Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate BWI76_RS20780 BWI76_RS20780 alcohol dehydrogenase EutG
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__Koxy:BWI76_RS20780 Length = 395 Score = 253 bits (645), Expect = 9e-72 Identities = 148/376 (39%), Positives = 212/376 (56%), Gaps = 6/376 (1%) Query: 6 ALPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFD 65 ++P ++L G GA++ + ++ D L + GL L +L ++ ++ Sbjct: 25 SVPPVTLCGLGALSACGQEAQARGVNHLFVMVDSFLHQAGLTAGLARSLAVKGVAMTVWP 84 Query: 66 EVFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKV 125 P V A + A+CD ++AFGGGS +D AKAV +L NP + + V Sbjct: 85 CPPGEPCVTDVCAAVAQLREAKCDGVVAFGGGSVLDAAKAVALLVTNPEQTLSEMTESSV 144 Query: 126 KNAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPAS 185 +PL+A+ TTAGT +E T+ VIID+ K+V+ +++PD+A+ DA++ +P Sbjct: 145 LRPRLPLIAVPTTAGTGSETTNVTVIIDAVSGRKQVLAHASLMPDVAILDAALTEGVPPQ 204 Query: 186 VTAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFG 245 VTA TG+DALTHAVEAY ++ A P TD+ AL AI +I LPKAV GH+L ARE M Sbjct: 205 VTAMTGIDALTHAVEAYSALNATPFTDSLALGAIAMIGQALPKAVGYGHDLAARESMLLA 264 Query: 246 QYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQA 305 +AGMAF+SAGLGL HA+AHQPGA ++PHG NA+LLP V FNR RF +I +A Sbjct: 265 SCMAGMAFSSAGLGLCHAMAHQPGAALHIPHGQANAMLLPTVMAFNRMVCRERFRQIGRA 324 Query: 306 MGVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCN 365 + ++ + EAI A+ L VG+ + S G E W A D C N Sbjct: 325 L------IAKKTDDHEAIAAVEALIAEVGLSKRLSDAGAKPEHFSAWAQAAQEDICLRAN 378 Query: 366 PRTASRDEVRGLYLEA 381 PRTA+R+++ LY A Sbjct: 379 PRTATREQIIDLYAAA 394 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: 414 Number of extensions: 16 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: 395 Length adjustment: 30 Effective length of query: 352 Effective length of database: 365 Effective search space: 128480 Effective search space used: 128480 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