Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate BPHYT_RS25160 BPHYT_RS25160 NAD/NADP-dependent betaine aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__BFirm:BPHYT_RS25160 Length = 489 Score = 337 bits (865), Expect = 4e-97 Identities = 191/479 (39%), Positives = 278/479 (58%), Gaps = 14/479 (2%) Query: 4 KLLINGELVSG-EGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKV 62 +L I G V GE +PATG+ L + +ASA VD AVR+A EW T Sbjct: 8 RLYIGGGYVDATSGETFDTLDPATGETLASVQQASAADVDRAVRSAKQGQREWAALTAMQ 67 Query: 63 RAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLA 122 R+ L + D++ E A LE+R+ GKP+ +I DV ++AG A + G Sbjct: 68 RSRILRRAVDLLRERNDELAALETRDTGKPIAETLAVDIVTGADVIEYYAGLATAIEGQ- 126 Query: 123 AGEYLEGHTSMI--RRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180 + TS + RR+PLGV A I WNYP+ +A WK APALAAGN ++ KPSEITPL+ Sbjct: 127 --QIPLRPTSFVYTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEITPLS 184 Query: 181 ALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHT-AS 238 ALKLAE+ + PAGV N++ G G+ VG L HP + +S TG + TG+ ++S AS Sbjct: 185 ALKLAEIFTEAGVPAGVFNVVQGDGR-VGAMLAAHPDIEKISFTGGVETGKKVMSMAGAS 243 Query: 239 SIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298 S+K MELGGK+P++VFDDA++E + + ++++GQ CT R++ Q+G+ D Sbjct: 244 SLKEVTMELGGKSPLLVFDDANLERAADIATSANFFSSGQVCTNGTRVFVQRGVLDRFEA 303 Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK---- 354 + V ++ G P D +T GPL S A L +V +E K G +++ GG++ Sbjct: 304 LVLERVKRIRVGKPTDAATNFGPLVSAAQLHKVLGYIESGKQEG-ARLVAGGKRLTEGHF 362 Query: 355 GNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKD 414 G Y PT+ A D IV++E+FGPV+S+ FD+E++ + AN + YGLA+ V T++ Sbjct: 363 AGGQYVEPTVFADCRDDMRIVREEIFGPVMSILVFDDEDEAIARANHTAYGLAAGVVTEN 422 Query: 415 VGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 + RAHRV RL+ G W+NT +EMP GG K SG G++ + LE YT ++ V V+ Sbjct: 423 LARAHRVIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGITTLEHYTRIKSVQVE 481 Lambda K H 0.317 0.134 0.397 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: 577 Number of extensions: 24 Number of successful extensions: 5 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: 474 Length of database: 489 Length adjustment: 34 Effective length of query: 440 Effective length of database: 455 Effective search space: 200200 Effective search space used: 200200 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