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_099619682.1 CLH62_RS18535 acetyl-CoA C-acyltransferase FadA
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_002744735.1:WP_099619682.1 Length = 391 Score = 306 bits (784), Expect = 7e-88 Identities = 176/407 (43%), Positives = 246/407 (60%), Gaps = 28/407 (6%) Query: 2 REAFICDGIRTPIGRY-GGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 R+ + D +RTP+GR G +VRA+ L+A + L RNP+LD + ++DVI GC NQ Sbjct: 6 RDVVVVDCVRTPMGRAKNGCFRNVRAETLSAALIEALFERNPKLDPKEVEDVIWGCVNQT 65 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 E NVAR +LL +P + T+NRLCGS + A+ AA+AI G+GD+ + GGVE M Sbjct: 66 KEQGFNVARQISLLTRIPHESAAQTVNRLCGSSMSAIHTAAQAIMTGNGDVFVVGGVEHM 125 Query: 121 SRAPFVMG----KAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKI 176 P G AAS ++ +A ++ M TAE +A++ I Sbjct: 126 GHVPMTEGFDHNPAASKYTAKA---------------------SNMMGLTAEMLAKMHGI 164 Query: 177 SREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLR 236 +R+ QD F RS + +A G EIVP+ ++ G V I+ DE +RP+TT+E L Sbjct: 165 TRKQQDEFGARSHRLAHEATLEGRFNNEIVPIEGHDENGFVKLIEEDETIRPDTTVESLG 224 Query: 237 GLKAPFRA-NGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLM 295 LK F NG +TAG +S + DGAAA+++ S + A A GL P AR+ +MA AG +P +M Sbjct: 225 QLKPAFDPKNGTVTAGTSSQLTDGAAAMVLMSAERAEALGLKPIARVRSMAVAGCDPAIM 284 Query: 296 GLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPD-DAPHVNPNGGAIA 354 G GPVPAT++ L+RAGL + D+D ELNEAFA Q+L VL++L L A VN NGGAIA Sbjct: 285 GYGPVPATKKALKRAGLKVEDIDFWELNEAFAGQSLPVLKDLKLLGVMAEKVNLNGGAIA 344 Query: 355 LGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 LGHPLG SGAR++ + + + G+ + TMCIG+GQGIA + ER+ Sbjct: 345 LGHPLGCSGARISTTLLNVMQAKGGKLGVSTMCIGLGQGIATVWERL 391 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: 400 Number of extensions: 15 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: 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 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