Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Pf6N2E2_4979 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4979 Length = 506 Score = 345 bits (886), Expect = 2e-99 Identities = 200/477 (41%), Positives = 280/477 (58%), Gaps = 14/477 (2%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 +I GE+ V G+ F SPV+G+ +A+ D +A++ A A ++ W + Sbjct: 22 YIGGEFVAPVKGQYFTNTSPVNGQPIAEFPRSTAEDIEKALDAAHAAADA--WGATSAQA 79 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L++ AD + N+E LA+ E+ D GK + ++ + DIP AA + A + Sbjct: 80 RSLILLKIADRIEANLETLAITESWDNGKAVRETLNADIPLAADHFRYFAGCLRAQEGAA 139 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 A + + EP+GVVG I+PWNFPLLMA WKL PALA GN VVLKP+E++PL Sbjct: 140 AEIDGNTVAYHIHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCVVLKPAEQTPLGICV 199 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 + +L + +P GVLNV+ G+G G+ALA + + FTGST + +M A E N+ Sbjct: 200 LMELIGDL-LPPGVLNVVQGFGKEAGEALATSKRIAKIAFTGSTPVGSHIMKCAAE-NII 257 Query: 263 RIWLEAGGKSPNIVFADAPD-----LQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317 +E GGKSPNI F D ++ AAE A FNQGEVCT SR LV+ SI D+ Sbjct: 258 PSTVELGGKSPNIFFEDIMQAEPSFIEKAAEGLVLAF-FNQGEVCTCPSRALVQESIYDE 316 Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377 F+ +V++ + K G+PLD T VGA QQ + +LSY+E +GA+LL GGK E Sbjct: 317 FMQVVMKKVLQIKRGDPLDTDTMVGAQASEQQFDKILSYLEIAKGEGAELLTGGKVEKLE 376 Query: 378 TG---GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIW 434 G Y++PT+ G TN MR+ QEEIFGPV+S+ F EA+AIANDT +GL AG+W Sbjct: 377 GNLATGYYIQPTLLKG-TNKMRVFQEEIFGPVVSITTFKDEAEALAIANDTEFGLGAGLW 435 Query: 435 TSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 T DI++A++ RA++AG VW N Y A FGG+K+SG GR+ L+ Y + K Sbjct: 436 TRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHYQQTK 492 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: 638 Number of extensions: 39 Number of successful extensions: 6 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: 506 Length adjustment: 34 Effective length of query: 463 Effective length of database: 472 Effective search space: 218536 Effective search space used: 218536 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