Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate PfGW456L13_2419 Aldehyde dehydrogenase (EC 1.2.1.3), PaaZ
Query= BRENDA::Q13WK4 (531 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2419 Length = 689 Score = 389 bits (999), Expect = e-112 Identities = 224/521 (42%), Positives = 315/521 (60%), Gaps = 12/521 (2%) Query: 5 LKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRALTYAQ 64 L++ +AG+WI GA + L + G + R E D A A R G + L AL + Q Sbjct: 12 LQSFIAGRWIGQHGAQV-LRSAIDGHEIARTHEERPDFAEAIEHGRRQGISGLMALDFQQ 70 Query: 65 RAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGA-SLGEVH 123 RA RL + L ++ YAI+ +SG TR DS +DI+GG TL YA LG+ L + Sbjct: 71 RAQRLKALALYLSERKEQLYAISH-HSGATRADSWIDIEGGNSTLFTYASLGSRELPSGN 129 Query: 124 ALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVKP 183 + +G A LSK +F+ H+L P G+A+ INAFNFP WG+ EK AP+ L+G+P IVKP Sbjct: 130 IVHEGPAMQLSKMGTFAGTHILVPRGGLAVHINAFNFPIWGMLEKFAPSFLAGMPCIVKP 189 Query: 184 ATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAATLRA 243 A+AT++LT+ +V + ++G+LP G+L +I GS+ LLD+++ DVV+FTGSADTAA LR Sbjct: 190 ASATSYLTEAVVRLMDESGLLPAGSLQLIIGSTGDLLDRLQGQDVVTFTGSADTAAKLRV 249 Query: 244 HPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIRRAF 303 +P ++ N EADSLN AIL D TPD F+LFIKEV REMT K+GQKCTAIRRA Sbjct: 250 NPNLIRNSVPFNAEADSLNCAILAPDVTPDDEEFELFIKEVAREMTTKAGQKCTAIRRAI 309 Query: 304 VPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVLAYD 363 VP ++ V L+ +LAK+ VG+P + VRMG+L S +Q ++V + +L + + + + Sbjct: 310 VPAKHIDAVATRLRDRLAKVVVGDPSVEGVRMGALASHDQQKDVAERLESLLQSSDMLFG 369 Query: 364 S-SAVPLIDADANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNALPE 422 + + + A AP L DP HD+E FGPV+++ Y + L E Sbjct: 370 ARDGFEPRGENVDKGAFFAPTLLQARDPHAEGGAHDIEAFGPVSTLMAY------DDLDE 423 Query: 423 AHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVMPM 482 A+ALA RG+GSLVAS+ + D + A HGR+ + TGHG+ +P Sbjct: 424 --ALALAARGKGSLVASLVTKDPQIAAKAIPVAAAWHGRLLVLDRHSAGESTGHGSPLPQ 481 Query: 483 SLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTLT 523 HGGPGRAGGGEELGGLRA+ Y +R+A+Q + + +T Sbjct: 482 LKHGGPGRAGGGEELGGLRAVKHYLQRAAVQGSPTMLAAVT 522 Lambda K H 0.318 0.132 0.379 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: 764 Number of extensions: 33 Number of successful extensions: 6 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: 531 Length of database: 689 Length adjustment: 37 Effective length of query: 494 Effective length of database: 652 Effective search space: 322088 Effective search space used: 322088 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: 53 (25.0 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