Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate SMc02689 SMc02689 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Smeli:SMc02689 Length = 502 Score = 362 bits (930), Expect = e-104 Identities = 205/476 (43%), Positives = 282/476 (59%), Gaps = 12/476 (2%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 FI GE+ + V+G F+ +P+ G L +VA D AD A++ A A W + + + Sbjct: 18 FIGGEWREPVAGRYFDNTTPITGGTLCEVARSDAADIEIALDAAHAAREK--WGRTSTTE 75 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L++ A + N+E LA ET D GKPI ++ + DIP A + A I + Sbjct: 76 RSNILMKIAARMEDNLELLARAETWDNGKPIRETMAADIPLAIDHFRYFAACIRAQEGSI 135 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 HD + EP+GVVG I+PWNFP+LMA WKL PALA GN VVLKP+E++P + + Sbjct: 136 GEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQTPGSILV 195 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 A+L I +P GVLN++ G+G GK LA + + FTG T + +M YA + N+ Sbjct: 196 WAEL-IGDLLPPGVLNIVNGFGLEAGKPLATSPRIAKIAFTGETTTGRLIMQYASQ-NLI 253 Query: 263 RIWLEAGGKSPNIVFADA----PDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318 + LE GGKSPNI FAD D A + A NQGEVCT SR LV+ SI D+F Sbjct: 254 PVTLELGGKSPNIFFADVASEDDDFFDKALEGFAMFALNQGEVCTCPSRALVQESIYDRF 313 Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE- 377 + V+ ++ + GNPLD T +GA ++Q+ +L+YIE G ++GA++L GG R + E Sbjct: 314 MERAVKRVEAIRQGNPLDEATMIGAQASSEQLEKILAYIEIGKEEGAEVLTGGGRNVLEG 373 Query: 378 --TGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435 +GG YV+PT+F G N MRI QEEIFGPV+SV F T EA+ IANDT YGL AG+W+ Sbjct: 374 DLSGGYYVKPTVFHG-HNRMRIFQEEIFGPVVSVTTFKTEAEALEIANDTLYGLGAGVWS 432 Query: 436 SDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 D ++ ++ RA+ AG VW N Y A FGG+KQSG GR+ L+ Y + K Sbjct: 433 RDANRCYRFGRAIEAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTK 488 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: 642 Number of extensions: 30 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: 502 Length adjustment: 34 Effective length of query: 463 Effective length of database: 468 Effective search space: 216684 Effective search space used: 216684 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