Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_041950131.1 VEIS_RS17310 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000015565.1:WP_041950131.1 Length = 496 Score = 365 bits (937), Expect = e-105 Identities = 200/480 (41%), Positives = 288/480 (60%), Gaps = 6/480 (1%) Query: 19 EGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQL 78 +GR I+G++ DA E SP G+ +A A + DA RA+ AR F+ G W L Sbjct: 11 QGRLLIDGQWCDAADARRLERRSPAHGQLVAVYAEAGVPDAQRAIGAARQAFDKGPWPLL 70 Query: 79 APAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKV 138 A+R L AD + LA +E+L+ GKP+ S + +I GAA + A + Sbjct: 71 KGAERARILRHVADGILARRHALARMESLENGKPLAQSLA-EIEGAADLWQYAASLARNL 129 Query: 139 Y-DEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSP 197 + D L LV REP+GVVG I PWNFP L+ KL ALA G + V+KP+E + Sbjct: 130 HGDSYNTLGAATLALVLREPIGVVGIITPWNFPFLIVSQKLPFALAAGCTAVVKPAEVTS 189 Query: 198 LTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAG 257 T + + ++ +EAGIPAGV+N+L G G VG+A+ H DVD L FTGST + KQ + + Sbjct: 190 GTTVMLGEILLEAGIPAGVVNILVGQGAVVGEAMVSHPDVDMLSFTGSTAVGKQAVARSA 249 Query: 258 ESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317 + +K++ LE GGK+P IVFAD D +AA +AA I FN G+ C +GSR+LV+ ++ DK Sbjct: 250 -ATLKKVALELGGKNPQIVFADC-DWEAAVDAAVYGIFFNAGQCCNSGSRILVQDAVADK 307 Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377 F V+ + + G+P D +T VGA+ +Q++T+L+++E + GA + GG R + Sbjct: 308 FAEAVIARSRQVRVGDPFDERTQVGAITTERQLHTILAHVEGARQAGATVALGGARL--D 365 Query: 378 TGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSD 437 G Y+EPT+ GVT M IA++E+FGPVLS++ F T +EAV +AN T YGL+A +W+ D Sbjct: 366 RPGLYMEPTVLTGVTRDMAIARQEVFGPVLSMLRFGTLDEAVDLANSTLYGLSAAVWSQD 425 Query: 438 ISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497 I+ AR + AG+VWVN + G PFGG+++SG GR+ A E YTE K + L Sbjct: 426 INTCITAARRIEAGTVWVNTFLEGHAELPFGGYRESGIGRELGRFAAEDYTETKTVHLHL 485 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: 593 Number of extensions: 20 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 497 Length of database: 496 Length adjustment: 34 Effective length of query: 463 Effective length of database: 462 Effective search space: 213906 Effective search space used: 213906 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