Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate AZOBR_RS31000 AZOBR_RS31000 aldehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__azobra:AZOBR_RS31000 Length = 479 Score = 269 bits (688), Expect = 1e-76 Identities = 173/463 (37%), Positives = 248/463 (53%), Gaps = 14/463 (3%) Query: 20 GDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGI 79 G ++V+NPATE V + G EDA++A+ AA A + P ER L + A Sbjct: 19 GATVMEVLNPATEQVSGTVALGGPEDAQRAVAAAHAAFDGFSRTPLNERLELLAAVCALF 78 Query: 80 RERASEISALIVEE-GGKIQQLAEVEVAFTA-DYIDYMAEWARRYEGEIIQSDRPGENIL 137 +R E++ I EE G + L++ AF + E AR Y E R Sbjct: 79 EKRMDEVADAITEEMGAPLAALSKPAQAFMGLAHFKTALEAAREYPFE-----RTRGTTR 133 Query: 138 LFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGL 197 + + +GV I PWN+P IA K+APAL TG T+V+KPSEF P +A FA+I+ E G+ Sbjct: 134 ILREPVGVCAMITPWNWPINQIACKVAPALATGCTMVLKPSEFAPYSAWIFAEILHEAGV 193 Query: 198 PRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAP 257 P GVFN+ G G VG LA +P V MVS+TGS AG + AA +I +V LELGGK+ Sbjct: 194 PAGVFNMFYGDGAVVGPVLASHPLVDMVSLTGSTRAGASVSHNAADSIKRVSLELGGKSA 253 Query: 258 AIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNP 317 I+ + ADL AV V S + N+GQ CN R+YV D+ + + G+P Sbjct: 254 NIICESADLTKAVTHGVRSMMSNTGQSCNAPSRMYVPASRLDEAETIAAQVCARLVVGDP 313 Query: 318 AERND-IAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEG---KGYYYPPTLLLDV 373 R D +GP+ N ERV++ + +EEGA + GG +G+Y PT+ Sbjct: 314 --RGDRTGVGPIANQRQYERVQRLIQAGIEEGATLLCGGPGRPDGLERGFYAKPTVFSRA 371 Query: 374 RQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFG 433 M+IM EE FGPVL + ++ +E+AI ANDS YGL+ +Y ++ A K L+ G Sbjct: 372 TDGMTIMREEIFGPVLTIRPYEDIEEAIRSANDSLYGLSGYVYAGTVDEARAVAKRLRTG 431 Query: 434 ETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVY 476 ++N + + F G+++SGIG G+ G E+L+T+ VY Sbjct: 432 MVHLNGASIDLAAPF-GGYKQSGIGREWGEVGFEEFLETKSVY 473 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: 475 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: 479 Length adjustment: 34 Effective length of query: 445 Effective length of database: 445 Effective search space: 198025 Effective search space used: 198025 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