Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized)
to candidate SMa2213 SMa2213 aldehyde dehydrogenase
Query= BRENDA::Q9S795 (501 letters) >FitnessBrowser__Smeli:SMa2213 Length = 494 Score = 365 bits (937), Expect = e-105 Identities = 205/490 (41%), Positives = 281/490 (57%), Gaps = 9/490 (1%) Query: 5 MPTRQLFIDGEWREPILKKRIPIVNPATEEVIGDIPAATTEDVDVAVNAARRALSRNKGK 64 +P ++IDG+W P + I V+P T +P ED D AV AA RA S+ Sbjct: 4 LPKLSMYIDGQWVAPASGEYIETVDPFTARPWALVPRGNAEDADRAVRAAHRAFSQGP-- 61 Query: 65 DWAKAPGAVRAKYLRAIAAKVNERKTDLAKLEALDCGKPLDEAVWDMDDVAGCFEFYADL 124 W K R + ++ AA + E LA +E D G+ L E + + + +YA Sbjct: 62 -WGKMHPTERGRIIQRFAALIEEHADALADIEVRDNGRLLAEMTHQIRYIPRWYHYYAGF 120 Query: 125 AEGLDAKQKAPVSLPMESFKSYVLKQPLGVVGLITPWNYPLLMAVWKVAPSLAAGCTAIL 184 A+ ++ P P SF + +PLGV I PWN PLL+ K AP+LAAG T ++ Sbjct: 121 ADKIEGTLH-PCDKPALSFSRH---EPLGVCVGIVPWNAPLLLFSLKAAPALAAGNTLVM 176 Query: 185 KPSELASVTCLELADICREVGLPPGVLNVLTGFGSEAGAPLASHPGVDKIAFTGSFATGS 244 KP+E S T L+L ++ + G P GV+NV+TG+G E G PL +HP + FTGS TG+ Sbjct: 177 KPAEFTSATALKLMELVEKAGFPTGVINVVTGYGPEVGEPLVTHPLTRHVGFTGSTKTGA 236 Query: 245 KVMTAAAQLVKPVSMELGGKSPLIVFDDVDLDKAAEWALFGCFWTNGQICSATSRLLVHE 304 + + AA+ VK VS+ELGGKSP IVF D DLD A + G F GQ C A SRLLVH Sbjct: 237 HLYSLAAKDVKRVSLELGGKSPNIVFGDADLDNAVRGVVGGIFGAVGQTCIAGSRLLVHR 296 Query: 305 SIASEFIEKLVKWSKNIKISDPMEEGCRLGPVVSKGQYEKILKFISTAKSEGATILHGGS 364 SI EF+EKL ++K +I DP + ++GP+ + Q+EK+L +I A+ EGA ++ GG Sbjct: 297 SIHDEFLEKLAVFTKTARIGDPRKVETQIGPIANSMQFEKVLGYIDIARREGAELILGGG 356 Query: 365 RP--EHLEKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFASEDEAIELANDSHYGLG 422 RP E G+FIEPTI V+ M+I REEVFGPVL F +EA+ +ANDS +GLG Sbjct: 357 RPDLEECGTGYFIEPTIFAGVSNDMRIAREEVFGPVLSAIVFDEPEEALAIANDSEFGLG 416 Query: 423 AAVISNDTERCDRISEAFEAGIVWINCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSV 482 A V ++D ++SE EAG VW+N + P+GG K+SG GRE G G+ YL Sbjct: 417 AGVWTSDMRLALKMSERLEAGSVWVNTYRDISYTTPFGGYKKSGIGRENGVAGIYEYLQT 476 Query: 483 KQVTLYTSND 492 K V L T+ + Sbjct: 477 KAVWLSTAEE 486 Lambda K H 0.318 0.135 0.416 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: 656 Number of extensions: 30 Number of successful extensions: 4 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: 501 Length of database: 494 Length adjustment: 34 Effective length of query: 467 Effective length of database: 460 Effective search space: 214820 Effective search space used: 214820 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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