Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF3619 PGA1_262p00230 betaine aldehyde dehydrogenase BetB
Query= BRENDA::C0P9J6 (505 letters) >FitnessBrowser__Phaeo:GFF3619 Length = 494 Score = 318 bits (816), Expect = 2e-91 Identities = 195/481 (40%), Positives = 265/481 (55%), Gaps = 12/481 (2%) Query: 10 RQLFVDGEWRPPAQGRRLPVVNPTTEAHIGEIPAGTAEDVDAAVAAARAALKRNRGRDWA 69 R F+DG P G R+ +P + AG A DVD AV +A A + W+ Sbjct: 21 RDHFIDGRAVAPGAGGRMESFDPGRGTAFDDFAAGDAADVDHAVTSAVAGFEI-----WS 75 Query: 70 RAPGAVRAKYLRAIAAKVIERKPELAKLEALDCGKPYDEAAWDMDDVAGCFEYFADQAEA 129 P A R L A + LA +E +D GK EA D+ A EY+A A+ Sbjct: 76 ATPPARRCAILNEAARLMRHEAEHLAVVECVDSGKTLAEARGDIAGSARLLEYYAGAADK 135 Query: 130 LDKRQNSPVSLPMETFKCHLRREPIGVVGLITPWNYPLLMATWKIAPALAAGCTAVLKPS 189 LD R V+L + LR EP+GV I PWNYP IAPALAAGC+AV+KP+ Sbjct: 136 LDGRS---VNLGNDNAAFTLR-EPVGVTAHIVPWNYPSSTLVRGIAPALAAGCSAVVKPA 191 Query: 190 ELASVTCLELADICKEVGLPSGVLNIVTGLGPDAGAPLSAHPDVDKVAFTGSFETGKKIM 249 E T L +AD+ GLP+GV+N+VTG G AGAPL P V V FTGS TG +M Sbjct: 192 ETTPFTALMIADLLIRAGLPAGVVNVVTGTGIAAGAPLVRDPRVRHVTFTGSVATGVGVM 251 Query: 250 ASAAPMVKPVTLELGGKSPIVVFDDVDIDKAVEWTLFGCFWTNGQICSATSRLLIHTKIA 309 S AP V +TLELGGKSP+V F D ++D VE L+ F GQICSA SRL+IH + Sbjct: 252 QSVAPNVTGLTLELGGKSPLVAFGDANVDAVVEGALWAIFSNAGQICSAGSRLVIHRSLH 311 Query: 310 KKFNERMVAWAKNIKVSDPLEEGCRLGPVVSEGQYEKIKKFISNAKSQGATILTGGVRPA 369 + +++VA A+ ++V L G +G V S +I +S A+++G I+TGG Sbjct: 312 AEVRDKLVARAQRLRVGHGL-RGPDIGAVNSARHLAQIDDHVSRARTRGVEIVTGGEILT 370 Query: 370 HLE--KGFFIEPTIITDITTSMEIWREEVFGPVLCVKEFSTEDEAIELANDTQYGLAGAV 427 +E KG+F PTI+ D+ + + +E+FGPVL ++ F E EA+ LAN T++ LA + Sbjct: 371 DVESGKGWFYAPTILDDLAANDDAVLQEIFGPVLAIQVFEDEAEALALANGTEFALAAGI 430 Query: 428 ISGDRERCQRLSEEIDAGCIWVNCSQPCFCQAPWGGNKRSGFGRELGEGGIDNYLSVKQV 487 + D R++ +DAG + VN + P+GGN++SGFGRE G G+D Y K V Sbjct: 431 YTRDIATALRMARRVDAGQVTVNDYWAGGIELPFGGNRKSGFGREKGLEGLDAYTRSKAV 490 Query: 488 T 488 T Sbjct: 491 T 491 Lambda K H 0.318 0.135 0.422 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: 611 Number of extensions: 22 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: 505 Length of database: 494 Length adjustment: 34 Effective length of query: 471 Effective length of database: 460 Effective search space: 216660 Effective search space used: 216660 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