Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein
Query= BRENDA::Q402C7 (499 letters) >NCBI__GCF_000009985.1:WP_011385953.1 Length = 496 Score = 375 bits (962), Expect = e-108 Identities = 201/477 (42%), Positives = 291/477 (61%), Gaps = 6/477 (1%) Query: 20 HFIGGEWVSGDSGKTIDLINPATGAVLTKIQAGNAKDIQRAVAAAKAAFPKWSESSPAER 79 H IGG+ V G+ ++ NPATG ++ G +D+ AV +AKAA W++ S R Sbjct: 20 HLIGGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIAVISAKAAQKDWAKQSARAR 79 Query: 80 QEILIEVARRLKARHQHYATLETLNNGKPIRESMYFDMPQAISQFEVFAGAAYGLHGQTL 139 +++ E R L A + L L GK +R + F F G L G+T+ Sbjct: 80 GKLVAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVLADMFTFFGGLGSELKGETI 139 Query: 140 DY-PDAIGIVHREPLGVCAQIIPWNVPILMMACKIAPALASGNTVVLKPAETVCLSVIEF 198 + PD + + REP+GV IIPWNVP+L+MA K A AL +GN+VV+K AE L+V+ Sbjct: 140 PFNPDMLTVTVREPVGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEAPLTVLRV 199 Query: 199 FVEMADLLPPGVINVVTGYGADVGEALVTHEDVRKVAFTGSVATARRIIQYASSNIIPQT 258 M +LPPG+ N+++G+G + G LV H DV+KV FTGSV T R + + A+ +IP T Sbjct: 200 AEIMNTVLPPGLFNMLSGFGPECGAPLVEHPDVKKVTFTGSVETGRIVYKAAAEKLIPVT 259 Query: 259 LELGGKSAHIVCADADIDAAVESATMSTVFNK-GEVCLAGSRLFLHQSIQDEFLAKFKVA 317 LELGGKS IVCADAD+D AV A F + G+ C A SRLF+H+SI DEF+AK K Sbjct: 260 LELGGKSPMIVCADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHESIHDEFVAKVKAK 319 Query: 318 LEGIRQGDPLDFATQLGAQASQMQMDKVQSYLQLATE-EGAT--VLTGGSRNESLADGHF 374 ++ + GDPLD T +G S Q+++V+SY+++ E +GAT V + + LA G F Sbjct: 320 VDAMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSALPTDPKLAKGRF 379 Query: 375 IKPTVFTNVSNSMRIAREEIFGPVTSVLTWNDEDDMMALANDTTYGLAGGVWTRDISRAH 434 ++P +FT + NS R+ +EEIFGPV +V+ W+D +D++A AND+ YGLA +WTRD A Sbjct: 380 VQPVIFTGMKNSDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASIWTRDFKLAM 439 Query: 435 RIARKLETGTVWVNRYYNLKPNMPLGGYKQSGFGREFSHE-VLHHYTQTKSVVINLQ 490 ++LE G V VN+ ++P + GG K SG G+E S E +L H+T K+++ N++ Sbjct: 440 DATKRLEAGFVQVNQNLVVQPGLSYGGVKTSGIGKEASLESMLEHFTHKKTIIFNMK 496 Lambda K H 0.318 0.133 0.390 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: 518 Number of extensions: 15 Number of successful extensions: 4 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: 499 Length of database: 496 Length adjustment: 34 Effective length of query: 465 Effective length of database: 462 Effective search space: 214830 Effective search space used: 214830 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 (21.7 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