Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__PV4:5211158 Length = 506 Score = 359 bits (921), Expect = e-103 Identities = 202/477 (42%), Positives = 287/477 (60%), Gaps = 14/477 (2%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 FI G++ V GE F+ SPVDG+ +VA D D A++ A A ++ W + + + Sbjct: 22 FIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIELALDAAHAAKDA--WGKTSVTE 79 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L++ AD + +N+E LA+ ET + GK + ++ + D+P + A I Sbjct: 80 RSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEGSA 139 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 A ++ + EP+GVVG I+PWNFPLLMA WK+ PALA GN +VLKP+E++P++ + Sbjct: 140 ADIDNNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQTPVSILV 199 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 + +L I+ +PAGVLN++ G+G G+ALA+ + L FTGST+I ++ A ES + Sbjct: 200 MVEL-IQDLLPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTGSTQIGHHILKCAAESLIP 258 Query: 263 RIWLEAGGKSPNIVFADAPD-----LQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317 +E GGKSPNI FAD + L A E A FNQGEVCT SR+L+ SI DK Sbjct: 259 ST-VELGGKSPNIYFADVMEQEDEYLDKAVEGMLLAF-FNQGEVCTCPSRVLIAESIYDK 316 Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGG---KRT 374 F+ V+ K K GNPLD T VGA +Q + +LSY+E G +GA++L GG + + Sbjct: 317 FIDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGRNEGAEVLIGGTSCQLS 376 Query: 375 LEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIW 434 +++ G Y+EPTI G N MR+ QEEIFGPV+SV F EA+AIANDT YGL AG+W Sbjct: 377 GDQSSGFYIEPTILKG-HNKMRVFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGAGVW 435 Query: 435 TSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 T D+++A + R ++AG VW+N Y A FGG+K+SG GR+ L Y K Sbjct: 436 TRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLSHYQNTK 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: 648 Number of extensions: 40 Number of successful extensions: 7 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