Align lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein
Query= BRENDA::Q58806 (463 letters) >MicrobesOnline__882:208821 Length = 464 Score = 232 bits (591), Expect = 2e-65 Identities = 157/458 (34%), Positives = 238/458 (51%), Gaps = 16/458 (3%) Query: 15 VINPYSLEVIKKIPALSREEAKEAIDTAEK-YKEVMKNLPITKRYNILMNIAKQIKEKKE 73 V NP+ L + ++P +S EA A++ A + + +P +R IL +A ++ E Sbjct: 6 VRNPFDLSTVGEVPLMSEAEAFAALERAHALHGDPAHRIPAHERLAILERLATLMRTHAE 65 Query: 74 ELAKILAIDAGKPIKQARVEVERSIGTFKLAAFYVKEHRDEVIP------SDDRLIFTRR 127 L + + GKP + VEVER+I + AA + + +P S RL FT R Sbjct: 66 ALVRDAVREGGKPWADSVVEVERAIDGVRWAARELAQLGGREVPMGLTPASAGRLAFTVR 125 Query: 128 EPVGIVGAITPFNFPLNLSAHKIAPAIATGNVIVHHPSSKAPLVCIELAKIIENALKKYN 187 EP G+V AI+ FN P+NL H+ PA A G ++ P+S PL C + +++ A Sbjct: 126 EPRGVVLAISAFNHPVNLIVHQAVPAFAAGCPVLVKPASATPLSCRNVLRLMHEA----G 181 Query: 188 VPLGVYNLLTGAGEVVGDEIVVNEKVNMISFTGSSKVG-ELITKKAGFKKIALELGGVNP 246 VP +L A +++V + +V +SF GSS+VG L +K A ALE GG P Sbjct: 182 VPEAWATMLPCAA-ATAEKLVADPRVAFLSFIGSSRVGWHLRSKLAPGATCALEHGGAAP 240 Query: 247 NIVLKDADLNKAVNALIKGSFIYAGQVCISVGMILVDESIADKFIEMFVNKAKVLNVGNP 306 ++ ADL+ A+ L+KG F +AGQVC+SV + A F E A L G+P Sbjct: 241 VVLDASADLDAALPLLLKGGFYHAGQVCVSVQRVFAPHETARTFAERLAAAAAQLPTGDP 300 Query: 307 LDEKTDVGPLISVEHAEWVEKVVEKAIDEGGKLLLGG-KRDKALFYPTIL-EVDRDNILC 364 + T VGPLI V + VE+A GG +L GG + L+ PT++ + + L Sbjct: 301 MRHDTAVGPLIDPREVSRVHEWVEEARAGGGTVLCGGAPLSETLYSPTVVYDPPQGCRLA 360 Query: 365 KTETFAPVIPIIRTNE-EEMIDIANSTEYGLHSAIFTNDINKSLKFAENLEFGGVVINDS 423 + E F PV+ + T + +E I AN + +A+F D++ +L A L GV++ND Sbjct: 361 RNEVFGPVVAVFSTRDRDEAIARANDVPFIFQAAVFARDVDVALDTARRLNATGVMVNDH 420 Query: 424 SLFRQDNMPFGGVKKSGLGREGVKYAMEEMSNIKTIII 461 + FR D MPFGG +SG+G G+ AM EM+ K I++ Sbjct: 421 TAFRVDWMPFGGRGESGMGTGGIGPAMHEMTTEKLIVL 458 Lambda K H 0.317 0.137 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: 449 Number of extensions: 26 Number of successful extensions: 7 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: 463 Length of database: 464 Length adjustment: 33 Effective length of query: 430 Effective length of database: 431 Effective search space: 185330 Effective search space used: 185330 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 (21.6 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