Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__SB2B:6938545 Length = 498 Score = 239 bits (609), Expect = 2e-67 Identities = 151/476 (31%), Positives = 251/476 (52%), Gaps = 11/476 (2%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPE---WEALPAI 66 +I+G + G D ++P +++++ Q DA A+ A RA E W + Sbjct: 24 FINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADIAV-ANARAVFESGVWSLQSPV 82 Query: 67 ERASWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEWARRYEGE 125 +R + + + + A E++ L + GK I V+VA A I + E + E Sbjct: 83 KRKKVMIRFAELLEAHADELALLETLDMGKPIAHSKAVDVAGAARAIRWSGEAIDKIYDE 142 Query: 126 IIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNA 185 + + E ++ + +GV I+PWNFP + K+ PAL TGN++V+KPSE +P A Sbjct: 143 LAPTPH-NEIGMITREPVGVVAAIVPWNFPMLMACWKLGPALATGNSVVLKPSEKSPLTA 201 Query: 186 IAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK-N 244 I A++ E GLP GV N++ G G TVGQ LA + V + TGS +++M A + N Sbjct: 202 IRMAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDTLVFTGSTKIAKQLMVYAGQSN 261 Query: 245 ITKVCLELGGKAPAIVMDDA-DLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVN 303 + +V LE GGK+P IV +DA DL+ A +A + N G+VC R+ V+ G+ D+ + Sbjct: 262 MKRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEVCTAGSRLLVESGVKDELIK 321 Query: 304 RLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAV--EGK 361 + + M+A Q G+P + G +++ L+ V + +EGA++ GG V E Sbjct: 322 LIVKEMEAWQPGHPLD-PATTCGAVVDKQQLDTVLGYIKAGHDEGAKLMCGGSQVLAETG 380 Query: 362 GYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLN 421 G Y PT+ V +M I EE FGPV+ V+ FD +++A+++AND+ YGL + ++T +++ Sbjct: 381 GVYVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAIANDTIYGLAAGVWTSDIS 440 Query: 422 VAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 A K K L+ G +IN + M G+++SG G H +Y + + ++ Sbjct: 441 KAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFEKYTEVKATWI 496 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: 532 Number of extensions: 28 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: 498 Length adjustment: 34 Effective length of query: 445 Effective length of database: 464 Effective search space: 206480 Effective search space used: 206480 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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