Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate WP_086510128.1 BZY95_RS11880 alcohol dehydrogenase
Query= metacyc::STM4044-MONOMER (382 letters) >NCBI__GCF_002151265.1:WP_086510128.1 Length = 387 Score = 256 bits (653), Expect = 1e-72 Identities = 143/371 (38%), Positives = 216/371 (58%) Query: 12 LHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNP 71 + G GA + N V + L+V+D +V G ++ + + L E + F V PNP Sbjct: 17 IFGDGARRAVANFVGTFGAERVLLVSDPGVVLAGWVEEVEADLAEQGIFSQRFTSVSPNP 76 Query: 72 TEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVP 131 E V G AY+ I+A GGGSP+D AK + I+ A+ G + GV ++ P Sbjct: 77 RAEEVMAGAMAYREMGAQAIVAIGGGSPMDCAKGIGIVVAHDGHIIDFEGVDTLRVPIPP 136 Query: 132 LVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATG 191 L+ + TTAGT+A+++ A+I D R++K I+ +++PD+++ D V L + +TA TG Sbjct: 137 LIFVPTTAGTSADISQFAIISDQQRRMKFSIVSKSVVPDVSLIDPQVTLTMSPFLTACTG 196 Query: 192 MDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGM 251 +DAL HA+EA+VS G+ PLTDA+ALEA+RLIN L V H+LE R Q+ G AG+ Sbjct: 197 VDALVHAIEAFVSTGSGPLTDAHALEAMRLINGHLVALVQAPHDLELRSQVMLGSMQAGL 256 Query: 252 AFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGVETR 311 AF++A LG VHA++H G +LPHG+CN++LL V +N A RF RIA+ +G++ R Sbjct: 257 AFSNAILGAVHAMSHSLGGFLDLPHGLCNSLLLEHVVAYNFEAAPERFTRIAETLGIDCR 316 Query: 312 GMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCNPRTASR 371 G++ I+ + L + VG+ +LGV D+ AL DPC NPR +S Sbjct: 317 GLNSTQVKARLIDHLIELKRAVGLTGSLGRLGVHTSDVPFLARHALEDPCILTNPRRSSP 376 Query: 372 DEVRGLYLEAL 382 +V+ +Y EA+ Sbjct: 377 RDVQVVYEEAM 387 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: 378 Number of extensions: 15 Number of successful extensions: 1 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: 387 Length adjustment: 30 Effective length of query: 352 Effective length of database: 357 Effective search space: 125664 Effective search space used: 125664 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