Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate Ac3H11_178 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_178 Length = 394 Score = 321 bits (823), Expect = 2e-92 Identities = 183/402 (45%), Positives = 245/402 (60%), Gaps = 12/402 (2%) Query: 2 REAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAG 61 RE + +RT IG +GG+L + DL A+ ++E L R ++ + + V+ G Sbjct: 3 REVVVVSAVRTAIGTFGGSLKDIAPTDLGALVVKESLAR-ASVEGKDVGHVVFGHVVNTE 61 Query: 62 EDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMS 121 + ++R+A + G + +NRLCGSGL A+ AA+AI+ GD D+ I G E MS Sbjct: 62 PKDMYLSRVAAINGGCAEGTPAFNVNRLCGSGLQAIVSAAQAIQLGDADVTIGAGAEVMS 121 Query: 122 RAPFV-MGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180 RAPF + A +M D IG + F T M TAEN+A ISRED Sbjct: 122 RAPFASLNMRWGARMGDTKMVDMMIG------ALHDPFHTIHMGVTAENIAAKWGISRED 175 Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240 QD A+ S R +A ++G ++IVPV LK+KKG V + DEH RP TL+ LK Sbjct: 176 QDKLAVESHNRAERATAAGYFKDQIVPVTLKSKKGDV-QYATDEHFRPGATLDDFAKLKP 234 Query: 241 PF-RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGP 299 F + NG +TAGNASG+ND AAA+++ A A+G P AR+VA A AGV+P+ MG+GP Sbjct: 235 VFVKENGTVTAGNASGINDAAAAVVLMDAAAAKARGAKPLARLVAYAHAGVDPKYMGIGP 294 Query: 300 VPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPL 359 VPAT+ L++AGL++ D+DVIE NEAFAAQA V ++LGL D VNPNG I+LGHP+ Sbjct: 295 VPATQLALKKAGLTVADLDVIEANEAFAAQACAVTKDLGL--DPAKVNPNGSGISLGHPI 352 Query: 360 GMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 G +GA + + A HEL R GRYAL TMCIG GQGIA I ER+ Sbjct: 353 GATGALITVKAIHELQRVQGRYALVTMCIGGGQGIAAIFERL 394 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: 385 Number of extensions: 16 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: 394 Length adjustment: 31 Effective length of query: 370 Effective length of database: 363 Effective search space: 134310 Effective search space used: 134310 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