Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 535 bits (1378), Expect = e-156 Identities = 264/479 (55%), Positives = 349/479 (72%), Gaps = 3/479 (0%) Query: 45 DLLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEIS 104 +L+ + + G+W+ A+F V +PA G + VAD G E A+ AA+ A +W + Sbjct: 8 NLVETAALIDGQWVRGEASFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALPAWAART 67 Query: 105 VKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYG 164 KER ++LR+W DL++ + D+LA+++T E GKPL EA+GE++Y A F++WF+EEA+R YG Sbjct: 68 AKERGAILRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEEAKRAYG 127 Query: 165 DIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYS 224 I T KR +KQPVGV + I PWNFP AMITRKVG ALAAGCTVVVKPA +TP S Sbjct: 128 HTIPTPMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAETPLS 187 Query: 225 ALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHA 284 ALA+A+LA +AG+P GV N++ + T++ EVG+VLC D V K+SFTGST GK+L Sbjct: 188 ALAIARLATEAGVPAGVLNIV--TTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQC 245 Query: 285 ANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSF 344 A ++K++S+ELGG APFIVFD A+++ AV GA+ASK+RNAGQTCVC+NR +VQ GIHD+F Sbjct: 246 AGTMKKLSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDAF 305 Query: 345 VTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSG 404 + AE + +L+VG G EG GPLINEKA+ KV V+ AV GA V+TGG H G Sbjct: 306 AARLAEKV-AALKVGPGTGEGVQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGDVHGLG 364 Query: 405 GNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPA 464 G+F++PT+L T +M EE FGPVAP++KF+ E EAV +ANA GLA YFYS+D Sbjct: 365 GHFYQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRDVG 424 Query: 465 QIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 + WRVAEQ+E GMVG+NEGLIS+ PFGGVK+SGLGREG+ G+DEYLE KY+C+GG+ Sbjct: 425 RCWRVAEQIEAGMVGINEGLISTEVAPFGGVKESGLGREGASEGLDEYLETKYLCFGGV 483 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: 678 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: 485 Length adjustment: 34 Effective length of query: 489 Effective length of database: 451 Effective search space: 220539 Effective search space used: 220539 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