Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011811026.1 VEIS_RS16060 gamma-aminobutyraldehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_000015565.1:WP_011811026.1 Length = 477 Score = 311 bits (798), Expect = 2e-89 Identities = 186/463 (40%), Positives = 258/463 (55%), Gaps = 8/463 (1%) Query: 11 YIDGAFVESAAHLE-VFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAG 69 +IDG F++ E + NP+ G L+ V AS ++ RA+ AA A WA A +RA Sbjct: 6 FIDGQFLQGEESAERILNPSTGELICEVREASPTQISRAVDAAHRAWPAWASTSAKDRAA 65 Query: 70 HLRRIAAKIRADAGRIARTITLEQGKI--ASLAEVEVNFTADYLDYMAEWARRLEGEIIA 127 L ++A I +A +A+ L GK A+LA+ E+ AD + A R + + Sbjct: 66 MLLKVADHIEQNAAGLAQLEALNCGKPYQAALAD-EMPAIADVFRFFAGAVRCMTAPVAT 124 Query: 128 SDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEF 187 PG + R LGVVA I PWN+P + A K+ PA+ TGNTIV+KPSE+TP + Sbjct: 125 EYLPGHTSMIRRDSLGVVASISPWNYPLMMAAWKICPAVATGNTIVLKPSEQTPLTTLKL 184 Query: 188 ARLVAETDLPRGVFNVVCGAGQVGGA-LSSHPGVDLISFTGSVETGARIMAAAAPNLTKL 246 A +A P GV N+VCG G+ GA L + P V +IS TG V TG ++M AA + + Sbjct: 185 AEFIASI-FPPGVINIVCGRGESAGATLIAQPQVRMISVTGDVSTGQKVMEAAVRGIKRT 243 Query: 247 NLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAA 306 +LELGGKAP IV DAD+ V IR N+GQ C A RVY Q+ + + + +AAA Sbjct: 244 HLELGGKAPVIVFDDADIGEVVAGIRTFGYYNAGQDCTAACRVYAQKGIYDKLVADLAAA 303 Query: 307 MAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQ-GATLVTGGAIAERPGHHYQP 365 ++ R G+P + VEMGP I+ ++ A V A + +V GG IA+R G YQP Sbjct: 304 VSTIRIGEP-GDVGVEMGPCISERQRSRVAAFVERAREEKHIKVVAGGKIADRRGFFYQP 362 Query: 366 TVLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHAL 425 T+L C+ I+R+E+FGPV+ + DLDE I LAND +YGL SSV++ D+ KAM Sbjct: 363 TLLANCKQSDEIVRKEVFGPVVSVTPFSDLDEVIGLANDSDYGLASSVWSSDVGKAMRVA 422 Query: 426 RELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYT 468 L +G T+IN + H G++KSG G L EYT Sbjct: 423 AALHYGTTWINTHFMLVAEMPHGGMKKSGYGKDQSMFALEEYT 465 Lambda K H 0.320 0.136 0.395 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: 536 Number of extensions: 24 Number of successful extensions: 3 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: 477 Length of database: 477 Length adjustment: 33 Effective length of query: 444 Effective length of database: 444 Effective search space: 197136 Effective search space used: 197136 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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