Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-16246 (477 letters) >FitnessBrowser__Dino:3608018 Length = 484 Score = 305 bits (781), Expect = 2e-87 Identities = 176/464 (37%), Positives = 264/464 (56%), Gaps = 6/464 (1%) Query: 8 HRNYIDGAFVESAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIER 67 +R+ I+GA V+SA EVFNPA +++ P AS ++VE+A+AAA+AAQ WA ER Sbjct: 19 YRHAINGALVDSAGSFEVFNPATDEVVAHAPNASRDQVEQAIAAAKAAQPGWAALSQDER 78 Query: 68 AGHLRRIAAKIRADAGRIARTITLEQGKIA-SLAEVEVNFTADYLDYMAEWARRLEGEII 126 ++ A + A + +T EQGK S+A EV + ++ +A+ RRLE E+I Sbjct: 79 GAYIAAYADALDAHKQELITLLTTEQGKPRHSMATTEVEYAIFWVREVAK--RRLEDEVI 136 Query: 127 ASDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFE 186 D P + + PLGVV I PWNFP L K+AP L+TGNT+V+KPS TP Sbjct: 137 -EDTPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNTMVMKPSPYTPLCTLR 195 Query: 187 FARLVAETDLPRGVFNVVCGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKL 246 F +A+ P GV NVV G + G L+ HP + ISFTGS TG ++MA+++ NL ++ Sbjct: 196 FGE-IAQQVFPAGVLNVVAGGNEQGAWLTEHPDIAKISFTGSTATGRKVMASSSCNLKRI 254 Query: 247 NLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAA 306 LELGG PAI+L D + + + D+ NSGQ C +R+YV + + F+ A Sbjct: 255 TLELGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDDFLRDFVAH 314 Query: 307 MAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPT 366 A G+ + +P ++GP+ N++ K+ AQG ++ GG I + PG+ T Sbjct: 315 AAEKTVGNGM-DPNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGEIPDGPGNFVPIT 373 Query: 367 VLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALR 426 ++ D+R++REE FGP+LPI DLDE + AND E+GL +SV+ D + A+ Sbjct: 374 IVDNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVWGPDRDTAIGVAN 433 Query: 427 ELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHT 470 L+ G ++N H + G ++SG+G +G+ GL E+T+T Sbjct: 434 RLEAGTVWVNEIHIHGIDIPFGGHKQSGMGVENGQEGLKEFTNT 477 Lambda K H 0.320 0.136 0.395 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: 545 Number of extensions: 36 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: 477 Length of database: 484 Length adjustment: 34 Effective length of query: 443 Effective length of database: 450 Effective search space: 199350 Effective search space used: 199350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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