Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate GFF1188 PGA1_c12030 3-ketoacyl-CoA thiolase FadA
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Phaeo:GFF1188 Length = 403 Score = 249 bits (636), Expect = 1e-70 Identities = 166/425 (39%), Positives = 222/425 (52%), Gaps = 46/425 (10%) Query: 1 MNEALIIDAVRTPIG--RYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCAN 58 M EA I DAVRTP G R G+L V A L A+ L AL R+ L+ AV+DVI+G Sbjct: 1 MTEAYIYDAVRTPRGKGRKDGSLHEVTAARLSAVALNALKDRN-NLEGHAVEDVIWGNVT 59 Query: 59 QAGEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVE 118 Q GE +AR A L + L S+PG ++NR C SGL+AV AA +R +AGGVE Sbjct: 60 QVGEQGACLARTAVLASDLDESIPGVSINRFCASGLEAVNMAANQVRGRAGHAYIAGGVE 119 Query: 119 SMSRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178 SMSR P M A + I N + QG +A+ +A ++ SR Sbjct: 120 SMSRVPMGMDGGAIAVDPAIAI---------ENYFVPQGI-------SADIIATEYGFSR 163 Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKL 238 D DA A+ SQ +A AA + R A IV V I++HDE+ R T ++ L L Sbjct: 164 DDADAMAMESQRRAKAAWDDNRFAGSIVPVRDING---LTILDHDEYMRPGTDMQSLGGL 220 Query: 239 GTPFRQGGSVT----------------------AGNASGVNDGACALLLASSEAAQRHGL 276 F+ G AGN+SG+ DGA A+L+ E + GL Sbjct: 221 NPAFQMMGEQMPGFDKIAMLKYPHLERINHIHHAGNSSGIVDGAAAVLIGDKEFGEAMGL 280 Query: 277 KARARVVGMATAGVEPRIMGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRE 336 K RAR+ A G +P IM GPVP T K+L G+A+ D+D+ E+NEAFA+ + + Sbjct: 281 KPRARIKATAKIGTDPTIMLTGPVPVTEKILRDNGMAIGDIDLFEVNEAFASVVMRFEQA 340 Query: 337 LGLADDDERVNPNGGAIALGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIAL 396 G+ D ++VN NGG+IA+GHPLG +GA ++ L ELE L T+CIG G G A Sbjct: 341 FGV--DHDKVNVNGGSIAMGHPLGATGAMILGALLDELERSDRETGLATLCIGSGMGAAT 398 Query: 397 IIERI 401 IIER+ Sbjct: 399 IIERV 403 Lambda K H 0.319 0.134 0.384 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: 431 Number of extensions: 23 Number of successful extensions: 5 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: 401 Length of database: 403 Length adjustment: 31 Effective length of query: 370 Effective length of database: 372 Effective search space: 137640 Effective search space used: 137640 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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