Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate 1937156 b3845 acetyl-CoA acetyltransferase (NCBI)
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__Keio:1937156 Length = 387 Score = 291 bits (744), Expect = 3e-83 Identities = 174/406 (42%), Positives = 242/406 (59%), Gaps = 25/406 (6%) Query: 1 MRDVFICDAIRTPIGRF-GGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQ 59 M V I DAIRTP+GR GGA VRA+DL+A +++L+ NPA++ +D++++GC Q Sbjct: 1 MEQVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQ 60 Query: 60 AGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVES 119 E N+AR A LLA +P S+P VT+NRLC S M A+ A R I +G+ + + GGVE Sbjct: 61 TLEQGFNIARNAALLAEVPHSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEH 120 Query: 120 MSRAPFVMG-KAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSR 178 M P G G SRN+ +G TA+ +A + +SR Sbjct: 121 MGHVPMSHGVDFHPGLSRNVAKAAGMMGL------------------TAEMLARMHGISR 162 Query: 179 ADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVE--RDEHLRPETTLEALTK 236 QDAFA RS +A AA + F EI+P H + + DE +RPETT+EAL Sbjct: 163 EMQDAFAARSHARAWAATQSAAFKNEIIPTG-GHDADGVLKQFNYDEVIRPETTVEALAT 221 Query: 237 LKPVNGP-DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMG 295 L+P P + VTAG +S ++DGAAA+++ S + GL PRARV MA G P +MG Sbjct: 222 LRPAFDPVNGMVTAGTSSALSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMG 281 Query: 296 IGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQ-VNPNGGAIAL 354 GPVPA + ++ G++ SD V E+NEAFA+Q L +++LG+ + + +N NGGAIAL Sbjct: 282 YGPVPASKLALKKAGLSASDIGVFEMNEAFAAQILPCIKDLGLIEQIDEKINLNGGAIAL 341 Query: 355 GHPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 GHPLG SGAR+ T L+ +E+ + GLATMC+G+GQG+A ERV Sbjct: 342 GHPLGCSGARISTTLLNLMERKDVQFGLATMCIGLGQGIATVFERV 387 Lambda K H 0.318 0.134 0.383 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: 378 Number of extensions: 18 Number of successful extensions: 7 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: 400 Length of database: 387 Length adjustment: 31 Effective length of query: 369 Effective length of database: 356 Effective search space: 131364 Effective search space used: 131364 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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