Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate Ac3H11_2497 Alcohol dehydrogenase (EC 1.1.1.1)
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2497 Length = 378 Score = 187 bits (476), Expect = 3e-52 Identities = 124/360 (34%), Positives = 187/360 (51%), Gaps = 23/360 (6%) Query: 32 KALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTEELVQKGFAAYQSAECDYI 91 + LIVTD + G+L AL M+ +FD+ NPTE V+ Y++ CD + Sbjct: 31 RPLIVTDPGVKAAGVLQKALDALPG--MTVAVFDQTPSNPTEAAVRAAVEMYKAQGCDGL 88 Query: 92 IAFGGGSPIDTAKAVKILTANPGPSTAYS----GVGKVKNAGVPLVAINTTAGTAAEMTS 147 IA GGGS ID AK + I + GP T Y+ G ++ + PL+A+ TT+GT +E+ Sbjct: 89 IAVGGGSAIDCAKGIAIAATHEGPLTHYATIEGGSPRITDRAAPLIAVPTTSGTGSEVAR 148 Query: 148 NAVII-DSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATGMDALTHAVEAYVSVG 206 A+II D RK+ N++P A+ D + L +P +TAATGMDA+ H +E ++S Sbjct: 149 GAIIIVDDHRKLG--FHSWNLVPKTAICDPELTLGLPPMLTAATGMDAIAHCMETFMSAA 206 Query: 207 AHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMAFNSAGLGLVHALAH 266 +P D AL+ + + +A +G + +AR M MAF GLG VH+L+H Sbjct: 207 FNPPADGIALDGLTRGWANIEQATKNGSDRDARLHMMSASMQGAMAFQK-GLGAVHSLSH 265 Query: 267 QPGATH-NLPHGVCNAILLPIVENFNRP----NAVARFARIAQAMGVETRGMSDEAASQE 321 G + L HG NA+ LP V FN R R+A AMG+ + G E Sbjct: 266 SLGGVNPRLHHGTLNAMFLPAVVRFNAQAESVQKEKRLERMAHAMGLASAGDIPE----- 320 Query: 322 AINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCNPRTASRDEVRGLYLEA 381 AIR ++ R+G+P G + +GV + + + A+AD C NPR A+ +E R + ++ Sbjct: 321 ---AIRDMNARLGLPTGLAAMGVNEAMFDDIIKGAMADHCHKTNPRIATPEEYRDMLAQS 377 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: 413 Number of extensions: 21 Number of successful extensions: 6 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: 378 Length adjustment: 30 Effective length of query: 352 Effective length of database: 348 Effective search space: 122496 Effective search space used: 122496 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