Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate H281DRAFT_02299 H281DRAFT_02299 aldehyde dehydrogenase
Query= BRENDA::A0A0E3T552 (503 letters) >FitnessBrowser__Burk376:H281DRAFT_02299 Length = 506 Score = 335 bits (859), Expect = 2e-96 Identities = 208/498 (41%), Positives = 280/498 (56%), Gaps = 24/498 (4%) Query: 11 FIDGEWREPVLKKRIPIINPATEEIIGHIPAATAEDVELAVEAARRALSRNKGRDWASAP 70 FI GEW +P + ++P T E IP + DVELA++AA RA + W Sbjct: 22 FIGGEWVKPAGGEYFDNVSPITGEPFTSIPRSREADVELALDAAHRAKAA-----WGKTS 76 Query: 71 GAVRAKYLRAIAAKIGERKPEIAKLEAIDCGKPLDEA-AWDIDDVSGCFEYYAELAEGLD 129 RA L IA ++ +A E ID GKPL E A DI F Y+A G Sbjct: 77 TTDRANILNRIADRMEANLQRLAVAETIDNGKPLRETMAADIPLAIDHFRYFA----GAV 132 Query: 130 AQQKAPISLPMEQFKSHVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCAAILKPSEL 189 Q+ IS + ++ EP+GVVG I PWN+P+LMA WK+APALAAG +LKP+E Sbjct: 133 RAQEGSISEIDDDTVAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQ 192 Query: 190 ASVTCLELADVCREVGLPPGVLNILTGLGHEAGAPLVSHPHVDKIAFTGSTMTGSKIMTA 249 + L L ++ +++ LP GVLN++ G G EAG PL S + KIAFTG T TG IM Sbjct: 193 TPASILVLVELIQDL-LPAGVLNVVNGFGLEAGKPLASSKRIAKIAFTGETTTGRLIMQY 251 Query: 250 AAQLVKPVSLELGGKSPIVVF------DDVDIDKAAEWTAFGCFWTN-GQICSATSRLIL 302 A+Q + PV+LELGGKSP + F DD DKA E F F N G++C+ SR+++ Sbjct: 252 ASQNIIPVTLELGGKSPNIFFADVMNQDDSYFDKALE--GFAMFALNQGEVCTCPSRVLI 309 Query: 303 HENIATEFLDRLLKWCKNIKIADPLEEGCRLGPVVSGGQYEKILKSIETAKSEGARVLSG 362 E I F++R LK I PL+ +G S Q EKIL ++ K EGA L G Sbjct: 310 DEKIYDSFMERALKRVAAITQGHPLDTRTMIGAQASQEQLEKILSYVDLGKQEGAECLIG 369 Query: 363 GDRPE---HLKKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFSSEDEALELANDTHY 419 G+R L KG++++PT+ M+I++EE+FGPV+ V TF +E+EALE+ANDT Y Sbjct: 370 GERNTLSGELSKGYYVKPTVFRG-HNKMRIFQEEIFGPVVSVTTFKTEEEALEIANDTLY 428 Query: 420 GLGAAVISKDLERCDRFSKGLQAGIVWINCSQPCFCQAPWGGNKRSGFGRELGKWGLDNY 479 GLGA V ++D R RF + +QAG VW NC A +GG K+SG GRE K LD+Y Sbjct: 429 GLGAGVWTRDGTRAYRFGRQIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHY 488 Query: 480 LTVKQVTEYVSDDPWGWY 497 K + S+ P G++ Sbjct: 489 QQTKNLLVSYSEKPLGFF 506 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: 646 Number of extensions: 30 Number of successful extensions: 6 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: 506 Length adjustment: 34 Effective length of query: 469 Effective length of database: 472 Effective search space: 221368 Effective search space used: 221368 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 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