Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate PP_2487 PP_2487 putative aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Putida:PP_2487 Length = 503 Score = 400 bits (1028), Expect = e-116 Identities = 213/489 (43%), Positives = 305/489 (62%), Gaps = 10/489 (2%) Query: 28 PNQQPEVFCNQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAF 87 PN P+ C +FI+N+W A +T +NP+ G+++ + DVD+AV+AA+ AF Sbjct: 13 PNHLPDS-CYGLFIDNQWVTAEYGETLDIINPANGKILTNIPNATAADVDRAVQAAQRAF 71 Query: 88 QLGSPWRRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLR 147 WR + R L ++ADL+E D A LETLD GKP S VD+ + + R Sbjct: 72 VT---WRTTSPAERANALLKIADLLEADADRFAVLETLDVGKPIRESRSVDIPLAIDHFR 128 Query: 148 YYAGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVV 207 Y+AG + + +D S EP+GV GQ+IPWNFPLLM AWK+ PA+A GN VV Sbjct: 129 YFAGVIRSQSDEAVMLDEQTLSIALSEPLGVVGQVIPWNFPLLMAAWKIAPAIAAGNTVV 188 Query: 208 MKVAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIG 267 +K +E TP+T L +A + + P GVVNIV G G T G A+ H D+ K+AFTGST +G Sbjct: 189 IKPSELTPVTILELAKIFAKV-LPAGVVNIVTGLGTTVGQALLDHPDLRKLAFTGSTRVG 247 Query: 268 RVIQVAAGSSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFV 327 ++ AA + + TLELGGKS NI+ DA+ D AVE A A+ +NQGQ C +G+R FV Sbjct: 248 ELVANAA-AKKIIPATLELGGKSANIVFPDANWDKAVEGAVLAILWNQGQVCESGARLFV 306 Query: 328 QEDIYDEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCG 387 E IY+ F+ + ++ VG+P + T G QV +TQ ++ILGY++ K+EGA++L G Sbjct: 307 HESIYERFLAELKHKFEAVRVGDPLNPDTMMGAQVSKTQMERILGYVDIAKEEGAEVLIG 366 Query: 388 GGIAA----DRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYG 443 GG D G+FIQPT+ V++ M +A EEIFGPV+ ++ FK EV+ AN+S YG Sbjct: 367 GGRLTGADYDAGFFIQPTILVGVRNDMRVAYEEIFGPVLCVIPFKDEAEVIAMANDSEYG 426 Query: 444 LAAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYT 503 LA AV+T+D+++A +++A++ G +WVN Y A +PFGGYK SG GRE + L+AY+ Sbjct: 427 LAGAVWTQDINRALRVARAVETGRMWVNTYHEIPAHAPFGGYKKSGLGRETHKSMLEAYS 486 Query: 504 EVKTVTVKV 512 + K + V + Sbjct: 487 QKKNIYVSL 495 Lambda K H 0.319 0.136 0.409 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: 591 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 517 Length of database: 503 Length adjustment: 34 Effective length of query: 483 Effective length of database: 469 Effective search space: 226527 Effective search space used: 226527 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: 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