Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_033099889.1 JG50_RS0104290 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000763315.1:WP_033099889.1 Length = 474 Score = 493 bits (1269), Expect = e-144 Identities = 249/471 (52%), Positives = 332/471 (70%), Gaps = 5/471 (1%) Query: 52 FVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKERSSL 111 ++ GRW+ V +PA+ +G+V + G EA+ AV AAY AF W + +ER L Sbjct: 7 YINGRWIDAINKIDVINPATKKIIGSVPNGGATEAKMAVEAAYPAFQKWSKQPAEERGKL 66 Query: 112 LRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIYTSA 171 L KW+DL+ ++KDELA+I+T E GKPL+EA+GEI Y+ F+ W++EE +R+YG+ I S+ Sbjct: 67 LMKWFDLIEKHKDELAEIMTLEQGKPLQEARGEITYANSFISWYAEEGKRIYGETIPASS 126 Query: 172 KDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALALAQL 231 DKR V KQPVGV + ITPWNFP+AMITRKV ALAAGCTVV+KP+E+TP++AL LA+L Sbjct: 127 PDKRIFVQKQPVGVIAAITPWNFPAAMITRKVAPALAAGCTVVLKPSEETPFTALKLAEL 186 Query: 232 ANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSVKRV 291 A+QAGIP GV NV+ A+ + D V K++FTGST GKIL+ AA++VK++ Sbjct: 187 ADQAGIPNGVLNVV---TGDAESIANAWQKDSRVRKLTFTGSTPVGKILMRGAADTVKKI 243 Query: 292 SMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKFAEA 351 S+ELGG AP IV A++D+AV GA+ASKFRNAGQTC+C+NR L I + F K AE Sbjct: 244 SLELGGHAPLIVTAQADIDKAVDGAIASKFRNAGQTCICTNRILADESIAEEFTVKLAEK 303 Query: 352 MKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKR-HQSGGNFFEP 410 K L+VGNG EE T GPLINE+AV+KV KH+ DA KG V+TGG R G F EP Sbjct: 304 AAK-LKVGNGLEESTDIGPLINEEAVKKVIKHIEDAKQKGGRVLTGGNRLTNQKGYFIEP 362 Query: 411 TLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIWRVA 470 T+++N DMLC+ EETFGP+ PV F +EA+ AN + GLA Y Y+++ + ++ Sbjct: 363 TVIANAKDDMLCMVEETFGPLIPVATFKTIDEAIERANNSSYGLAAYVYTENLREAVYIS 422 Query: 471 EQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521 E LE G+VGVN+G S+ + PFGG K+SGLGREGS+YGI+E+LE+KY+ G Sbjct: 423 EALEYGIVGVNDGAPSAAQAPFGGFKESGLGREGSRYGIEEFLEIKYISLG 473 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: 632 Number of extensions: 24 Number of successful extensions: 4 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: 474 Length adjustment: 34 Effective length of query: 489 Effective length of database: 440 Effective search space: 215160 Effective search space used: 215160 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 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