Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF2918 PGA1_c29650 succinate-semialdehyde dehdyrogenase GabD
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__Phaeo:GFF2918 Length = 491 Score = 511 bits (1316), Expect = e-149 Identities = 262/497 (52%), Positives = 352/497 (70%), Gaps = 19/497 (3%) Query: 23 LLREPAGAQRRSYVGGPADLHADLLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCG 82 LL +P+ + R+Y+GG +FV G TF V +PA G + VAD Sbjct: 11 LLTDPSLLEPRAYIGG------------AFVDG----ADGTFAVKNPARGDVIANVADVS 54 Query: 83 VPEARAAVRAAYDAFSSWKEISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQ 142 + A+ A A W + + KER+++LRKW+DLM++N+++LA I+TAE GKPL E++ Sbjct: 55 RSQVAGAIAQAEVAQKDWAKWTGKERANVLRKWFDLMMENQEDLAVILTAEMGKPLAESR 114 Query: 143 GEILYSAFFLEWFSEEARRVYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRK 202 GEI Y A F+E+F+EEA+R+YG+ I +DKR VLKQP+GVA+ ITPWNFP+AMITRK Sbjct: 115 GEIGYGASFIEFFAEEAKRIYGETIPGHQRDKRITVLKQPIGVAASITPWNFPNAMITRK 174 Query: 203 VGAALAAGCTVVVKPAEDTPYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTD 262 G ALAAGC V +PAE TP SA ALA LA++AGIP GV+NV+ S A E G+ C + Sbjct: 175 AGPALAAGCAFVARPAELTPLSATALAVLADRAGIPAGVFNVVTSS--NASETGKEFCEN 232 Query: 263 PLVSKISFTGSTATGKILLHHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFR 322 V K++FTGST G+IL+ AA++V + SMELGG APFIVFD A++D AV GA+ KFR Sbjct: 233 NAVRKLTFTGSTEVGRILMRQAADTVMKCSMELGGNAPFIVFDDADLDAAVEGAIMCKFR 292 Query: 323 NAGQTCVCSNRFLVQRGIHDSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEK 382 N GQTCVC+NR VQ G++D+F K EA+ K + VG+G EGT GPLINEKAVEKV+ Sbjct: 293 NNGQTCVCANRIYVQAGVYDAFAAKLKEAVAK-MTVGDGLAEGTQFGPLINEKAVEKVQA 351 Query: 383 HVNDAVAKGATVVTGGKRHQSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEE 442 H+ DA KGA V+ GG + GG FFEPT+++ T+DM+ +ETFGP+AP+ KF+ E++ Sbjct: 352 HIADAKEKGAEVILGGNPSELGGTFFEPTIITGATQDMVFSQDETFGPMAPLFKFETEDD 411 Query: 443 AVAIANAADVGLAGYFYSQDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGR 502 + +AN GLA YFY++D +++++VAE LE G+VGVN G+IS+ PFGGVKQSGLGR Sbjct: 412 VIEMANDTIFGLASYFYAKDLSRVYKVAEALEYGIVGVNTGIISTELAPFGGVKQSGLGR 471 Query: 503 EGSKYGIDEYLEVKYVC 519 EGS +GI++YLE+KY+C Sbjct: 472 EGSHHGIEDYLEMKYIC 488 Lambda K H 0.318 0.135 0.400 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: 626 Number of extensions: 24 Number of successful extensions: 3 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: 523 Length of database: 491 Length adjustment: 34 Effective length of query: 489 Effective length of database: 457 Effective search space: 223473 Effective search space used: 223473 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 (21.7 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