Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate BPHYT_RS25160 BPHYT_RS25160 NAD/NADP-dependent betaine aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__BFirm:BPHYT_RS25160 Length = 489 Score = 366 bits (940), Expect = e-106 Identities = 193/476 (40%), Positives = 286/476 (60%), Gaps = 7/476 (1%) Query: 23 LFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQV 82 L+I +V + S +TF T+ P+T E + V +A + D+D AV +A W+ Sbjct: 9 LYIGGGYVDATSGETFDTLDPATGETLASVQQASAADVDRAVRSAKQG-QREWAALTAMQ 67 Query: 83 RMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSV 141 R ++L + DL+ E D LA +E D GK + + D+ A AG I+G Sbjct: 68 RSRILRRAVDLLRERNDELAALETRDTGKPIAETLAVDIVTGADVIEYYAGLATAIEGQQ 127 Query: 142 IETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201 I T F YTRREP+GVC I WN+P+ +A WK P L G + K +E TPLSAL Sbjct: 128 IPLRPTSFVYTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEITPLSALK 187 Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261 LA + EAG P GV NVV G G GA +++HP I+K++FTG TG+ +M A S+LK Sbjct: 188 LAEIFTEAGVPAGVFNVVQGDG-RVGAMLAAHPDIEKISFTGGVETGKKVMSMAGASSLK 246 Query: 262 KVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFK 321 +VT+ELGGKSP +VFDDA+++ + F+++G+VC G+R++VQ G+ D+ + Sbjct: 247 EVTMELGGKSPLLVFDDANLERAADIATSANFFSSGQVCTNGTRVFVQRGVLDRFEALVL 306 Query: 322 NAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN----KGY 377 + +++G P T G S QL K+L YI+ GK+EGA ++ GG+R G Sbjct: 307 ERVKRIRVGKPTDAATNFGPLVSAAQLHKVLGYIESGKQEGARLVAGGKRLTEGHFAGGQ 366 Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437 +++PT+F D ++D +IVR+EIFGPV++I F +E IA AN + YGLAAGV T NL+ A Sbjct: 367 YVEPTVFADCRDDMRIVREEIFGPVMSILVFDDEDEAIARANHTAYGLAAGVVTENLARA 426 Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 V +++ +G W+NT+ + +P GGY QSG+GRE G L++YT++K+V++ L Sbjct: 427 HRVIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGITTLEHYTRIKSVQVEL 482 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: 590 Number of extensions: 24 Number of successful extensions: 5 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: 489 Length adjustment: 34 Effective length of query: 461 Effective length of database: 455 Effective search space: 209755 Effective search space used: 209755 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