Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate WP_093396475.1 BM091_RS13300 L-threonine dehydrogenase
Query= metacyc::STM4044-MONOMER (382 letters) >NCBI__GCF_900114975.1:WP_093396475.1 Length = 388 Score = 328 bits (840), Expect = 2e-94 Identities = 179/377 (47%), Positives = 242/377 (64%), Gaps = 1/377 (0%) Query: 7 LPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQ-MSYHLFD 65 +P ++L G GA ++ + K L+VTD L K GL D + S + E + +FD Sbjct: 12 IPTVTLMGIGAHKEVGRQIKVLGGKKPLLVTDKGLTKAGLTDQIRSLIKEDTGIDVVVFD 71 Query: 66 EVFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKV 125 E PNPT++ V G ++ CD II+ GGGS D AK + IL N G Y G+ K Sbjct: 72 ETVPNPTDKNVHDGLKVFKDNGCDMIISLGGGSSHDCAKGIGILATNGGNIRNYEGIDKA 131 Query: 126 KNAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPAS 185 P +AINTTAGTA+EMT +I ++ KVK I+D + P++A++D +M+ +P + Sbjct: 132 TKPMPPFIAINTTAGTASEMTRFCIITNTDTKVKMAIVDWRVTPNVAINDPLLMMGMPPA 191 Query: 186 VTAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFG 245 +TAATGMDALTHAVEAYVS A P+TDA AL+AIRLI+ +L AV +G ++EAR++MA+ Sbjct: 192 LTAATGMDALTHAVEAYVSTLATPVTDACALQAIRLISKYLRSAVANGSDIEARDKMAYA 251 Query: 246 QYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQA 305 +YLAGMAFN+A LG VHA+AHQ G ++LPHGVCNAILLP VE FN + RFA IA A Sbjct: 252 EYLAGMAFNNASLGYVHAMAHQLGGFYDLPHGVCNAILLPHVERFNLIAKLDRFADIAVA 311 Query: 306 MGVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCN 365 MG G+S A+++A+ AI LS+ VGIP G +LGV KEDI A+ D C N Sbjct: 312 MGENVEGLSPRDAAEKALQAIEKLSRDVGIPGGLKELGVKKEDIPTMAQNAMKDACGLTN 371 Query: 366 PRTASRDEVRGLYLEAL 382 PR A+ +++ +Y AL Sbjct: 372 PRRATLEDIIMIYENAL 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: 367 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: 388 Length adjustment: 30 Effective length of query: 352 Effective length of database: 358 Effective search space: 126016 Effective search space used: 126016 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