Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PfGW456L13_3394 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394 Length = 391 Score = 312 bits (800), Expect = 9e-90 Identities = 184/407 (45%), Positives = 253/407 (62%), Gaps = 23/407 (5%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M + +I+DAVRTPIG++ G+L+ VRAD LG++ + L+ R + + VDDVI+G Q Sbjct: 1 MKDIVIVDAVRTPIGKFRGSLSGVRADHLGSLVISRLLER-VDVSPTLVDDVIFGNVTQI 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 GE + N+AR A L AG PV+V G T++R CGSG AV A A+ G A +++AGG E+M Sbjct: 60 GEQSANIARTALLGAGWPVTVAGLTIDRKCGSGEVAVHMAVGAIAAGAADIVVAGGAENM 119 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180 SR P G + EI GW + Q + + S E AE +A ++ +SR Sbjct: 120 SRVPM---------GSNREIHGAAFGW-----MAAQRYELTSQGEAAERMADKWALSRDA 165 Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKG-----PAKIVEHDEHPRGDTTLEQL 235 D FA S +AAAA G E + V + + + PA ++ HDE R DT+ E+L Sbjct: 166 LDDFAFASHQRAAAACDAGYFDNETIPVVVEELREKELSEPAGVLRHDETIRRDTSREKL 225 Query: 236 AKLGTPFRQG-GSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRI 294 + L T FR G +TAGN+S ++DGA ALLL S++ A++ GLKARARVV T G +P + Sbjct: 226 STLKTSFRPDTGRITAGNSSQISDGAAALLLMSADTAKKLGLKARARVVAFTTVGSDPTL 285 Query: 295 MGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIA 354 M GP+ AT+KVL GL++ D+D+ E+NEAFA+ LA ++E G+ ++N NGGAIA Sbjct: 286 MLTGPIAATQKVLAKAGLSINDIDLFEVNEAFASVPLAWMQETGV--PHSKLNVNGGAIA 343 Query: 355 LGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 LGHPLG SGARL+TT L+ELE R GRY L +C G G A IIER+ Sbjct: 344 LGHPLGASGARLMTTMLNELERRGGRYGLQAICCAGGMGTATIIERL 390 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: 441 Number of extensions: 21 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: 401 Length of database: 391 Length adjustment: 31 Effective length of query: 370 Effective length of database: 360 Effective search space: 133200 Effective search space used: 133200 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 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