Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate CCNA_00075 CCNA_00075 3-ketoacyl-CoA thiolase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Caulo:CCNA_00075 Length = 401 Score = 260 bits (664), Expect = 6e-74 Identities = 168/423 (39%), Positives = 230/423 (54%), Gaps = 44/423 (10%) Query: 1 MNEALIIDAVRTPIGRYA--GALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCAN 58 M +A I DAVRTP G+ G+L A L L+AL R+ LD S VDDV+ GC + Sbjct: 1 MADAYIFDAVRTPRGKGKKDGSLHETTALSLATQVLEALRDRNG-LDTSKVDDVVLGCVS 59 Query: 59 QAGEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVE 118 GE ++AR A L A SV G +NR C SGL+AV AA + GEAGL + GGVE Sbjct: 60 PVGEQGSDIARTAVLTADYAESVAGVQINRFCASGLEAVNMAAAKVASGEAGLAIGGGVE 119 Query: 119 SMSRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178 SMSR P G + T F QG +A+ +A + SR Sbjct: 120 SMSRVP---------MGSDGGAWPTDPSSAFKTYFAPQGV-------SADLIATLYGFSR 163 Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKL 238 D DA+A+ SQ +AAAA A+ R K ++ V+ + G +++HDE RG TT++ LA L Sbjct: 164 DDVDAYAVESQKRAAAAWADNRFKKSVIPVK--DQLG-LTLLDHDETVRGSTTMQTLASL 220 Query: 239 GTPFRQGGSVT--------------------AGNASGVNDGACALLLASSEAAQRHGLKA 278 F G + AGN+SG+ DGA +L+ + E + GLKA Sbjct: 221 NPSFTGMGEMAFDAVVTQRYPQVERVNHVHHAGNSSGIVDGAAGVLIGTKEMGEALGLKA 280 Query: 279 RARVVGMATAGVEPRIMGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELG 338 RAR+ G A+ G EP IM GP + K+L+ G+ + D+D+ ELNEAFA+ L +++ L Sbjct: 281 RARIKGAASIGSEPSIMLTGPALVSEKLLKKLGMEVKDIDLYELNEAFASVVLRMMQALD 340 Query: 339 LADDDERVNPNGGAIALGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALII 398 + D ++N NGGAIA+GHPLG +GA ++ T L ELE AL T+C+G G G A +I Sbjct: 341 IPHD--KMNVNGGAIAMGHPLGATGAMILGTVLDELERSDKETALITLCVGAGMGTATVI 398 Query: 399 ERI 401 ER+ Sbjct: 399 ERV 401 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: 431 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: 401 Length adjustment: 31 Effective length of query: 370 Effective length of database: 370 Effective search space: 136900 Effective search space used: 136900 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