Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate RR42_RS11330 RR42_RS11330 aldehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Cup4G11:RR42_RS11330 Length = 477 Score = 316 bits (809), Expect = 1e-90 Identities = 183/474 (38%), Positives = 279/474 (58%), Gaps = 25/474 (5%) Query: 9 MYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIER 68 ++I+G++V G I+V++ TEAV+ RIP+G A DA AI AA A W A P R Sbjct: 7 LFINGKWVAPHGTGLINVIHSTTEAVMGRIPEGHARDAEDAIQAARAAFDSWSATPPSVR 66 Query: 69 ASWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEV-------AFTADYIDYMAEWAR 120 A ++RKI+ G++ R+ E++ LI E G I+ ++V A A +D A Sbjct: 67 AGYIRKIAEGLKARSEELAQLIAGEVGMPIKMARAIQVGGPVYNWAQAAKLLDTFA---- 122 Query: 121 RYEGEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEF 180 +E E+ N L+ + +GV I PWN+P I K+APAL G T+V+KPSE Sbjct: 123 -FEEEV-------GNSLVVREPVGVVAAITPWNYPLNQITLKVAPALAAGCTVVLKPSEV 174 Query: 181 TPNNAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMAT 240 P NA A++++ GLP GVFNLV G G VG+ LA +P+V MVS TGS AG+++ Sbjct: 175 APLNAFVLAEVIEAAGLPPGVFNLVTGYGPVVGEVLASHPEVDMVSFTGSTRAGKRVSEL 234 Query: 241 AAKNITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQ 300 A+++ +V LELGGK+ ++++DDADL AVK V + +NSGQ C+ R+ V + YD+ Sbjct: 235 GAQSVKRVALELGGKSASVILDDADLAAAVKGTVGACFLNSGQTCSAHTRMLVPRARYDE 294 Query: 301 FVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGG-KAVE 359 + ++ G+P + +GPLI+AA +RV + R + EGA + GG +A E Sbjct: 295 VKAIARKVVEGYTVGDPLLESS-RLGPLISAAQKDRVTGYIQRGINEGAELVAGGPEAPE 353 Query: 360 G--KGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYT 417 G KG++ PT+L +V + ++ EE FGPVL ++ +DT EDA+ +ANDS YGL +++ Sbjct: 354 GLDKGFFVKPTVLGNVDPKATVAQEEIFGPVLSIICYDTEEDAVRIANDSIYGLGGGVWS 413 Query: 418 QNLNVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQ 471 + A++ + ++ G+ IN F MQ G+++SG G GK+GL E+L+ Sbjct: 414 GDEARAIRVARRIRTGQVDINGGPFN-MQAPFGGYKQSGNGREAGKYGLEEFLE 466 Lambda K H 0.318 0.135 0.392 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: 530 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: 479 Length of database: 477 Length adjustment: 34 Effective length of query: 445 Effective length of database: 443 Effective search space: 197135 Effective search space used: 197135 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: 51 (24.3 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