Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Pf1N1B4_171 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_171 Length = 477 Score = 415 bits (1066), Expect = e-120 Identities = 215/479 (44%), Positives = 310/479 (64%), Gaps = 10/479 (2%) Query: 23 LFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFH-SSWSTSDPQ 81 + I ++V++ +T +P+T E + V A ED+D AV AA AF S+W+ + P+ Sbjct: 1 MLIGGDWVEAGDGQTMPLHNPATGEVLCVVPRATPEDVDRAVLAARQAFDDSAWTRTRPR 60 Query: 82 VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGS 140 R +L+KLADL+ A+ LA +E L+NGKS ++ DV L+ + R AGW KI+GS Sbjct: 61 ERQNLLWKLADLMQRDAELLAQLECLNNGKSAAVAQVMDVQLSIDFLRYMAGWATKIEGS 120 Query: 141 VIETG------DTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAES 194 +E D ++ RRE +GV G I+ WNFPLL+A WKLGP L TGCT VLK A+ Sbjct: 121 SVEVSMPLMPNDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPADE 180 Query: 195 TPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKA 254 TPL+AL LA L+ EAG P GV NVV+G G TAG+ ++ +P + K+ FTGSTA G+ I K Sbjct: 181 TPLTALKLAELVLEAGYPAGVFNVVTGTGITAGSALTHNPLVDKLTFTGSTAVGKQIGKI 240 Query: 255 AAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYD 314 A ES + +VTLELGGKSP IV DAD+K+ + IF+N G+VCCAGSR+YVQ +D Sbjct: 241 AMES-MTRVTLELGGKSPTIVMADADLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKHFD 299 Query: 315 KIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN 374 +V++ + A ++K+G+ MG S Q +++ YI+ G++ GAT+ GGE+FG Sbjct: 300 NVVADIADIANAMKLGNGLDPSVEMGPLISARQQERVYGYIEKGRESGATIACGGEQFG- 358 Query: 375 KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNL 434 GYF+KPT+ DV + H +V++EIFGPV+ F + + +ANDS YGL A + + +L Sbjct: 359 PGYFVKPTVIVDVDQQHSLVQEEIFGPVLVAIPFDDEADALRMANDSPYGLGASIWSNDL 418 Query: 435 STAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 + + +I SG++WVN ++ P +PFGGY SG+GREMG A+++YT++K+V I L Sbjct: 419 AAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEHYTELKSVLIKL 477 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: 628 Number of extensions: 35 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: 495 Length of database: 477 Length adjustment: 34 Effective length of query: 461 Effective length of database: 443 Effective search space: 204223 Effective search space used: 204223 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