Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase; EC 1.2.1.77 (characterized)
to candidate WP_011382620.1 AMB_RS00880 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
Query= SwissProt::Q84HH8 (515 letters) >NCBI__GCF_000009985.1:WP_011382620.1 Length = 515 Score = 508 bits (1309), Expect = e-148 Identities = 263/479 (54%), Positives = 331/479 (69%), Gaps = 8/479 (1%) Query: 1 MKLANYVYGQWIEGAGEGAALTDPVTGEALVRVSSDGIDVARALEFARTAGGAALKALTY 60 ++L +Y+ G+W +GAG GA L DPV+GE L S DG+D+A AL FAR GG AL+AL++ Sbjct: 2 IRLQSYLAGRWQDGAGSGAQLKDPVSGEVLATASGDGLDIAEALAFARDRGGPALRALSF 61 Query: 61 EERAAKLAAIAELLQAKRAEYFDISLRNSGATEGDASFDVDGAIFTVKSYARAGKALGAG 120 RA + A+A +L R Y ++L NSG T DA DVDG I T+K YA G+ LG Sbjct: 62 AGRAGLINALAGVLAENRERYNTVALANSGNTAVDAGLDVDGGIGTLKYYASIGRKLGEA 121 Query: 121 RHLKEGGRVALAKTDVFQGQHFLMPLTGVAVFINAFNFPAWGLWEKAAPALLAGVPVFAK 180 R L E L K + F+G+H GVAV INAFNFP+WGLWEKAA +LLAGVP AK Sbjct: 122 RLLAEATDDQLTKDEAFRGRHIWTSNRGVAVHINAFNFPSWGLWEKAAVSLLAGVPFLAK 181 Query: 181 PATPTAWLAQRMVADVVEAGILPPGAISIVCGGARDLLDHVTECDVVSFTGSADTAARMR 240 PAT T+WLA MV DVV AG+LP GA+S++CGG RDL+DH+ DVV+FTGSA+TAA++R Sbjct: 182 PATATSWLAYEMVKDVVAAGVLPEGAMSLLCGGGRDLMDHLKPGDVVAFTGSAETAAQLR 241 Query: 241 THPNVVARSVRINIEADSVNSAILGPDAQPGTPEFDLAVKEIVREMTVKTGQKCTAIRRI 300 ++PNV+A +VR +EADS+N LGPDA P PEF +KE+ REMTVK GQKCTAIRR+ Sbjct: 242 SNPNVIAANVRFAVEADSLNLCALGPDAAPDAPEFAAFIKEVSREMTVKAGQKCTAIRRV 301 Query: 301 LAPAGVSRALADAVSGKLAGCKVGNPRSEGVRVGPLVSKAQQAAAFEGLAKLRQECEVVF 360 L P + A+ LA +G+PR+EGVR+GPLVS+AQ AA+ GL L+ E +VV Sbjct: 302 LVPRSRVDDVVAALKPALAKALMGDPRTEGVRMGPLVSRAQTVAAWAGLEALKAETQVVA 361 Query: 361 GGDPDFEPVDADAAVSAFVQPTLLYCDKGLAARHVHDVEVFGPVATMVPYADTRDAVAIA 420 GG D FV TLL C+ LAAR VH++EVFGPVAT++PY AV +A Sbjct: 362 GGGND--------DGGCFVPATLLLCNDPLAARAVHEIEVFGPVATLMPYDSVEQAVDLA 413 Query: 421 RRGHGSLVASVYSGDAAFLGELVPGIADLHGRVMVVDAAVGANHTGHGNVMPTCLHGGP 479 +G GSL ASV+SGDAAFL VP IA HGRV+VVD++V A+H+GHG VMP C+HGGP Sbjct: 414 HKGGGSLAASVFSGDAAFLAGFVPAIATSHGRVLVVDSSVAASHSGHGVVMPHCIHGGP 472 Lambda K H 0.319 0.135 0.399 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: 724 Number of extensions: 36 Number of successful extensions: 2 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: 515 Length of database: 515 Length adjustment: 35 Effective length of query: 480 Effective length of database: 480 Effective search space: 230400 Effective search space used: 230400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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