Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate HSERO_RS09465 HSERO_RS09465 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__HerbieS:HSERO_RS09465 Length = 506 Score = 376 bits (966), Expect = e-109 Identities = 214/479 (44%), Positives = 287/479 (59%), Gaps = 18/479 (3%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 FI G++ V GE FE +SPV GR +VA D A++ A A S W + +P + Sbjct: 22 FIGGKFVPPVKGEYFENISPVIGRAFCEVARSSAEDVELALDAAHAAKKS--WGKTSPTE 79 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L++ AD + N+E LA ETLD GKPI ++ + DIP A + A A+ + Sbjct: 80 RANMLLKIADRMEANLELLATAETLDNGKPIRETMAADIPLAIDHFRYFAAAVRTQEGSI 139 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 P +D EP+GVVG I+PWNFP+LMA WKL PALA GN VVLKP+E++P + + Sbjct: 140 CPIDNDTYAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQTPASIMV 199 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 + +L + IP GV+N++ G+G GK LA + + + FTG T + +M YA + N+ Sbjct: 200 LIELIADL-IPPGVVNIVQGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYASQ-NLI 257 Query: 263 RIWLEAGGKSPNIVFADAPD-----LQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317 + LE GGKSPNI FAD D A E A A NQGEVCT SR+LV+ SI ++ Sbjct: 258 PVTLELGGKSPNIFFADVLDKDDDFFDKALEGFA-MFALNQGEVCTCPSRVLVQESIYER 316 Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377 F+ ++ + K GNPLD T +GA +Q+ +LSYI+ G ++GAK+LAGG R EE Sbjct: 317 FIERALKRVAAIKQGNPLDKSTMIGAQASQEQLEKILSYIDIGKQEGAKVLAGGGR--EE 374 Query: 378 TGGT-----YVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAG 432 GG YV+PT+F G N MRI QEEIFGPV+SV F EEA+AIANDT YGL AG Sbjct: 375 LGGDLASGYYVKPTVFQG-NNKMRIFQEEIFGPVVSVTTFKDEEEALAIANDTLYGLGAG 433 Query: 433 IWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 +WT D ++A + R ++AG VW N Y A FGG+KQSG GR+ L+ Y + K Sbjct: 434 LWTRDGTRAFRMGREIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQQTK 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: 607 Number of extensions: 27 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