Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate PfGW456L13_2360 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2360 Length = 496 Score = 414 bits (1064), Expect = e-120 Identities = 217/501 (43%), Positives = 317/501 (63%), Gaps = 13/501 (2%) Query: 1 MSLPLFVPIKLPNGTTYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDI 60 MSLP +P ++ + I ++V++ +T +P+T E + V A ED+ Sbjct: 1 MSLPNLLPA---TSAFIQRAPRMLIGGDWVEAADGQTMPLHNPATGEVLCVVPRATPEDV 57 Query: 61 DDAVEAATAAFH-SSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG- 118 D AV AA AF S+W+ + P+ R +L+KLADL+ A+ LA +E L+NGKS ++ Sbjct: 58 DRAVLAARQAFDDSAWTRTRPRERQNLLWKLADLMQRDAELLAQLECLNNGKSAAVAQVM 117 Query: 119 DVALTAAYFRSCAGWTDKIKGSVIETG------DTHFNYTRREPIGVCGQIIPWNFPLLM 172 DV L + R AGW KI+GS ++ D ++ RRE +GV G I+ WNFPLL+ Sbjct: 118 DVQLAIDFLRYMAGWATKIEGSTVDVSAPLMPNDQFHSFIRREAVGVVGAIVAWNFPLLL 177 Query: 173 ASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISS 232 A WKLGP L TGCT VLK A+ TPL+AL LA L+ EAG P GV NVV+G G TAG+ ++ Sbjct: 178 ACWKLGPALATGCTVVLKPADETPLTALKLAELVLEAGYPEGVFNVVTGTGITAGSALTH 237 Query: 233 HPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGI 292 +P + K+ FTGSTA G+ I K A +S + +VTLELGGKSP IV DAD+K+ + I Sbjct: 238 NPLVDKLTFTGSTAVGKQIGKIAMDS-MTRVTLELGGKSPTIVMADADLKTAAAGAASAI 296 Query: 293 FYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKIL 352 F+N G+VCCAGSR+YVQ +D +V++ + A ++K+G+ MG S Q +++ Sbjct: 297 FFNQGQVCCAGSRLYVQRKHFDNVVADISDIANAMKLGNGLDPSVDMGPLISARQQERVY 356 Query: 353 KYIDIGKKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVE 412 YI+ G++ GAT+ GGE+FG G+F+KPT+ DV + H +V++EIFGPV+ F Sbjct: 357 GYIEKGRESGATIACGGEQFG-PGFFVKPTVIVDVDQKHSLVQEEIFGPVLVAIPFDDEA 415 Query: 413 EVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIG 472 + + +ANDS YGL A + + +L+ + +I SG++WVN ++ P +PFGGY SG+G Sbjct: 416 DALRMANDSPYGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVG 475 Query: 473 REMGEEALDNYTQVKAVRIGL 493 REMG A+++YT++K+V I L Sbjct: 476 REMGYAAIEHYTELKSVLIKL 496 Lambda K H 0.316 0.133 0.389 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: 638 Number of extensions: 34 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: 495 Length of database: 496 Length adjustment: 34 Effective length of query: 461 Effective length of database: 462 Effective search space: 212982 Effective search space used: 212982 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: 52 (24.6 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