Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate WP_017219751.1 A923_RS0100900 iron-containing alcohol dehydrogenase
Query= metacyc::STM4044-MONOMER (382 letters) >NCBI__GCF_000276805.1:WP_017219751.1 Length = 389 Score = 219 bits (557), Expect = 1e-61 Identities = 133/374 (35%), Positives = 204/374 (54%), Gaps = 12/374 (3%) Query: 14 GAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTE 73 G G I D+ L++TD L L ++ + + + +F ++ NPT Sbjct: 19 GIGRIEDLPAACQELGMTSPLLITDPGLADLPMVQTALINCQKAGLKCGIFSQIKGNPTG 78 Query: 74 ELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVG----KVKNAG 129 + + G A++ E D +IAFGGGS +D KAV ++ P + VG KV AG Sbjct: 79 DNISDGVRAFKGGEHDGVIAFGGGSALDAGKAVALMVGQDRPIWDFDDVGDNWLKVNAAG 138 Query: 130 -VPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTA 188 VP+VA+ TT+GT +E+ +VI DS +K +I PN++P I + D + + +PA +TA Sbjct: 139 MVPVVAVPTTSGTGSEVGRASVITDSNNHIKRIIFHPNMLPAIVILDPQLSVGLPAKLTA 198 Query: 189 ATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYL 248 ATG+DAL+HA+EAY + G HP+ + ALE IRLI +LP+AV+DG +LEAR QM + Sbjct: 199 ATGLDALSHALEAYCANGYHPMAEGIALEGIRLIKEYLPRAVEDGCDLEARAQMMTASTM 258 Query: 249 AGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGV 308 AF GLG +HALAH GA ++ HG+ NAIL+P V NR A+ R+++ + + Sbjct: 259 GSTAF-QRGLGGMHALAHPIGALYDSHHGLLNAILMPYVLKANRSAIEAKLTRLSRYLAL 317 Query: 309 ETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCNPRT 368 E +A + I TL K++ IP ++G+ + + A DP A NP Sbjct: 318 E------DADFDGFLEWILTLRKQLDIPHSLGEIGIDADRVVEIGAMAEQDPSAGGNPIM 371 Query: 369 ASRDEVRGLYLEAL 382 + + ++L A+ Sbjct: 372 LNAQQYADIFLSAV 385 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: 412 Number of extensions: 25 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: 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 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