Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_061532096.1 CAter10_RS02100 acetyl-CoA C-acyltransferase family protein
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_001584165.1:WP_061532096.1 Length = 396 Score = 323 bits (828), Expect = 5e-93 Identities = 197/400 (49%), Positives = 247/400 (61%), Gaps = 10/400 (2%) Query: 3 EALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAGE 62 E +I+ A RT IG Y GAL +LGAI +K AR +D +I+G Sbjct: 6 EVVIVGAARTAIGSYGGALKDFAPGELGAIAVKEAFAR-AGVDPLQAGQIIFGNVIHTEA 64 Query: 63 DNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSR 122 + V+R+ L AG+ TLNRLCGSGL A+ +AA A++ GE + + GGVESMSR Sbjct: 65 RDMYVSRVVGLNAGMGKESTALTLNRLCGSGLQAIITAANAIQLGETDVAVGGGVESMSR 124 Query: 123 APFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRADQD 182 + + + QA A + D + V L FG M TAENVA ++ ISR +QD Sbjct: 125 SMY----ATQAARWGARMGDIKMVDMMVGALSDP-FGAGHMGITAENVAEKYGISREEQD 179 Query: 183 AFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGTPF 242 AFAL SQ +A AAIA G +IV VEI RKG + + DE+P+ D T+E LAKL F Sbjct: 180 AFALESQRRATAAIAAGHFKSQIVPVEIKTRKG-VTLFDTDEYPKADATMESLAKLKPAF 238 Query: 243 R-QGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPVP 301 + +GG+VTAGNASG+NDGA A +L +++AA + GLK ARVV AGV+P IMG GP+P Sbjct: 239 KKEGGTVTAGNASGINDGAAACVLMAADAAAQAGLKPLARVVSYGVAGVDPTIMGTGPIP 298 Query: 302 ATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLGM 361 A + L+ GL L+DM+VIE NEAFAAQ L V + LGL D N NGGAIALGHPLG Sbjct: 299 AVQLALKRAGLHLSDMEVIESNEAFAAQSLGVCKGLGL--DPALTNVNGGAIALGHPLGA 356 Query: 362 SGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 SGA + L+EL RY L TMCIG GQGIALIIERI Sbjct: 357 SGAIIAVKCLYELIRTNKRYGLITMCIGGGQGIALIIERI 396 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: 450 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: 396 Length adjustment: 31 Effective length of query: 370 Effective length of database: 365 Effective search space: 135050 Effective search space used: 135050 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