Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate BPHYT_RS23175 BPHYT_RS23175 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__BFirm:BPHYT_RS23175 Length = 497 Score = 363 bits (932), Expect = e-105 Identities = 212/479 (44%), Positives = 286/479 (59%), Gaps = 14/479 (2%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTSDPQV 82 FI+ E+ ++ +TF +SP + + +V ++ + D+D AV AA AF S WS +P+ Sbjct: 23 FIDGEYRDAEGGRTFDCLSPIDGKLLAKVADSGAADVDAAVAAARRAFDSGVWSGLNPRQ 82 Query: 83 RMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGW----TDKIK 138 R VL + A I EH D LA +E LD GK + + AAY C W DKI Sbjct: 83 RKAVLLRWAASIREHMDELALLETLDAGKPIADTTSVDVPGAAY---CVEWFAEAIDKIG 139 Query: 139 GSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLS 198 G V REPIGV ++PWNFP+LMASWK GP L G + VLK +E +PL+ Sbjct: 140 GEVAPADHHLLGLVTREPIGVVAAVVPWNFPILMASWKFGPALAAGNSVVLKPSEKSPLT 199 Query: 199 ALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAES 258 A+ LA L +AG P GV NVV G G G ++ H + +AFTGST G+ IM+ A +S Sbjct: 200 AIRLAQLALDAGIPAGVFNVVPGAGEP-GKLLALHQDVDCLAFTGSTNVGKLIMQYAGQS 258 Query: 259 NLKKVTLELGGKSPNIVFDDA-DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317 NLK+V LELGGKSPNIV D D+ IFYN GE+C AGSR+ V I D + Sbjct: 259 NLKRVWLELGGKSPNIVMPDCPDMDRAANAAAGAIFYNMGEMCTAGSRLLVHRDIKDVFI 318 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNK-- 375 + AA S G+P DT MGA ++QL+++L YI+ G+ E A ++ GG R Sbjct: 319 DKLIAAARSYTPGNPLDPDTSMGAIVDKVQLERVLGYIEAGRAE-AKLLLGGARVKEDTG 377 Query: 376 GYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLS 435 G++I+PTIF ++ R+EIFGPV+++ F TVEE I +ANDSEYGLAA V T+NL+ Sbjct: 378 GFYIEPTIFEIPGSGAKVAREEIFGPVLSVITFDTVEEAIRIANDSEYGLAAAVWTSNLT 437 Query: 436 TAISVSNKINSGTIWVNTYNDFHPM-VPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 TA VS K+ +GT+WVN Y++ M PFGGY QSG GR+ AL+ YT++K+ + L Sbjct: 438 TAHEVSRKLRAGTVWVNCYDEGGDMNFPFGGYKQSGNGRDKSLHALEKYTELKSTLVRL 496 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: 558 Number of extensions: 17 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: 497 Length adjustment: 34 Effective length of query: 461 Effective length of database: 463 Effective search space: 213443 Effective search space used: 213443 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