Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase
Query= BRENDA::Q9S795 (501 letters) >FitnessBrowser__Dyella79:N515DRAFT_2488 Length = 463 Score = 236 bits (602), Expect = 1e-66 Identities = 151/460 (32%), Positives = 228/460 (49%), Gaps = 9/460 (1%) Query: 28 VNPATEEVIGDIPAATTEDVDVAVNAARRALSRNKGKDWAKAPGAVRAKYLRAIAAKVNE 87 +NP T E + P+AT +V A++ A+ W A R K L+ A + E Sbjct: 6 INPYTGETVKTFPSATDAEVTQALDQAQAMFEA-----WKDVGVAARVKVLQKAADLLRE 60 Query: 88 RKTDLAKLEALDCGKPLDEAVWDMDDVAGCFEFYADLAEGLDAKQKAPVSLPMESFKSYV 147 T AK+ L+ GK + EA +++ A E+YAD AE L A +K P + +S+V Sbjct: 61 SHTQYAKVLTLEMGKVIGEAEGEVELCAQILEYYADHAEQLLAPEKLSSRHPSYT-QSWV 119 Query: 148 LKQPLGVVGLITPWNYPLLMAVWKVAPSLAAGCTAILKPSELASVTCLELADICREVGLP 207 P G++ + PWN+P V AP LAAG ILK + + RE GLP Sbjct: 120 EHVPQGILLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLP 179 Query: 208 PGVLNVLTGFGSEAGAPLASHPGVDKIAFTGSFATGSKVMTAAAQLVKPVSMELGGKSPL 267 G L + A + P V +A TGS G+ V A Q +K +MELGG Sbjct: 180 QGGFTNLYATRDQLKA-IIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGADAF 238 Query: 268 IVFDDVDLDKAAEWALFGCFWTNGQICSATSRLLVHESIASEFIEKLVKWSKNIKISDPM 327 +V D DLDKA +WA+ G W GQ+C ++ R++V + I F+EK ++ DPM Sbjct: 239 VVLADADLDKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPM 298 Query: 328 EEGCRLGPVVSKGQYEKILKFISTAKSEGATILHGGSRPEHLEKGFFIEPTIITDVTTSM 387 E L P+ S+G + + K + A + GA + G+ E +G F P +++ V+ Sbjct: 299 EPSTTLAPMSSRGAVDDLKKQLEQAVAHGAKVEVIGA--EVPSRGAFFRPVLLSHVSDDN 356 Query: 388 QIWREEVFGPVLCVKTFASEDEAIELANDSHYGLGAAVISNDTERCDRISEAFEAGIVWI 447 E FGPV V E +AI +ANDS +GLG +V + D + +++ G+V+I Sbjct: 357 PARYWEFFGPVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVYI 416 Query: 448 NCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVKQVTL 487 N P+GGV+RSG+GREL G+ +++ K + + Sbjct: 417 NHPTGVAADLPFGGVRRSGYGRELTGLGIKEFVNHKLIAV 456 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: 523 Number of extensions: 20 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: 463 Length adjustment: 34 Effective length of query: 467 Effective length of database: 429 Effective search space: 200343 Effective search space used: 200343 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