Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF3406 PS417_17430 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__WCS417:GFF3406 Length = 506 Score = 351 bits (900), Expect = e-101 Identities = 198/477 (41%), Positives = 284/477 (59%), Gaps = 14/477 (2%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 +I GE+ +SGE F SPV G +A+ + AD ++A++ A A ++ W + +P Sbjct: 22 YIGGEFVAPLSGEYFTNTSPVTGEVIAEFPRSNAADIDKALDAAHAAADA--WGKTSPQD 79 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L++ AD + +++E LA+ E+ D GK + ++ + D+P AA + A I Sbjct: 80 RSLVLLKIADRIEQHLEVLAVTESWDNGKAVRETLNADVPLAADHFRYFAGCIRAQEGGA 139 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 A EP+GVVG I+PWNFPLLMA WKL PALA GN +VLKP+E++PL+ + Sbjct: 140 AEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVLKPAEQTPLSIMV 199 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 A+L I +P GVLN++ G+G G+ALA + + FTGST I +M +A N+ Sbjct: 200 FAEL-INDLLPPGVLNIVQGFGREAGEALATSKRIAKIAFTGSTPIGAHIM-HAAAENLI 257 Query: 263 RIWLEAGGKSPNIVFADAPD-----LQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317 +E GGKSPNI F D ++ AAE A FNQGEVCT SR LV+ SI D Sbjct: 258 PSTVELGGKSPNIFFEDIMQAEPQFIEKAAEGLVLAF-FNQGEVCTCPSRALVQESIYDD 316 Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377 F+ +V++ + K GNPLD +T VGA QQ + +LSY++ ++GA+LL GG E Sbjct: 317 FMKVVMKKIVKIKRGNPLDTETMVGAQASEQQYDKILSYLKIAQEEGAELLTGGAAERLE 376 Query: 378 ---TGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIW 434 + G Y++PT+ G N MR+ QEEIFGPV+ + F EA+AIAND+ +GL AG+W Sbjct: 377 GDLSSGYYIQPTLLKG-HNKMRVFQEEIFGPVVGITTFKDEAEALAIANDSEFGLGAGLW 435 Query: 435 TSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 T DI++A++ RA++AG VW N Y A FGG+K+SG GR+ L+ Y + K Sbjct: 436 TRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRENHKMMLDHYQQTK 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: 623 Number of extensions: 34 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