Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase; EC 1.2.1.77 (characterized)
to candidate WP_058857816.1 AS188_RS04315 aldehyde dehydrogenase family protein
Query= SwissProt::Q84HH8 (515 letters) >NCBI__GCF_001482365.1:WP_058857816.1 Length = 491 Score = 112 bits (281), Expect = 2e-29 Identities = 124/438 (28%), Positives = 181/438 (41%), Gaps = 37/438 (8%) Query: 5 NYVYGQWIEGAG-EGAALTDPVTGEALVRV-SSDGIDVARALEFARTAGGAALKALTYEE 62 +++ G ++ G + + DP T E V ++ D+ RA+ A A A A T E Sbjct: 23 HFIDGAYLASTGAQRNDVVDPATEEVWASVPNATEEDLDRAVGAAERAF-AGWAARTPAE 81 Query: 63 RAAKLAAIAELLQAKRAEYFDISLRNSGATEGDASFDVDGAIFTVKSYARAGKALGAGRH 122 RA L AE ++ +R + R +G + A + +A +A Sbjct: 82 RAQVLLRAAEEIETRREPMALTNTRENGTPLAETRGAAANAAGIFRYFAPWLEAEDVRPF 141 Query: 123 LKEGGRVALAKTDVFQGQHFLMPLTGVAVFINAFNFPAWGLWEKAAPALLAGVPVFAKPA 182 G + + V GV I +NFP + K APALLAG V KPA Sbjct: 142 PNGAGETVVHENPV-----------GVCALIAPWNFPINLVVAKLAPALLAGCTVVIKPA 190 Query: 183 TPTAWLAQRMVADVVEAGILPPGAISIVCGGAR--DLLDHVTECDVVSFTGSADTAARMR 240 +PT L+ R V D + A +P G +++V G R D L V+FTG R+ Sbjct: 191 SPTP-LSVRFVVDALTAAGVPAGVVNLVTGNGRMGDRLVRHPAVRKVAFTGCTPVGRRIA 249 Query: 241 THPNVVARSVRINIEADSVNSAILGPDAQPGTPEFDLAVKEIVREMTVKTGQKCTAIRRI 300 + V +E +SAI+ PDA + + ++R TGQ C RI Sbjct: 250 AACGEQLKPV--TLELGGKSSAIVLPDA-----DLEHMSSVLLRSCLRNTGQTCYISTRI 302 Query: 301 LAPAGVSRALADAVSGKLAGCKVGNPRSEGVRVGPLVSKAQQAAAFEGLAKLRQE-CEVV 359 L P + + V +A G+P EG GP+ ++AQ L R E VV Sbjct: 303 LDPESRYDEVVEMVGATVAAAPQGDPLEEGTVFGPMANRAQYDVVMGYLETARAEGARVV 362 Query: 360 FGGDPDFEPVDADAAVSAFVQPTLL--YCDKGLAARHVHDVEVFGPVATMVPYADTRDAV 417 GG AD +V PT+L + AR E+FGPV T++ Y D +AV Sbjct: 363 TGGG------RADRETGFYVAPTVLADVTPEMTVARE----EIFGPVITVLRYRDVDEAV 412 Query: 418 AIARRGHGSLVASVYSGD 435 A+A L V+S D Sbjct: 413 ALANNTPFGLGGIVFSAD 430 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: 604 Number of extensions: 31 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: 515 Length of database: 491 Length adjustment: 34 Effective length of query: 481 Effective length of database: 457 Effective search space: 219817 Effective search space used: 219817 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 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