Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011841815.1 RSPH17029_RS13480 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000015985.1:WP_011841815.1 Length = 492 Score = 537 bits (1384), Expect = e-157 Identities = 271/476 (56%), Positives = 346/476 (72%), Gaps = 5/476 (1%) Query: 46 LLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 LL +FV G W+ ATF V +PA G + TV D G E A+ AA +A W Sbjct: 17 LLETRAFVAGEWVDADDGATFEVTNPARGDVICTVPDLGRAETARAIAAAEEAMKEWAAR 76 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + KER+ ++RKW+DLM+ N+D+L I+TAE GKPL EA+GEI Y A F+EWF EEA+R+Y Sbjct: 77 TGKERAQVMRKWFDLMMANQDDLGAILTAEMGKPLAEAKGEIAYGASFIEWFGEEAKRIY 136 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 G+ I +DKR VLKQP+GV ITPWNFP+AMITRK G ALAAGC V +PA +TP Sbjct: 137 GETIPGHMRDKRITVLKQPIGVVGSITPWNFPNAMITRKCGPALAAGCGFVARPAAETPL 196 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 SALALA L +AG+P G+ +VI SR + ++G+ +C +P+V K++FTGST G+ILL Sbjct: 197 SALALAVLGERAGLPKGILSVITSSR--SSDIGKEMCENPIVRKLTFTGSTEVGRILLRQ 254 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 AA+ V + SMELGG APFIVFD A++D AV GAMASKFRN GQTCVC+NR VQ G++D+ Sbjct: 255 AADQVMKCSMELGGNAPFIVFDDADLDAAVQGAMASKFRNNGQTCVCANRIYVQSGVYDA 314 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F K A A+KK L+VG+G EGT GPLINEKAV KVE+H+ D + G V+TGGKRH Sbjct: 315 FAEKLAAAVKK-LKVGDGLVEGTEAGPLINEKAVAKVEEHIRDVLDGGGQVLTGGKRHAL 373 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 GG FFEPT+++ V ++M TEETFGP+AP+ +F+ EEEAV AN GLA YFY++D Sbjct: 374 GGTFFEPTVVTGVKQEMKVSTEETFGPLAPLFRFETEEEAVGYANDTIFGLASYFYARDV 433 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVC 519 +I RV E LE G+VGVN G+IS+ PFGGVKQSGLGREGS++GI++YLE+KY+C Sbjct: 434 GRITRVQEALEYGIVGVNTGIISTEVAPFGGVKQSGLGREGSRHGIEDYLEMKYIC 489 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: 649 Number of extensions: 27 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: 492 Length adjustment: 34 Effective length of query: 489 Effective length of database: 458 Effective search space: 223962 Effective search space used: 223962 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 Apr 10 2024. 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