Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate 1937064 b3589 predicted Fe-containing alcohol dehydrogenase (NCBI)
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__Keio:1937064 Length = 383 Score = 340 bits (873), Expect = 3e-98 Identities = 176/376 (46%), Positives = 244/376 (64%) Query: 7 LPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDE 66 +P +++ GA ++ D +N++A+ + + LIVTD L KLG+ + AL+E + ++D Sbjct: 8 IPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDG 67 Query: 67 VFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVK 126 PNPT E V G + CD +I+ GGGSP D AK + ++ AN G Y GV + Sbjct: 68 TQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRSA 127 Query: 127 NAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASV 186 +P++AINTTAGTA+EMT +I D AR +K I+D ++ P ++V+D+S+M+ +P S+ Sbjct: 128 KPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSL 187 Query: 187 TAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQ 246 TAATGMDALTHA+EAYVS+ A P+TDA AL+A+ +I LP AV+DG N +ARE MA+ Q Sbjct: 188 TAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQ 247 Query: 247 YLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAM 306 +LAGMAFN+A LG VHA+AHQ G +NLPHGVCNA+LLP V+ FN A AR A AM Sbjct: 248 FLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAM 307 Query: 307 GVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCNP 366 GV G +D ++ INAIR L+K+V IP G L V +ED AL D C NP Sbjct: 308 GVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTNP 367 Query: 367 RTASRDEVRGLYLEAL 382 A+ +E+ +Y A+ Sbjct: 368 IQATHEEIVAIYRAAM 383 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: 384 Number of extensions: 17 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: 383 Length adjustment: 30 Effective length of query: 352 Effective length of database: 353 Effective search space: 124256 Effective search space used: 124256 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