Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate AZOBR_RS22315 AZOBR_RS22315 aldehyde dehydrogenase
Query= BRENDA::Q402C7 (499 letters) >FitnessBrowser__azobra:AZOBR_RS22315 Length = 497 Score = 387 bits (993), Expect = e-112 Identities = 205/476 (43%), Positives = 291/476 (61%), Gaps = 5/476 (1%) Query: 20 HFIGGEWVSGDSGKTIDLINPATGAVLTKIQAGNAKDIQRAVAAAKAAFPKWSESSPAER 79 HF GGE+ SGK ++NPATG + + G A D+ AVAAA AA +W++ ER Sbjct: 22 HFFGGEFRPASSGKGFPVVNPATGETVAEAAFGEAADVDAAVAAAVAAQKEWAKRPVRER 81 Query: 80 QEILIEVARRLKARHQHYATLETLNNGKPIRESMYFDMPQAISQFEVFAGAAYGLHGQTL 139 +++ E R L A + A L L GK +R + F F G A L G+T+ Sbjct: 82 GKLVAECGRVLDAHKEEIAKLIALETGKALRTESRVEAGVLSDAFVFFGGLAPELKGETI 141 Query: 140 DY-PDAIGIVHREPLGVCAQIIPWNVPILMMACKIAPALASGNTVVLKPAETVCLSVIEF 198 + P + + REP+GV IIPWNVP+L+MA KIAPA+ +GN VV+K AE L+V+ Sbjct: 142 PFNPSMLTMTVREPVGVVGAIIPWNVPLLLMALKIAPAMVAGNAVVVKSAEEAPLAVLRV 201 Query: 199 FVEMADLLPPGVINVVTGYGADVGEALVTHEDVRKVAFTGSVATARRIIQYASSNIIPQT 258 + ++P GV+N+++GYG + G LV H+DV+KV FTGSV T + + + A+ +IP T Sbjct: 202 VQLINTVIPAGVVNILSGYGPECGAPLVAHKDVKKVTFTGSVETGKIVYKTAAEKLIPVT 261 Query: 259 LELGGKSAHIVCADADIDAAVESATMSTVFNK-GEVCLAGSRLFLHQSIQDEFLAKFKVA 317 LELGGKS IVC DAD+D A+ A F + G+ C A SR+F+H SI D F+ K K Sbjct: 262 LELGGKSPMIVCGDADLDQAIAGAIAGMRFTRQGQSCTASSRIFVHDSIHDAFVEKLKEK 321 Query: 318 LEGIRQGDPLDFATQLGAQASQMQMDKVQSYLQLATEEGAT--VLTGGSRNESLADGHFI 375 + ++ GDPLD +T +G S Q+D+VQSY+ + E GAT V + + L G ++ Sbjct: 322 VNAMKMGDPLDESTDIGTIVSPQQLDRVQSYIAIGKEGGATPHVCSAMPSDPKLTKGLYV 381 Query: 376 KPTVFTNVSNSMRIAREEIFGPVTSVLTWNDEDDMMALANDTTYGLAGGVWTRDISRAHR 435 +P +FT V NS RIA+EEIFGPV V+ W D ++++A ANDT YGLA +WTRD+ A Sbjct: 382 QPHIFTGVKNSDRIAQEEIFGPVCCVIRWTDYEEVIAQANDTEYGLAATIWTRDLKVAMD 441 Query: 436 IARKLETGTVWVNRYYNLKPNMPLGGYKQSGFGREFSHE-VLHHYTQTKSVVINLQ 490 +LE G V VN+ ++PN+ GG K SG G+E S E +L H+T K+++IN++ Sbjct: 442 AVHRLEAGFVQVNQNLVVQPNLSYGGVKSSGLGKEASLEAMLEHFTHKKTIIINMK 497 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: 558 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: 499 Length of database: 497 Length adjustment: 34 Effective length of query: 465 Effective length of database: 463 Effective search space: 215295 Effective search space used: 215295 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