Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate GFF2074 PGA1_c21070 betaine aldehyde dehydrogenase BetB
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Phaeo:GFF2074 Length = 488 Score = 340 bits (873), Expect = 5e-98 Identities = 188/464 (40%), Positives = 274/464 (59%), Gaps = 6/464 (1%) Query: 30 VQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHS-SWSTSDPQVRMKVLY 88 V S F + P++ E + EA + D++ AV AA AAFH+ W+ R K+LY Sbjct: 11 VFSDGSARFESRDPASGEVWAMMPEARASDVEAAVAAARAAFHAPDWAGMTATGRGKLLY 70 Query: 89 KLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIETGDTH 148 +LADLI E+A+TLA +E D GK + + +A A Y+R AG DKI+G+ + Sbjct: 71 RLADLIAENAETLAQLETRDTGKIIRETSAQIAYVADYYRYYAGLADKIEGAHLPIDKPD 130 Query: 149 FN-YTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIK 207 + RREP+GV ++PWN L +A+ K+GP L GCT VLK +E P L A + Sbjct: 131 MEVWLRREPLGVVAAVVPWNSQLFLAAVKIGPALAAGCTVVLKASEEAPAPLLEFARIFD 190 Query: 208 EAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLEL 267 +AG P GV+NV++GFG GA +++HP I +AFTG T RH+++ +AE NL +LEL Sbjct: 191 QAGFPRGVLNVITGFGADCGAVLTAHPGIDHIAFTGGPDTARHVVRNSAE-NLASTSLEL 249 Query: 268 GGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESL 327 GGKSP IVF+D D+ S + V+ IF TG+ C AGSR+ + I + + K AE++ Sbjct: 250 GGKSPFIVFEDVDIDSAVNAQVSAIFAATGQSCVAGSRLIISNQIKAQFLHRLKEKAENI 309 Query: 328 KIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPTIFGDV 387 +IG P +T +G + Q+ + ++ + GA ++TGG+ +G F PTI D Sbjct: 310 RIGAPELPETEVGPLCTDAQMRRAVELVAASLAAGARIVTGGQPLEGEGNFFPPTIL-DC 368 Query: 388 KE--DHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKIN 445 E + +R+E FGPV+++ F T E +ALAND+ +GLA+GV T +L+ A + I Sbjct: 369 SEAPEAPCLREEFFGPVLSVCGFDTEAEALALANDTAHGLASGVFTRDLTRAHRMIRGIR 428 Query: 446 SGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 +G +WVNTY P+ PFGG SG GRE G +A +YT+VK V Sbjct: 429 AGIVWVNTYRAVSPIAPFGGQGLSGHGREGGLQAALDYTRVKTV 472 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: 532 Number of extensions: 19 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: 488 Length adjustment: 34 Effective length of query: 461 Effective length of database: 454 Effective search space: 209294 Effective search space used: 209294 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