Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_010532097.1 ON01_RS16395 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000224785.1:WP_010532097.1 Length = 506 Score = 355 bits (910), Expect = e-102 Identities = 206/479 (43%), Positives = 284/479 (59%), Gaps = 18/479 (3%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 +I GEY +G+ FE +SPV G+ ++A D AV+ A ++ W+Q + A+ Sbjct: 22 YIGGEYRPPANGKYFENVSPVTGKVFCELARSTKEDVEAAVDAGYAAKDA--WAQTSVAE 79 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L + AD + +N+E LA+ ET D GK + + + DIP A + A AI V Sbjct: 80 RADILNKIADRMEENLESLAVAETWDNGKAVREGLAADIPLAVDHFRYFAGAIRAQEGGV 139 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 + +D + EP+GVVG I+PWNFP+LMA WKL PALA GN VVLKP+E++P +I Sbjct: 140 SQIDNDTVAYHFHEPLGVVGQIIPWNFPILMATWKLAPALAAGNCVVLKPAEQTP-ASIH 198 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 + I+ +PAGVLN++ G+G GK LA + + + FTG T + +M YA E N+ Sbjct: 199 VLLDLIKDLLPAGVLNIVNGFGVEAGKPLASNSRISKIAFTGETTTGRLIMQYASE-NII 257 Query: 263 RIWLEAGGKSPNIVFADAPD-----LQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317 + LE GGKSPNI F D D L A E A NQGEVCT SR LV SI D+ Sbjct: 258 PVTLELGGKSPNIFFPDVMDKDDGFLDKAIEGLV-MFALNQGEVCTCPSRALVHESIYDE 316 Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGG-----K 372 F+ ++ + K G+PLD T +GA +QM + SY++ G ++GA++L GG K Sbjct: 317 FMERAIKRVNEIKIGHPLDTDTMMGAQASLEQMEKIKSYLDIGRQEGAEVLVGGGVNQLK 376 Query: 373 RTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAG 432 +EE G Y+EPTIF G N MRI QEEIFGPVL+V F+ +EA+ IANDT YGL AG Sbjct: 377 GDMEE--GYYIEPTIFKG-DNKMRIFQEEIFGPVLAVTTFNENDEAMKIANDTLYGLGAG 433 Query: 433 IWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 +WT +I+ A++ R + AG VW+N Y A FGG+K+SG GR+ L L+ Y + K Sbjct: 434 VWTRNINTAYRFGRGIEAGRVWMNCYHQYPAHAAFGGYKKSGIGRENHLMMLDHYQQTK 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: 644 Number of extensions: 28 Number of successful extensions: 8 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 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