Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate BPHYT_RS25160 BPHYT_RS25160 NAD/NADP-dependent betaine aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__BFirm:BPHYT_RS25160 Length = 489 Score = 402 bits (1032), Expect = e-116 Identities = 210/479 (43%), Positives = 298/479 (62%), Gaps = 6/479 (1%) Query: 21 RAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAP 80 R +I G Y DA SGETF+ L P G LA V AD +RAV +A+ W+ L Sbjct: 8 RLYIGGGYVDATSGETFDTLDPATGETLASVQQASAADVDRAVRSAKQ--GQREWAALTA 65 Query: 81 AKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYD 140 +R L R DLLR+ +ELA LET D GKPI ++ ++DI A I + A + Sbjct: 66 MQRSRILRRAVDLLRERNDELAALETRDTGKPIAETLAVDIVTGADVIEYYAGLATAIEG 125 Query: 141 EVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTA 200 + P REP+GV I WN+P+ +ACWK PALA GN+++ KPSE +PL+A Sbjct: 126 QQIPLRPTSFVYTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEITPLSA 185 Query: 201 IRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESN 260 +++A++ EAG+PAGV NV+ G G VG LA H D++ + FTG + K++M AG S+ Sbjct: 186 LKLAEIFTEAGVPAGVFNVVQGDGR-VGAMLAAHPDIEKISFTGGVETGKKVMSMAGASS 244 Query: 261 MKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLP 320 +K + +E GGKSP +VF DA +L+ AA+ A SA F+ G+VCT G+R+ V+R + D+F Sbjct: 245 LKEVTMELGGKSPLLVFDDA-NLERAADIATSANFFSSGQVCTNGTRVFVQRGVLDRFEA 303 Query: 321 MVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE--T 378 +V+E +K + G P D T G LV Q++ VL YIE+G ++GA+L+AGGKR E Sbjct: 304 LVLERVKRIRVGKPTDAATNFGPLVSAAQLHKVLGYIESGKQEGARLVAGGKRLTEGHFA 363 Query: 379 GGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDI 438 GG YVEPT+F + MRI +EEIFGPV+S++ FD +EA+A AN T YGLAAG+ T ++ Sbjct: 364 GGQYVEPTVFADCRDDMRIVREEIFGPVMSILVFDDEDEAIARANHTAYGLAAGVVTENL 423 Query: 439 SKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497 ++AH+ + AG W+N + P GG+KQSG GR+ + LE YT +K+ ++L Sbjct: 424 ARAHRVIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGITTLEHYTRIKSVQVEL 482 Lambda K H 0.316 0.132 0.390 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: 654 Number of extensions: 35 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: 497 Length of database: 489 Length adjustment: 34 Effective length of query: 463 Effective length of database: 455 Effective search space: 210665 Effective search space used: 210665 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 (21.6 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