Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_067912398.1 AQZ52_RS14300 aldehyde dehydrogenase family protein
Query= BRENDA::A0A0E3T552 (503 letters) >NCBI__GCF_001519075.1:WP_067912398.1 Length = 500 Score = 322 bits (825), Expect = 2e-92 Identities = 199/498 (39%), Positives = 279/498 (56%), Gaps = 24/498 (4%) Query: 11 FIDGEWREPVLKKRIPIINPATEEIIGHIPAATAEDVELAVEAARRALSRNKGRDWASAP 70 FI G++ P + P ++ + + A D+ELA++AA RA +W + Sbjct: 16 FISGKFLPPASGRYFANPTPVDGTVLCEVARSDAADIELALDAAHRAAP-----NWGTTS 70 Query: 71 GAVRAKYLRAIAAKIGERKPEIAKLEAIDCGKPLDEA-AWDIDDVSGCFEYYAELAEGLD 129 A RA L IA ++ E +A+ E+ D GKPL E+ A D+ F Y+A G Sbjct: 71 AAERAGILNRIADRMEENLALLAQAESWDNGKPLRESMAADLPLAIDHFRYFA----GCI 126 Query: 130 AQQKAPISLPMEQFKSHVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCAAILKPSEL 189 Q+ +S Q ++ EP+GVVG I PWN+PLLMA WK+APALAAG +LKP+E Sbjct: 127 RAQQGGLSEIDSQTVAYHFHEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQ 186 Query: 190 ASVTCLELADVCREVGLPPGVLNILTGLGHEAGAPLVSHPHVDKIAFTGSTMTGSKIMTA 249 + + A++ ++ LP GV+NI+ G G EAG PL S P + KIAFTG T TG IM Sbjct: 187 TPASIMIWAELVGDL-LPAGVINIVNGFGLEAGKPLASSPRISKIAFTGETSTGRLIMQY 245 Query: 250 AAQLVKPVSLELGGKSPIVVF------DDVDIDKAAEWTAFGCFWTN-GQICSATSRLIL 302 A++ + PV+LELGGKSP + F DD +DKA E F F N G++C+ SR ++ Sbjct: 246 ASENIIPVTLELGGKSPNIFFADVAQEDDEFLDKAIE--GFVMFALNQGEVCTCPSRALI 303 Query: 303 HENIATEFLDRLLKWCKNIKIADPLEEGCRLGPVVSGGQYEKILKSIETAKSEGARVLSG 362 HE+I F++R L IK PL+ +G S Q EKIL ++ + EGA L G Sbjct: 304 HESIYDRFMERALARVAQIKQGHPLDMETMIGAQASTEQVEKILSYLDLGEMEGALTLIG 363 Query: 363 GDR---PEHLKKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFSSEDEALELANDTHY 419 G R P LK G +I+PT++ M++++EE+FGPV+CV TF E EAL +ANDT Y Sbjct: 364 GGRASVPPALKGGNYIQPTVLKG-HNGMRVFQEEIFGPVVCVTTFKDEAEALSIANDTLY 422 Query: 420 GLGAAVISKDLERCDRFSKGLQAGIVWINCSQPCFCQAPWGGNKRSGFGRELGKWGLDNY 479 GLGA V S+D+ C R +G++AG VW NC A +GG K+SG GRE L +Y Sbjct: 423 GLGAGVWSRDISTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHLMMLSHY 482 Query: 480 LTVKQVTEYVSDDPWGWY 497 K + + G++ Sbjct: 483 QQTKNLLVSYAPQKLGFF 500 Lambda K H 0.319 0.136 0.424 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: 644 Number of extensions: 26 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: 503 Length of database: 500 Length adjustment: 34 Effective length of query: 469 Effective length of database: 466 Effective search space: 218554 Effective search space used: 218554 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