Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate RR42_RS21760 RR42_RS21760 succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__Cup4G11:RR42_RS21760 Length = 482 Score = 533 bits (1372), Expect = e-156 Identities = 261/478 (54%), Positives = 352/478 (73%), Gaps = 4/478 (0%) Query: 46 LLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISV 105 LLR ++ GRW V +PA+G ++G V G E R A+ AA A +W+ + Sbjct: 9 LLRQQCYIDGRWTDAQRHIDVTNPATGERVGQVPLLGADETRQAIEAANRALPAWRARTA 68 Query: 106 KERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGD 165 KERS+LLRKW++L++ N+D+LA+I+TAE GKP EA+GEI Y+A F+EWF+EE +RVYG+ Sbjct: 69 KERSALLRKWFELLLANQDDLARIMTAEQGKPFAEARGEIGYAASFIEWFAEEGKRVYGE 128 Query: 166 IIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSA 225 I ++R +V K+PVGV + ITPWNFP+AMITRK G ALAAGCT+VVKPA TP +A Sbjct: 129 TIPAPVSNQRIVVTKEPVGVCAAITPWNFPAAMITRKAGPALAAGCTMVVKPASQTPLTA 188 Query: 226 LALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAA 285 LA+ LA +AGIP GV +V+ S A +G L ++PLV K++FTGST G+ L+ A Sbjct: 189 LAMVALAERAGIPAGVLSVVTGS---AAAIGGELSSNPLVRKLTFTGSTEVGRTLMAQTA 245 Query: 286 NSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFV 345 +++K+VSMELGG APFIVF+ A++D AV GA+ SK+RNAGQTCVC+NR V ++D+F Sbjct: 246 STIKKVSMELGGNAPFIVFEDADLDAAVEGAIVSKYRNAGQTCVCANRLYVHSKVYDAFA 305 Query: 346 TKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGG 405 K A+ ++L+VGNG E+G GPLI+ KAV KVE+H+ DA++KGA V+ GGKRH G Sbjct: 306 EKLVAAV-RALKVGNGMEDGVRIGPLIDGKAVTKVEEHITDAISKGARVLQGGKRHALGQ 364 Query: 406 NFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQ 465 +FFEPT+L++VT ML EETFGP+AP+ +F+ E+E VA+AN + GLA YFY++D + Sbjct: 365 SFFEPTVLADVTPGMLVAREETFGPLAPLFRFETEDEVVAMANDTEFGLASYFYARDLGR 424 Query: 466 IWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 +WRV+E+LE GMVGVN GLIS+ PFGGVKQSG+GREGS YGI++YL +KY C G+ Sbjct: 425 VWRVSERLEYGMVGVNTGLISNEVAPFGGVKQSGVGREGSHYGIEDYLVIKYTCMAGI 482 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: 617 Number of extensions: 23 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: 482 Length adjustment: 34 Effective length of query: 489 Effective length of database: 448 Effective search space: 219072 Effective search space used: 219072 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