Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized)
to candidate WP_011612157.1 TERY_RS12430 aldehyde dehydrogenase family protein
Query= BRENDA::P11884 (519 letters) >NCBI__GCF_000014265.1:WP_011612157.1 Length = 490 Score = 677 bits (1748), Expect = 0.0 Identities = 329/485 (67%), Positives = 389/485 (80%), Gaps = 1/485 (0%) Query: 30 PNQQPEVFCNQIFINNEWHDAVSKKTFPTVNPSTGEVICQVAEGNKEDVDKAVKAAQAAF 89 P Q+ ++ ++ INNEW ++ S K F T+NP+TGEVIC VAE + DVDKAV AA+ AF Sbjct: 7 PEQKVKIGPTKLLINNEWVESASGKRFETINPATGEVICNVAEADAPDVDKAVIAARKAF 66 Query: 90 QLGSPWRRMDASDRGRLLYRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLR 149 G W ++ A+ RG LLY+LADLIE++ LA LETLDNGKP+ S DL + + C R Sbjct: 67 TSGE-WPKISAAKRGELLYKLADLIEKNIEELARLETLDNGKPFKDSLNTDLPLAIACYR 125 Query: 150 YYAGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVV 209 YYAGWADK GKTIPI G +F YTRHEPVGV GQIIPWNFPLLMQAWKL PALA GN +V Sbjct: 126 YYAGWADKVQGKTIPISGPYFCYTRHEPVGVVGQIIPWNFPLLMQAWKLAPALAMGNTLV 185 Query: 210 MKVAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEVG 269 MK AEQTPL+AL V L+ EAGFPPGVVNI+ G+GPTAGAAI+ H+D+DKVAFTGSTEVG Sbjct: 186 MKTAEQTPLSALRVGELVIEAGFPPGVVNILSGYGPTAGAAISHHKDIDKVAFTGSTEVG 245 Query: 270 HLIQVAAGSSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFV 329 LI AA SNLKRVTLELGGKSPNI+ +DADMD A+E +HFALFFNQGQCCCAGSR FV Sbjct: 246 RLIMEAAAKSNLKRVTLELGGKSPNIVFADADMDAAIEGSHFALFFNQGQCCCAGSRLFV 305 Query: 330 QEDVYDEFVERSVARAKSRVVGNPFDSRTEQGPQVDETQFKKILGYIKSGQQEGAKLLCG 389 +E YDEFV +SV RAK R+VG+PF R EQGPQVDE QF K++ YI+SGQQ+GA++LCG Sbjct: 306 EEKCYDEFVNKSVERAKLRMVGDPFTERVEQGPQVDEEQFNKVMSYIESGQQDGAQMLCG 365 Query: 390 GGAAADRGYFIQPTVFGDVKDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSKYGLAAA 449 G DRGYFI PTVF DV+D M IA+EEIFGPVM I+KFK I+E+V RANNS YGLAA Sbjct: 366 GSRVGDRGYFIAPTVFADVQDNMKIAQEEIFGPVMSIIKFKDIDELVERANNSMYGLAAG 425 Query: 450 VFTKDLDKANYLSQALQAGTVWINCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKT 509 V+T+D+ KA+ L+ L+AGTVW+NCYDVF A +PFGG+K SG GRELGEYGLQ YTE+KT Sbjct: 426 VWTQDVTKAHTLAHRLRAGTVWVNCYDVFDAAAPFGGFKQSGLGRELGEYGLQQYTEIKT 485 Query: 510 VTVKV 514 VT+K+ Sbjct: 486 VTMKM 490 Lambda K H 0.319 0.135 0.404 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: 729 Number of extensions: 20 Number of successful extensions: 2 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: 519 Length of database: 490 Length adjustment: 34 Effective length of query: 485 Effective length of database: 456 Effective search space: 221160 Effective search space used: 221160 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 (21.7 bits) S2: 52 (24.6 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