Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate BPHYT_RS31860 BPHYT_RS31860 alcohol dehydrogenase
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__BFirm:BPHYT_RS31860 Length = 393 Score = 197 bits (502), Expect = 3e-55 Identities = 130/387 (33%), Positives = 200/387 (51%), Gaps = 16/387 (4%) Query: 4 MLALPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHL 63 +L P++ G GA+ L LIVTD ++K L+ L L + + + Sbjct: 6 LLYSPRLLDIGGGAVRRTAALCRRFGISHPLIVTDPYMIKSKLICVLTDTLSAASIEFAI 65 Query: 64 FDEVFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILT--ANPGPSTA--- 118 F + +PT+E+V G S D +IAFGGGSPIDTAKA+ IL PS Sbjct: 66 FSDTVADPTDEVVDVGVELLNSGNFDAVIAFGGGSPIDTAKAINILAHARRTEPSACMRD 125 Query: 119 YSGVGKVKNAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASV 178 Y +A +PL+AI TTAGT +E+T VI D K +I +P A+ D + Sbjct: 126 YKMPELADHAALPLIAIPTTAGTGSEVTRFTVITDIGLDEKMLISGLGALPIAAIVDYQL 185 Query: 179 MLEIPASVTAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEA 238 L++P +TA TG+D+ THA+EA+VS A+ +D A A+ LI L A + HN A Sbjct: 186 TLDMPPRLTADTGIDSFTHALEAFVSRHANANSDLFARSALSLIGTHLKTAYTEPHNHAA 245 Query: 239 REQMAFGQYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVAR 298 RE M G AG+A + A + LVH +A GA ++PHG+ NA++LP V ++ +A+ R Sbjct: 246 REAMMLGATHAGIACSIAPVALVHGMARPIGAHFHVPHGLSNAMMLPAVTAYSLRSALPR 305 Query: 299 FARIAQAMGVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGW------ 352 +A +A+ G T +DE A + + +R +++ + +P G+ +GW Sbjct: 306 YAEVARLAGFATASDNDEEAGLKLVEGLREMNRDLTVPSP-RAYGINP---DGWHAKKTL 361 Query: 353 -LDKALADPCAPCNPRTASRDEVRGLY 378 ++ALA NP+ ++ ++ LY Sbjct: 362 MAEQALASGSPANNPKVPTKADIETLY 388 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: 392 Number of extensions: 20 Number of successful extensions: 2 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: 393 Length adjustment: 30 Effective length of query: 352 Effective length of database: 363 Effective search space: 127776 Effective search space used: 127776 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