEMYGIGNVKGARVPLVQMPTTAGTGSEVT-NISIVS 158 Query: 154 SARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATGMDALTHAVEAYVSVGA-HPLTD 212 K I+ P + D + DA + + +P TAATG+DA+ HA+EAY S + ++D Sbjct: 159 VGETTKMGIVAPQLYADRVILDAELTVGLPRQHTAATGIDAMVHAIEAYTSKHKKNAISD 218 Query: 213 ANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMAFNSAGLGLVHALAHQPGATH 272 A A EA+RL++ L A ++G++ ARE M G LAG AF +A + VHALA+ G Sbjct: 219 ALAREALRLLSANLLPACENGNDRGAREAMLLGATLAGQAFANAPVAAVHALAYPLGGHF 278 Query: 273 NLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGVETRGMSDEAASQEAINAIRTLSKR 332 ++PHG+ NA++L V FN A A++A +A A+G+ DEA + I + L R Sbjct: 279 HIPHGLSNALMLGPVLRFNAAAAAAQYAELAGALGIGQADGDDEARTAAFIGFMEDLMDR 338 Query: 333 VGIPEGFSKLGVTKEDI 349 G P GVT+E + Sbjct: 339 SGAPRRLRDAGVTRESL 355 Lambda K H 0.317 0.133 0.384 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: 332 Number of extensions: 12 Number of successful extensions: 3 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: 389 Length adjustment: 30 Effective length of query: 352 Effective length of database: 359 Effective search space: 126368 Effective search space used: 126368 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: 50 (23.9 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