Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate PP_2803 PP_2803 1,3-propanediol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Putida:PP_2803 Length = 394 Score = 204 bits (520), Expect = 3e-57 Identities = 129/351 (36%), Positives = 193/351 (54%), Gaps = 16/351 (4%) Query: 17 GALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPLET 76 G ++ +++LG +L++TD + GL+D V + L + G + D+ P + Sbjct: 25 GLRERTGEHLRQLGLARVLIVTDAGVKAAGLLDSVYASLDKAGIAYEEVADIKANPRSDD 84 Query: 77 GEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGLPK 136 R D ++ VGGGSA+D AK ++L HDG + DY G+ TL P Sbjct: 85 INHTAQRYRGTGIDGLLAVGGGSAMDAAKAISLLLTHDGRIEDY---EGSFTLTHAIPPI 141 Query: 137 ILIPTTSGTGSEVTNISVLSLETTKDVVTH------DYLLADV-AIVDPQLTVSVPPRVT 189 + IPTT+GTGSEVT SV++ D H DY + V A++D +T ++PP + Sbjct: 142 VAIPTTAGTGSEVTCFSVIT-----DTARHFKMNVLDYRIGPVLALLDSHITDTLPPSIA 196 Query: 190 AATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSY 249 AATG+DALTHA+EAY A+P SDGLA+ AIRLIS+ L+ AV ++ AR M S Sbjct: 197 AATGMDALTHAIEAYTCRVANPISDGLALHAIRLISQHLKAAVQEPDNQAAREQMLVASL 256 Query: 250 LAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALG 309 +AG+AF NA V VH ++ +GG + HG NA+ LP+V G+ R + R A + ALG Sbjct: 257 IAGMAFGNADVGSVHCISEAIGGMYDTPHGVGNAIFLPFVFGHNRDADIVRHAQVAYALG 316 Query: 310 GNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQ 360 + + LS V+A+ V L + D+GIP+ G+ E ++ + + Q Sbjct: 317 IDPT-LSPVDAAEAAVGHLFQMSKDLGIPRFAEVKGVREEDFPTIAEKSKQ 366 Lambda K H 0.318 0.135 0.381 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: 19 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: 395 Length of database: 394 Length adjustment: 31 Effective length of query: 364 Effective length of database: 363 Effective search space: 132132 Effective search space used: 132132 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