Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_067906566.1 AQZ52_RS03795 acetyl-CoA C-acyltransferase family protein
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_001519075.1:WP_067906566.1 Length = 392 Score = 317 bits (813), Expect = 3e-91 Identities = 179/402 (44%), Positives = 250/402 (62%), Gaps = 11/402 (2%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 M + FI G RT IG +GG+L+S R DL I ++E + R + A+ +++V++G Sbjct: 1 MTDIFIVSGARTAIGTFGGSLASFRPADLGTIVIKEAIAR-AGISADKVENVVIGTVVPT 59 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 + V+R+A + AG+P +NRLCGSGL A+ AA+ I G+ + + GG E M Sbjct: 60 QPKDAYVSRVAAVNAGVPIESPAMNVNRLCGSGLQAIVSAAQGIALGEQQIAVGGGCEVM 119 Query: 121 SRAPFVMGKAASAFSRQAE-MFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRE 179 S AP ++ A + + + D +G + F M TAENVAE +I+RE Sbjct: 120 SNAPHMVLTARNGQKMGDQVLMDAMLG------ALHDPFENIHMGVTAENVAERHQITRE 173 Query: 180 DQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLK 239 QD+ A+ S +R A A ++G E+IVPV +K +KGV T DEH R + ++E + LK Sbjct: 174 AQDALAVESHKRAAAATAAGYFKEQIVPVEIKTRKGV-TVFDTDEHFRADASVEAMATLK 232 Query: 240 APFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGP 299 F+ +G +TAGNASG+NDGA A+++AS + A GL P A+I+A AGVEP +MGLGP Sbjct: 233 PVFKKDGTVTAGNASGINDGAGAVVLASGEAVAEHGLKPIAKILAWGHAGVEPNVMGLGP 292 Query: 300 VPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPL 359 V A L+RAGL++ +DVIE NEAFAAQA GV +ELG D NPNG I+LGHP+ Sbjct: 293 VKAVPVALKRAGLTLDQIDVIESNEAFAAQACGVAKELGF--DPAKTNPNGSGISLGHPI 350 Query: 360 GMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 G +GA L + A++EL R G+Y L TMCIG GQGIAM++ERV Sbjct: 351 GATGAILTIKAAYELQRTGGQYGLITMCIGGGQGIAMVIERV 392 Lambda K H 0.319 0.135 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: 415 Number of extensions: 17 Number of successful extensions: 4 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: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 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 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