Align lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Ga0059261_0516 Ga0059261_0516 vanillin dehydrogenase (EC 1.2.1.67)
Query= BRENDA::Q58806 (463 letters) >FitnessBrowser__Korea:Ga0059261_0516 Length = 478 Score = 220 bits (561), Expect = 7e-62 Identities = 148/456 (32%), Positives = 238/456 (52%), Gaps = 12/456 (2%) Query: 16 INPYSLEVIKKIPALSREEAKEAIDTAEKYKEVMKNLPITKRYNILMNIAKQIKEKKEEL 75 +NP + EV + A + ++A EA++ A L R L A+ + K E+ Sbjct: 16 LNPVTGEVATEAQAFTVDQANEAVEAAAAAFPAWSTLGPNARRAALNKAAEALAAKAEDF 75 Query: 76 AKILAIDAGKPIKQARVEVERSIGTFKLAAFYVKEHRDEVIPSDDR--LIFTRREPVGIV 133 + + + G AR + ++ + AA + EVIPSD + REPVG++ Sbjct: 76 VEAMNGEIGATEGWARFNLMLAVSMVREAAALTTQIGGEVIPSDKPGCIAMAIREPVGVM 135 Query: 134 GAITPFNFPLNLSAHKIAPAIATGNVIVHHPSSKAPLVCIELAKIIENALKKYNVPLGVY 193 I P+N P+ L +A +A GN +V S + P +A+ + AL K V + V Sbjct: 136 LGIAPWNAPIILGVRAVAAPLACGNTVVLKASEQCPRTHSLIAEAFDEALPKGAVSI-VT 194 Query: 194 NLLTGAGEVVGDEIVVNEKVNMISFTGSSKVGELITKKAG--FKKIALELGGVNPNIVLK 251 N A E+VG ++ N + I+FTGS+ VG +I K+A K + LELGG P +VL+ Sbjct: 195 NAPEDAPEIVG-ALIDNPHIRRINFTGSTAVGRIIAKRAAEHLKPVLLELGGKAPMLVLE 253 Query: 252 DADLNKAVNALIKGSFIYAGQVCISVGMILVDESIADKFIEMFVNKAKVLNVGNPLDEKT 311 DADL++AV A G+F+ GQ+C+S I+V +++AD F+E F K + VG+P + KT Sbjct: 254 DADLDEAVKAAAFGAFMNQGQICMSTERIIVVDAVADAFVEKFAAKVGTMPVGDPREGKT 313 Query: 312 DVGPLISVEHAEWVEKVVEKAIDEGGKLLLGG---KRDKALFYP--TILEVDRDNILCKT 366 +G ++ + V+ ++ A+ G + GG + + P I V D L + Sbjct: 314 PLGAVVDQKTVAHVKALIGDALAAGAVQVNGGGVLEGTGGVLMPAHVIDHVTPDMKLFRD 373 Query: 367 ETFAPVIPIIRTNEE-EMIDIANSTEYGLHSAIFTNDINKSLKFAENLEFGGVVINDSSL 425 E+F PV+ +IR +E I +AN TEYGL +++FT D + L+ A ++ G +N ++ Sbjct: 374 ESFGPVVGVIRARDEAHAILLANDTEYGLSASVFTRDTARGLRVARQIKSGICHVNGPTV 433 Query: 426 FRQDNMPFGGVKKSGLGREGVKYAMEEMSNIKTIII 461 + MPFGGVK SG GR G K ++ + ++ I I Sbjct: 434 HDEAQMPFGGVKASGYGRFGGKAGIDAFTELRWITI 469 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: 482 Number of extensions: 24 Number of successful extensions: 6 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: 478 Length adjustment: 33 Effective length of query: 430 Effective length of database: 445 Effective search space: 191350 Effective search space used: 191350 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