Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate RR42_RS32140 RR42_RS32140 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Cup4G11:RR42_RS32140 Length = 496 Score = 393 bits (1009), Expect = e-114 Identities = 213/491 (43%), Positives = 295/491 (60%), Gaps = 11/491 (2%) Query: 8 PIKLPNGTTYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAA 67 P + +G + I+ E+ Q++S +TF P+T EEI +V + DID AV AA Sbjct: 4 PKEARSGLNQAIRNAMLIDGEWRQAESGETFAVFDPATGEEIARVPAGGAADIDAAVAAA 63 Query: 68 TAAFHS-SWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAA 125 AF +W P R ++L KLADL+++H D LA +E L+NGK L S+G +V +A Sbjct: 64 GRAFAGGTWRAMMPAQRERLLLKLADLVEQHGDELARLETLNNGKLLAFSQGLEVGGSAQ 123 Query: 126 YFRSCAGWTDKIKGSVIET------GDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGP 179 + R AGW KI+GS ++ G + TRR P+GV G I+PWNFPLLMA WK+ P Sbjct: 124 WLRYMAGWATKIEGSTLDVSVPFPPGTRYSAMTRRSPVGVVGAIVPWNFPLLMAVWKIAP 183 Query: 180 VLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKV 239 L GCT VLK AE TPL+AL LA L EAG PPGV+NVV+G G GA + +HP + K+ Sbjct: 184 ALACGCTVVLKPAEETPLTALRLAELALEAGFPPGVLNVVTGDG-VPGAALVAHPGVNKI 242 Query: 240 AFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEV 299 FTGST GR ++ A ++++V+LELGGKSP IV DD D IQ IF N G+V Sbjct: 243 TFTGSTEVGR-LIGARCGQDIRRVSLELGGKSPVIVLDDCDPAHAIQGAAGAIFLNQGQV 301 Query: 300 CCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGK 359 C AGSR+YV YD++V A + +G + MG S DK++ I G+ Sbjct: 302 CTAGSRLYVARRHYDQVVEGLGKVANATVLGSGLDPASQMGPLVSSRHRDKVMGLIGTGR 361 Query: 360 KEGATVITGGERFGNKGYFIKPTIFGDVK-EDHQIVRDEIFGPVVTITKFKTVEEVIALA 418 EGA ++ GG GYF++PT+ + +D +VR+E+FGPVV F E V+A A Sbjct: 362 SEGADIVAGGTALDRPGYFVRPTVVANAACKDLTLVREEVFGPVVVAMPFDDPEAVLAEA 421 Query: 419 NDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEE 478 N SEYGL A + + +L + + +++GT+WVNT+N P +PFGGY SG+GRE G Sbjct: 422 NRSEYGLGASIWSNDLRAVQRLVDGLDAGTVWVNTHNIVDPNMPFGGYKASGVGREHGRS 481 Query: 479 ALDNYTQVKAV 489 A++ YT++K+V Sbjct: 482 AIEAYTEIKSV 492 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: 629 Number of extensions: 28 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