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_089302604.1 CHB84_RS16865 acetyl-CoA acetyltransferase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_900188115.1:WP_089302604.1 Length = 403 Score = 288 bits (738), Expect = 1e-82 Identities = 180/423 (42%), Positives = 242/423 (57%), Gaps = 47/423 (11%) Query: 3 EAFICDGIRTPIGR-YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAG 61 EAFI + IRTP G+ G+L ++ DL + E+ R+P LD IDD+I+G + G Sbjct: 4 EAFIYEAIRTPRGKGKKGSLHGIKPIDLTIGLIEEIKRRHPGLDPAAIDDIIMGIVSPVG 63 Query: 62 EDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMS 121 + + R A + +GLP SV+G +NR C SGL+A+ AA+ + AG LL+AGGVESMS Sbjct: 64 DQGGVLPRAAAIASGLPDSVAGVQLNRFCASGLEAVNQAAQKVLAGWDRLLLAGGVESMS 123 Query: 122 RAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPET--AENVAELLKISRE 179 R P MG T G F++P A + T +P+ A+ +A L SRE Sbjct: 124 RVP--MG--------------TDGGAMFLDP--ATNYDTYFVPQGIGADLIATLEGFSRE 165 Query: 180 DQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLK 239 D D+FA RSQ+R A S G A+ +VPV N VT + HDEH RP TT+E L L Sbjct: 166 DVDAFAARSQERAEAAWSGGYFAKSVVPVTDING---VTVLDHDEHRRPGTTVEDLGKLN 222 Query: 240 APF---------------------RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTP 278 F + N V T GN+SG+ DGA+ +++ EQ GLTP Sbjct: 223 PSFAGIGEMGGFDAVALQKYHNVEKINHVHTGGNSSGIVDGASLVLLGDEQAGKDFGLTP 282 Query: 279 RARIVAMATAGVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELG 338 RAR+ A A G +P +M GP PAT +VL +AGL + D+D+ ELNEAFA+ L ++L Sbjct: 283 RARVAATAVTGSDPTIMLTGPTPATEKVLAKAGLGVDDIDLFELNEAFASVVLKYQKDLN 342 Query: 339 LPDDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMIL 398 +PD+ +N NGGAIA+GHPLG +GA + EL RRN R AL T+CIG G G+A I+ Sbjct: 343 IPDE--KLNVNGGAIAMGHPLGATGAMILGTMVDELERRNARRALVTLCIGGGMGLATII 400 Query: 399 ERV 401 ERV Sbjct: 401 ERV 403 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: 478 Number of extensions: 25 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: 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 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