Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate BPHYT_RS25160 BPHYT_RS25160 NAD/NADP-dependent betaine aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__BFirm:BPHYT_RS25160 Length = 489 Score = 397 bits (1021), Expect = e-115 Identities = 212/484 (43%), Positives = 294/484 (60%), Gaps = 9/484 (1%) Query: 34 VFCNQ-IFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSP 92 VF Q ++I + DA S +TF T++P+TGE + V + DVD+AV++A+ Q Sbjct: 3 VFATQRLYIGGGYVDATSGETFDTLDPATGETLASVQQASAADVDRAVRSAK---QGQRE 59 Query: 93 WRRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGW 152 W + A R R+L R DL+ LAALET D GKP + VD+ + YYAG Sbjct: 60 WAALTAMQRSRILRRAVDLLRERNDELAALETRDTGKPIAETLAVDIVTGADVIEYYAGL 119 Query: 153 ADKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAE 212 A G+ IP+ F YTR EP+GVC I WN+P+ + WK PALA GN ++ K +E Sbjct: 120 ATAIEGQQIPLRPTSFVYTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSE 179 Query: 213 QTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQV 272 TPL+AL +A + EAG P GV N+V G G GA +A+H D++K++FTG E G+ + Sbjct: 180 ITPLSALKLAEIFTEAGVPAGVFNVVQGDG-RVGAMLAAHPDIEKISFTGGVETGKKVMS 238 Query: 273 AAGSSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIY 332 AG+S+LK VT+ELGGKSP ++ DA+++ A + A A FF+ GQ C G+R FVQ + Sbjct: 239 MAGASSLKEVTMELGGKSPLLVFDDANLERAADIATSANFFSSGQVCTNGTRVFVQRGVL 298 Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAA 392 D F + R K VG P D+ T GP V Q K+LGYI +GKQEGA+L+ GG Sbjct: 299 DRFEALVLERVKRIRVGKPTDAATNFGPLVSAAQLHKVLGYIESGKQEGARLVAGGKRLT 358 Query: 393 D----RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAV 448 + G +++PTVF D +D M I +EEIFGPVM IL F +E + RAN++ YGLAA V Sbjct: 359 EGHFAGGQYVEPTVFADCRDDMRIVREEIFGPVMSILVFDDEDEAIARANHTAYGLAAGV 418 Query: 449 FTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTV 508 T++L +A+ + L+AG W+N + A+ P GGYK SG GRE G L+ YT +K+V Sbjct: 419 VTENLARAHRVIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGITTLEHYTRIKSV 478 Query: 509 TVKV 512 V++ Sbjct: 479 QVEL 482 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: 613 Number of extensions: 31 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: 517 Length of database: 489 Length adjustment: 34 Effective length of query: 483 Effective length of database: 455 Effective search space: 219765 Effective search space used: 219765 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