Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate WP_011766665.1 AZO_RS14770 aldehyde dehydrogenase family protein
Query= SwissProt::A1B4L2 (508 letters) >NCBI__GCF_000061505.1:WP_011766665.1 Length = 506 Score = 796 bits (2055), Expect = 0.0 Identities = 382/492 (77%), Positives = 436/492 (88%) Query: 17 FEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWGA 76 F+ RYDNFIGG+WVAPV G+Y N TPITG Q+ARS DI LALDAAHAA +KWG Sbjct: 15 FKSRYDNFIGGKWVAPVRGQYMDNITPITGKPFCQVARSTEEDINLALDAAHAAADKWGR 74 Query: 77 TSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLRA 136 TS ERAN + +IADR+E+NLEL+A AET DNGKPIRETMAAD+PLAIDHFRYFAG +RA Sbjct: 75 TSVIERANTLCRIADRLEQNLELIAYAETVDNGKPIRETMAADIPLAIDHFRYFAGCIRA 134 Query: 137 QEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQTP 196 QEGS++++D++TVAYHFHEPLGVVGQIIPWNFP+LMA WKLAPA+AAGN VVLKPAE TP Sbjct: 135 QEGSLAELDENTVAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNVVVLKPAESTP 194 Query: 197 AGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYASE 256 GI+V A LI DLLP GVLNIVNG G EAG PLA+S+RIAKIAFTG TTTGRLIMQ AS+ Sbjct: 195 VGILVIAELIADLLPAGVLNIVNGLGREAGVPLATSSRIAKIAFTGSTTTGRLIMQAASQ 254 Query: 257 NLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESIY 316 N+IPVTLELGGKSPNIFF DVA DD+FFDKA+EGF +FALNQGEVCTCPSR LI ESIY Sbjct: 255 NIIPVTLELGGKSPNIFFQDVAAADDEFFDKAVEGFVLFALNQGEVCTCPSRALIHESIY 314 Query: 317 DKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAAD 376 D+FM+RA+ RV+AIKQG+P +++TMIGAQAS+EQ +KILSY+++GK+EGA++L GG A Sbjct: 315 DRFMDRALARVKAIKQGNPLDTETMIGAQASTEQMKKILSYIELGKEEGAQLLAGGGEAK 374 Query: 377 LGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAGV 436 GGEL+ GYY++PT+F+G+NKMRIFQEEIFGPV+SVTTFKD+AEAL IANDTLYGLGAGV Sbjct: 375 FGGELAEGYYVQPTVFKGHNKMRIFQEEIFGPVLSVTTFKDEAEALSIANDTLYGLGAGV 434 Query: 437 WSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNM 496 WSRD +T YRMGR IKAGRVWTNCYH YPAHAAFGGYKQSGIGRETHKMMLDHYQQTKN+ Sbjct: 435 WSRDGSTAYRMGRNIKAGRVWTNCYHLYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNL 494 Query: 497 LVSYSPKKLGFF 508 LVSYSPK LGFF Sbjct: 495 LVSYSPKALGFF 506 Lambda K H 0.319 0.136 0.411 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: 875 Number of extensions: 20 Number of successful extensions: 1 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: 508 Length of database: 506 Length adjustment: 34 Effective length of query: 474 Effective length of database: 472 Effective search space: 223728 Effective search space used: 223728 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