Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate PP_2803 PP_2803 1,3-propanediol dehydrogenase
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__Putida:PP_2803 Length = 394 Score = 222 bits (565), Expect = 2e-62 Identities = 128/325 (39%), Positives = 192/325 (59%), Gaps = 1/325 (0%) Query: 32 KALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTEELVQKGFAAYQSAECDYI 91 + LIVTD + GLLDS++++LD+ ++Y ++ NP + + Y+ D + Sbjct: 41 RVLIVTDAGVKAAGLLDSVYASLDKAGIAYEEVADIKANPRSDDINHTAQRYRGTGIDGL 100 Query: 92 IAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVPLVAINTTAGTAAEMTSNAVI 151 +A GGGS +D AKA+ +L + G Y G + +A P+VAI TTAGT +E+T +VI Sbjct: 101 LAVGGGSAMDAAKAISLLLTHDGRIEDYEGSFTLTHAIPPIVAIPTTAGTGSEVTCFSVI 160 Query: 152 IDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATGMDALTHAVEAYVSVGAHPLT 211 D+AR K ++D I P +A+ D+ + +P S+ AATGMDALTHA+EAY A+P++ Sbjct: 161 TDTARHFKMNVLDYRIGPVLALLDSHITDTLPPSIAAATGMDALTHAIEAYTCRVANPIS 220 Query: 212 DANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMAFNSAGLGLVHALAHQPGAT 271 D AL AIRLI+ L AV + N AREQM +AGMAF +A +G VH ++ G Sbjct: 221 DGLALHAIRLISQHLKAAVQEPDNQAAREQMLVASLIAGMAFGNADVGSVHCISEAIGGM 280 Query: 272 HNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGVETRGMSDEAASQEAINAIRTLSK 331 ++ PHGV NAI LP V NR + R A++A A+G++ +S A++ A+ + +SK Sbjct: 281 YDTPHGVGNAIFLPFVFGHNRDADIVRHAQVAYALGIDPT-LSPVDAAEAAVGHLFQMSK 339 Query: 332 RVGIPEGFSKLGVTKEDIEGWLDKA 356 +GIP GV +ED +K+ Sbjct: 340 DLGIPRFAEVKGVREEDFPTIAEKS 364 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: 411 Number of extensions: 17 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: 394 Length adjustment: 30 Effective length of query: 352 Effective length of database: 364 Effective search space: 128128 Effective search space used: 128128 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