Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::A0A0E3T552 (503 letters) >FitnessBrowser__Dino:3607686 Length = 506 Score = 330 bits (846), Expect = 7e-95 Identities = 205/497 (41%), Positives = 279/497 (56%), Gaps = 22/497 (4%) Query: 11 FIDGEWREPVLKKRIPIINPATEEIIGHIPAATAEDVELAVEAARRALSRNKGRDWASAP 70 FI G++ PV + + P T E++G I ++A DVELA++AA A W Sbjct: 22 FIGGKFVPPVEGRYFDNVTPITGEVVGQIARSSAADVELALDAAHAAKDA-----WGKTS 76 Query: 71 GAVRAKYLRAIAAKIGERKPEIAKLEAIDCGKPLDEAAW-DIDDVSGCFEYYAELAEGLD 129 RA + IA +I E IAK E D GKP+ E DI F Y+A + G Sbjct: 77 VTERANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRG-- 134 Query: 130 AQQKAPISLPMEQFKSHVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCAAILKPSEL 189 Q+ +S ++ EP+GVVG I PWN+ +LMA WK+APA+AAG +LKP+E Sbjct: 135 --QEGSMSEIDNDTVAYHFHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQ 192 Query: 190 ASVTCLELADVCREVGLPPGVLNILTGLGHEAGAPLVSHPHVDKIAFTGSTMTGSKIMTA 249 + L ++ ++ LP GVLNI+ G G E GA L + + KIAFTGST TG KIM A Sbjct: 193 TPAAIMVLVELISDL-LPAGVLNIVNGYGGEVGAALATSDRIAKIAFTGSTATGRKIMEA 251 Query: 250 AAQLVKPVSLELGGKSPIVVF------DDVDIDKAAEWTAFGCFWTNGQICSATSRLILH 303 A + PV+LELGGKSP + F DD +DKA E F G++C+ SR ++H Sbjct: 252 ATVNLIPVTLELGGKSPNIFFKDVMAEDDAFLDKAVEGFVLFAF-NQGEVCTCPSRALIH 310 Query: 304 ENIATEFLDRLLKWCKNIKIADPLEEGCRLGPVVSGGQYEKILKSIETAKSEGARVLSGG 363 E+I EF+ R + K I DP + +G S Q +KIL + EGA VL+GG Sbjct: 311 EDIYEEFIARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGVEEGAEVLTGG 370 Query: 364 ---DRPEHLKKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFSSEDEALELANDTHYG 420 D + LK GF+IEPTI+ M++++EE+FGPV+ V TF +E+EALELANDT YG Sbjct: 371 KVADVSDDLKDGFYIEPTILKG-HNKMRVFQEEIFGPVVSVTTFKTEEEALELANDTMYG 429 Query: 421 LGAAVISKDLERCDRFSKGLQAGIVWINCSQPCFCQAPWGGNKRSGFGRELGKWGLDNYL 480 LGA V S+D C RF +G+QAG VW+N A +GG K+SG GRE K LD+Y Sbjct: 430 LGAGVWSRDQNTCYRFGRGVQAGRVWVNNYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQ 489 Query: 481 TVKQVTEYVSDDPWGWY 497 K + + + G++ Sbjct: 490 QTKNMLVSYNPNKLGFF 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: 638 Number of extensions: 37 Number of successful extensions: 7 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