Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate 16552 b2453 ethanolamine utilization; homolog of Salmonella enzyme, similar to iron-containing alcohol dehydrogenase (VIMSS)
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__Keio:16552 Length = 395 Score = 260 bits (664), Expect = 5e-74 Identities = 149/376 (39%), Positives = 217/376 (57%), Gaps = 6/376 (1%) Query: 6 ALPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFD 65 ++P ++L G G+++ + ++ D L + G+ L +L ++ L+ Sbjct: 25 SVPPVTLCGPGSVSSCGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLTVKGIAMTLWP 84 Query: 66 EVFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKV 125 P V A + + CD +IAFGGGS +D AKAV +L NP + A V Sbjct: 85 CPVGEPCITDVCAAVAQLRESGCDGVIAFGGGSVLDAAKAVTLLVTNPDSTLAEMSETSV 144 Query: 126 KNAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPAS 185 +PL+AI TTAGT +E T+ VIID+ K+V+ +++PD+A+ DA++ +P+ Sbjct: 145 LQPRLPLIAIPTTAGTGSETTNVTVIIDAVSGRKQVLAHASLMPDVAILDAALTEGVPSH 204 Query: 186 VTAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFG 245 VTA TG+DALTHA+EAY ++ A P TD+ A+ AI +I LPKAV GH+L ARE M Sbjct: 205 VTAMTGIDALTHAIEAYSALNATPFTDSLAIGAIAMIGKSLPKAVGYGHDLAARESMLLA 264 Query: 246 QYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQA 305 +AGMAF+SAGLGL HA+AHQPGA ++PHG+ NA+LLP V FNR RF++I +A Sbjct: 265 SCMAGMAFSSAGLGLCHAMAHQPGAALHIPHGLANAMLLPTVMEFNRMVCRERFSQIGRA 324 Query: 306 MGVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCN 365 + + ++ ++AINA+ L VGI + +G T W AL D C N Sbjct: 325 L------RTKKSDDRDAINAVSELIAEVGIGKRLGDVGATSAHYGAWAQAALEDICLRSN 378 Query: 366 PRTASRDEVRGLYLEA 381 PRTAS +++ GLY A Sbjct: 379 PRTASLEQIVGLYAAA 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: 417 Number of extensions: 13 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