Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_090443038.1 BLS63_RS09095 gamma-aminobutyraldehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_900100495.1:WP_090443038.1 Length = 474 Score = 312 bits (800), Expect = 1e-89 Identities = 188/468 (40%), Positives = 267/468 (57%), Gaps = 7/468 (1%) Query: 12 IDGAFVES-AAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAGH 70 I+G V A+L V +PA G+ L + ASAE+V+ A+ AA AA W++ +RA Sbjct: 7 INGRLVSGEGANLAVLDPALGSPLLHLNEASAEQVDAAVRAAAAAFAGWSQTAPKDRALL 66 Query: 71 LRRIAAKIRADAGRIARTITLEQGK-IASLAEVEVNFTADYLDYMAEWARRLEGEIIASD 129 L R+A KI A A +A+ + GK A+ E+ AD + A +R L G Sbjct: 67 LLRLADKIEAHAEELAKLESDNCGKPYAAALNDEIPAIADVFRFFAGASRCLSGSAAGEY 126 Query: 130 RPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFAR 189 G + R P+GVVA I PWN+P + A K+APAL GNT+V+KPSE+TP + A Sbjct: 127 LAGHTSMIRRDPIGVVASIAPWNYPLMMAAWKLAPALAAGNTVVLKPSEQTPLTALKLAE 186 Query: 190 LVAETDLPRGVFNVVCGAG-QVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNL 248 +AE P GV N+V G G VG L SHP V ++S TGSV TG+ I+A++A ++ +L++ Sbjct: 187 FLAEL-FPAGVVNIVFGRGASVGSPLVSHPQVRMVSLTGSVATGSSIIASSATSVKRLHM 245 Query: 249 ELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMA 308 ELGGKAP ++ DAD+ AV+ IR N+GQ C A R+Y Q+ + E F+ + AA+ Sbjct: 246 ELGGKAPVLIFDDADIAAAVEGIRTFGFYNAGQDCTAACRIYAQKGIYEKFVAELGAAVG 305 Query: 309 ATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQG-ATLVTGGAIAERPGHHYQPTV 367 + +YG +P E+GPLI+ + V A AQ +VTGG PG YQPTV Sbjct: 306 SLKYGLQ-GDPSTELGPLISAEHRTRASGFVERAAAQAHIEVVTGGKAVAGPGFFYQPTV 364 Query: 368 LTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRE 427 L G R D I+R E+FGPV+ + DD +A+A AND +YGL SSV+T D+ +A Sbjct: 365 LAGARQDDEIVRREVFGPVVSVTPFDDEAQALAWANDSDYGLASSVWTGDVGRAHRLAAR 424 Query: 428 LDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHT-HVVY 474 L +G T++N + H G++ SG G +GL +YT HV++ Sbjct: 425 LQYGCTWVNTHFMLVSEMPHGGLKLSGYGKDLSMYGLEDYTAVRHVMF 472 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: 506 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: 477 Length of database: 474 Length adjustment: 33 Effective length of query: 444 Effective length of database: 441 Effective search space: 195804 Effective search space used: 195804 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