Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate GFF1358 PS417_06905 alcohol dehydrogenase
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__WCS417:GFF1358 Length = 382 Score = 323 bits (827), Expect = 6e-93 Identities = 169/381 (44%), Positives = 237/381 (62%) Query: 1 MSFMLALPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMS 60 MS +P +++ G + + + + N + KALIVTD L K G+ + L + Sbjct: 1 MSSTFFIPAVNIMGTDCLDEAMIAIRNYGFRKALIVTDAGLAKAGVASMIAEKLAMQDID 60 Query: 61 YHLFDEVFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYS 120 ++D PNP E V+KG Q + CD++++ GGGSP D AK + + N G Y Sbjct: 61 SVIYDGAKPNPNVENVEKGLTLLQESACDFVVSLGGGSPHDCAKGIALCATNGGHIGDYE 120 Query: 121 GVGKVKNAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVML 180 GV + +PLVAINTTAGTA+EMT +I D R VK I+D N+ P ++V+D S+M+ Sbjct: 121 GVDQSSKPQLPLVAINTTAGTASEMTRFCIITDETRHVKMAIVDRNVTPLLSVNDPSLMV 180 Query: 181 EIPASVTAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEARE 240 +P +TAATGMDALTHA+EAYVS A+P+TDA A++AI LI+ L AV DG + ARE Sbjct: 181 GMPKGLTAATGMDALTHAIEAYVSTAANPITDACAIKAIELISANLRLAVRDGSDKAARE 240 Query: 241 QMAFGQYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFA 300 MA+ Q+LAGMAFN+A LG VHA+AHQ G ++LPHGVCNA+LLP V++FN + R + Sbjct: 241 NMAYAQFLAGMAFNNASLGFVHAMAHQLGGFYDLPHGVCNAVLLPHVQSFNASVSAKRLS 300 Query: 301 RIAQAMGVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADP 360 + +A+G + +G SDE +Q AI AIR+L+ V IP G +LG +DI AL D Sbjct: 301 DVGRALGADVKGFSDEEGAQAAIAAIRSLAHDVEIPAGLRELGAKLQDIPLLATNALKDA 360 Query: 361 CAPCNPRTASRDEVRGLYLEA 381 C NPR A + ++ ++ A Sbjct: 361 CGLTNPRRADQRQIEEIFRSA 381 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: 401 Number of extensions: 18 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: 382 Length adjustment: 30 Effective length of query: 352 Effective length of database: 352 Effective search space: 123904 Effective search space used: 123904 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