Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_041098592.1 SUTH_RS08615 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000828635.1:WP_041098592.1 Length = 480 Score = 545 bits (1404), Expect = e-159 Identities = 270/480 (56%), Positives = 353/480 (73%), Gaps = 5/480 (1%) Query: 45 DLLRGDSFVGGRWLP-TPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 +LLR + G WL T AT + +PA+G +G+V G E R A+ AA+ AF W+ Sbjct: 5 ELLRNACLINGEWLAATGATLDIRNPATGEAVGSVPGFGAAETRRAIDAAHAAFHPWRAK 64 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + ER+ +LR+W++LM++N+++LA+++T E GKPL EA+GEI Y+A F+EWF+EEARR+Y Sbjct: 65 TAAERAKILRRWFELMMENQEDLARLMTQEQGKPLAEARGEIAYAASFIEWFAEEARRIY 124 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 GD+I + D+R +VLKQPVGV + ITPWNFP+AMITRKV ALAAGCT+VVKPAE TP Sbjct: 125 GDVIPSPLADRRLIVLKQPVGVCAAITPWNFPAAMITRKVAPALAAGCTMVVKPAEQTPL 184 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 SALALA L QAG+PPGV NV+ + +G L ++P V K+SFTGST G++L+ Sbjct: 185 SALALAWLGQQAGLPPGVLNVV---TGEPVAIGGELTSNPKVLKLSFTGSTEIGRLLMGQ 241 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 A ++K++S+ELGG APFIVFD A++D AVAGAM SK+RN GQTCVC+NRFLVQ G+HD+ Sbjct: 242 CAPTIKKMSLELGGNAPFIVFDDADLDAAVAGAMLSKYRNTGQTCVCTNRFLVQEGVHDA 301 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F + A A+ L+VG G EEG TQGPLI+ + KVE+ + DA+AKGA V+ GGKRH Sbjct: 302 FAQRLAAAV-AGLKVGYGLEEGVTQGPLIDGAGLAKVEELLADALAKGARVLCGGKRHAK 360 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 GG FFEPT+L+ T M EE FGPVAP+ F E +A+ +AN + GLA YF+S+D Sbjct: 361 GGTFFEPTVLAGATPAMRLAREEIFGPVAPIFSFKDEADAIRMANDTEFGLAAYFFSRDI 420 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 A+ WRV E L+ GMVG+N G+IS+ PFGGVKQSGLGREGSKYGI+EYLE+KY+ GL Sbjct: 421 ARAWRVGEALDYGMVGINSGMISNEVAPFGGVKQSGLGREGSKYGIEEYLEIKYLAMAGL 480 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: 668 Number of extensions: 26 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: 480 Length adjustment: 34 Effective length of query: 489 Effective length of database: 446 Effective search space: 218094 Effective search space used: 218094 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 09 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