Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate 8500233 DvMF_0990 iron-containing alcohol dehydrogenase (RefSeq)
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__Miya:8500233 Length = 386 Score = 238 bits (607), Expect = 2e-67 Identities = 137/351 (39%), Positives = 198/351 (56%), Gaps = 1/351 (0%) Query: 32 KALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTEELVQKGFAAYQSAECDYI 91 + L+V+D + G D++ L + ++ F V NP + V +G +++ CD I Sbjct: 35 RCLVVSDQGVAAAGHTDAVARTLRDEGIACATFLGVSENPRDTEVMQGSEVFRAEGCDAI 94 Query: 92 IAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVPLVAINTTAGTAAEMTSNAVI 151 +A GGGSP+D AK + I+ AN G Y GV + PLV + TTAG++A+++ A+I Sbjct: 95 VAVGGGSPMDCAKGIGIVVANGGHILDYEGVDAIPKPMPPLVCVPTTAGSSADVSQFAII 154 Query: 152 IDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATGMDALTHAVEAYVSVGAHPLT 211 D+ R+VK I+ +PD+A+ D L P +TAATG+DALTHAVEAY S P+T Sbjct: 155 RDTPRRVKIAIVSKANVPDVALVDPLTTLTKPRELTAATGLDALTHAVEAYASNAHSPVT 214 Query: 212 DANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMAFNSAGLGLVHALAHQPGAT 271 D ALEA+R I L +DD N +AR +MA G AG+AF++A LG VHAL+H G Sbjct: 215 DMFALEAVRGIGSALFDVLDDLGNRDARARMALGSMNAGLAFSNAILGAVHALSHSLGGL 274 Query: 272 HNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGV-ETRGMSDEAASQEAINAIRTLS 330 +LPHG CNA+LLP V N A R+ R+A+A+GV + D+ + + Sbjct: 275 LDLPHGECNALLLPFVVRRNYVAAPQRYRRVAEALGVADALAAPDDEVRDALFARLGAMR 334 Query: 331 KRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCNPRTASRDEVRGLYLEA 381 +R G +G ++ GVT++ + AL DPC NP E+ LY EA Sbjct: 335 RRAGFDKGLAQYGVTRDQLAELARLALEDPCLSTNPVPLDARELEQLYAEA 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: 398 Number of extensions: 16 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: 386 Length adjustment: 30 Effective length of query: 352 Effective length of database: 356 Effective search space: 125312 Effective search space used: 125312 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