Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_104913141.1 C3B54_RS02765 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_002950575.1:WP_104913141.1 Length = 507 Score = 352 bits (903), Expect = e-101 Identities = 200/476 (42%), Positives = 280/476 (58%), Gaps = 12/476 (2%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 +I G++T V G FE +SPV+G+ ++A D + A++ A A + W + + + Sbjct: 23 WIGGQWTKPVKGNYFEDISPVNGKPFCEIARGTAEDIDAALDAAHAA--APAWGKASTTE 80 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R A L + AD++ NVE LA+ ET D GKPI ++ + DIP AA + A+ + Sbjct: 81 RAAVLNKIADVIDANVEMLAVAETWDNGKPIRETLNADIPLAADHFRYFVAAVRAQDGDF 140 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 D EP+GVVG I+PWNFP+LMA WKL PAL+ GN+VVLKP+E++P + + Sbjct: 141 QEMDGDTTAYHYHEPLGVVGQIIPWNFPILMAAWKLAPALSAGNAVVLKPAEQTPASILV 200 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 +A+L + +P GVLN++ G+G GK LA + + FTG T + ++ YA +N+ Sbjct: 201 LAELIGDI-LPPGVLNIVNGFGAEAGKPLASSPRIRKIAFTGETTTGRLILQYAS-ANII 258 Query: 263 RIWLEAGGKSPNIVFADAP----DLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318 LE GGKSPNI F D D A+ AFNQGEVCT SR L+++S D F Sbjct: 259 PTTLELGGKSPNIFFDDVSQEKDDFYDKAQEGFVLFAFNQGEVCTCPSRALIQKSHYDSF 318 Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL--- 375 L VE K GNPLD T VGA Q+ +LSYI+ G ++GA L+ GG R Sbjct: 319 LGDAVERTKKAIQGNPLDTDTQVGAQASNDQLEKILSYIDIGKQEGATLVCGGDRVDLGG 378 Query: 376 EETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435 + G YVEP IF+G N MR+ QEEIFGPV++V +FD ++A+ IANDT YGL AG+W+ Sbjct: 379 DLADGYYVEPAIFEG-NNKMRLFQEEIFGPVVAVTSFDDYDDAIQIANDTLYGLGAGVWS 437 Query: 436 SDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 + + A++ R ++AG VWVN Y A FGG+K SG GR+ + AL Y + K Sbjct: 438 RNGNTAYRAGRDIQAGRVWVNNYHAYPAGAAFGGYKSSGIGRENNKLALSHYQQTK 493 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: 678 Number of extensions: 39 Number of successful extensions: 9 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: 507 Length adjustment: 34 Effective length of query: 463 Effective length of database: 473 Effective search space: 218999 Effective search space used: 218999 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 24 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