Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate PP_2803 PP_2803 1,3-propanediol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Putida:PP_2803 Length = 394 Score = 234 bits (598), Expect = 2e-66 Identities = 137/378 (36%), Positives = 207/378 (54%), Gaps = 5/378 (1%) Query: 6 FFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIY 65 F +PS V+ + G R LIVTD + G+ V +L++ I Sbjct: 14 FLLPSKIVMEPGLRERTGEHLRQLGLARVLIVTDAGVKAAGLLDSVYASLDKAGIAYEEV 73 Query: 66 DGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDR 125 + NP ++++ + + D ++++GGGS D AK I+L+ + G I DYEG Sbjct: 74 ADIKANPRSDDINHTAQRYRGTGIDGLLAVGGGSAMDAAKAISLLLTHDGRIEDYEGSFT 133 Query: 126 SAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPK 185 P++AI TTAGT SE+T F +ITD ARH KM ++D + P+L++ DS + +P Sbjct: 134 LTHAIPPIVAIPTTAGTGSEVTCFSVITDTARHFKMNVLDYRIGPVLALLDSHITDTLPP 193 Query: 186 SLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAY 245 S+ AATGMDALTHAIEAY A PI+D AL A+ +I+++L AV++ N ARE M Sbjct: 194 SIAAATGMDALTHAIEAYTCRVANPISDGLALHAIRLISQHLKAAVQEPDNQAAREQMLV 253 Query: 246 AQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAA 305 A +AGMAF NA +G VH ++ +GG Y+ PHGV NA+ LP V N R A Sbjct: 254 ASLIAGMAFGNADVGSVHCISEAIGGMYDTPHGVGNAIFLPFVFGHNRDADIVRHAQVAY 313 Query: 306 AMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFT 365 A+G++ T + + AEA + + +++K + IP V+EEDF +A + ++ + Sbjct: 314 ALGIDPT-LSPVDAAEAAVGHLFQMSKDLGIPRFAEVKGVREEDFPTIAEKSKQNFSDAS 372 Query: 366 N----PIQATHEEIVAIY 379 N ++A H+ I Y Sbjct: 373 NAKAMSVEAYHDIITTAY 390 Lambda K H 0.318 0.131 0.373 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: 376 Number of extensions: 13 Number of successful extensions: 4 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: 383 Length of database: 394 Length adjustment: 30 Effective length of query: 353 Effective length of database: 364 Effective search space: 128492 Effective search space used: 128492 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 (21.8 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