Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate PP_1481 PP_1481 medium chain aldehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Putida:PP_1481 Length = 474 Score = 302 bits (774), Expect = 1e-86 Identities = 172/467 (36%), Positives = 262/467 (56%), Gaps = 5/467 (1%) Query: 5 VQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALP 64 +Q M I+GQ V +G AW V+NPA +++I + A+ AA++A W Sbjct: 1 MQTQMLINGQLVAGQGPAWT-VLNPALGTALAQINEATEAQVDSAVRAADQAFDSWSQTS 59 Query: 65 AIERASWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEWARRYE 123 ER+ L ++ I E++ L + GK + E+ AD + A AR Sbjct: 60 PKERSQALLALADAIEAHGDELARLESQNCGKPLSAALNDEIPAIADVFRFFAGAARCLG 119 Query: 124 GEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPN 183 G PG ++ + LGV I PWN+P ++A K+APAL GNT+VIKPSE TP Sbjct: 120 GSAAGEYLPGHTSMIRRDPLGVVASIAPWNYPLMMLAWKIAPALAAGNTVVIKPSELTPL 179 Query: 184 NAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK 243 A+ ++ ++ LP GV N++ GRG+TVG L +PKV MVS+TGS+ G I++ A Sbjct: 180 TALRLGELAQDL-LPPGVLNILFGRGQTVGNPLITHPKVRMVSLTGSIPTGAHIISATAD 238 Query: 244 NITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVN 303 ++ ++ +ELGGKAP +V DDAD++ A+ I N+GQ C A R+YVQ GIY++FV Sbjct: 239 SVKRMHMELGGKAPVLVFDDADIDAAIDGIRTFGFYNAGQDCTAACRLYVQDGIYERFVE 298 Query: 304 RLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAV-EEGARVAFGGKAVEGKG 362 RLG+A+ +++ G E + +GPLI+A ++V V RA+ + R+ GGK + G G Sbjct: 299 RLGKAVASLKPG-LQESEETELGPLISAQHRDKVAGLVQRAIAQPHIRLVTGGKPIAGDG 357 Query: 363 YYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNV 422 +++ PT+L D Q+ I+ E FGPV+ V F A+ ANDS+YGL SS++T++ Sbjct: 358 FFFEPTVLADALQDDEIVRNEVFGPVVSVTRFTDEAQALEWANDSNYGLASSVWTRDTGR 417 Query: 423 AMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEY 469 A + L++G T++N + H G + SG G +GL +Y Sbjct: 418 AHRLAARLQYGCTWVNTHFMLVSEMPHGGQKHSGYGKDMSMYGLEDY 464 Lambda K H 0.318 0.135 0.392 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: 528 Number of extensions: 24 Number of successful extensions: 5 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: 479 Length of database: 474 Length adjustment: 33 Effective length of query: 446 Effective length of database: 441 Effective search space: 196686 Effective search space used: 196686 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: 51 (24.3 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