Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PP_3754 PP_3754 Beta-ketothiolase BktB
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Putida:PP_3754 Length = 394 Score = 343 bits (879), Expect = 7e-99 Identities = 196/401 (48%), Positives = 260/401 (64%), Gaps = 13/401 (3%) Query: 3 EALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAGE 62 E ++ AVR+ IG + G+L + DL + +A I R L V ++ G Sbjct: 5 EIYVVSAVRSAIGGFGGSLKDLPLADLASAVTRAAIERSG-LAAEQVGHMVMGTVIPTEP 63 Query: 63 DNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSR 122 + +AR+AA+ AG+P P +NRLCGSGL A+ SAA+ L G+ + +A G ESMSR Sbjct: 64 RDAYLARVAAMNAGIPKETPAFNVNRLCGSGLQAIVSAAQGLLLGDTDVAVAAGAESMSR 123 Query: 123 APFVMGKSEQAFGRSAEI--FDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180 P+++ ++ R ++ D T+G ++Q F M TAENV+A++ I+R Sbjct: 124 GPYLLPQARWG-ARMGDLQGIDYTVG------VLQDPFQHFHMGITAENVSAKYGITREM 176 Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240 QD AL SQ +AA AIA GR A +IVA+E+ RKG + DEH R D T EQLA + Sbjct: 177 QDELALTSQRRAARAIAEGRFASQIVALELKTRKGSVQF-SVDEHVRADVTAEQLAGMKP 235 Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300 F++ G+VTAGNASG+NDGA L+LA+ +A +R GLK AR+VG A AGVEP +MG+GP+ Sbjct: 236 VFKKDGTVTAGNASGINDGAAGLVLATGDAVRRLGLKPLARLVGYAHAGVEPELMGLGPI 295 Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360 PATRKVLE TGL L D+DVIE NEAFAAQ AV RELG D E+VNPNG I+LGHP+G Sbjct: 296 PATRKVLEKTGLNLQDLDVIESNEAFAAQACAVARELGF--DPEKVNPNGSGISLGHPVG 353 Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 +GA + T A+HEL+ QGRYAL TMCIG GQGIA++ ER+ Sbjct: 354 ATGAIIATKAIHELQRIQGRYALATMCIGGGQGIAVVFERV 394 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: 436 Number of extensions: 20 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: 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