Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate 7022768 Shewana3_0023 3-ketoacyl-CoA thiolase (RefSeq)
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__ANA3:7022768 Length = 387 Score = 320 bits (821), Expect = 3e-92 Identities = 185/406 (45%), Positives = 253/406 (62%), Gaps = 24/406 (5%) Query: 1 MREAFICDGIRTPIGRY-GGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQ 59 M++A I D IRTP+GR G +VRA+ L+A ++ LL+RNP+LD I+DVI GC Q Sbjct: 1 MKQAVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKGLLLRNPQLDPNTIEDVIWGCVQQ 60 Query: 60 AGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVES 119 E N+AR A+LLAG+P++ T+NRLCGS ++A+ AARAI G GD I GGVE Sbjct: 61 TLEQGFNIARNASLLAGIPKTAGAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIIGGVEH 120 Query: 120 MSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDS--MPETAENVAELLKIS 177 M P G +P +A S M TAE + +L I+ Sbjct: 121 MGHVPMNHGVD-------------------FHPGLANNVAKASGMMGLTAEMLGKLHGIT 161 Query: 178 REDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRG 237 RE QD+FA+RS QR A G A+EI + + G + ++ HDE +RPET++E L Sbjct: 162 REQQDAFAVRSHQRAHAATVEGRFAKEIYGIEGHDANGALIKVLHDEVIRPETSMESLAA 221 Query: 238 LKAPFR-ANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMG 296 L+ F ANG +TAG +S ++DGA+A+++ E A A GL RARI +MA AG + +MG Sbjct: 222 LRPVFDPANGTVTAGTSSALSDGASAMLVMEESKARALGLPIRARIRSMAVAGCDAAIMG 281 Query: 297 LGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDA-PHVNPNGGAIAL 355 GPVPAT++ L RAG++++D+DVIELNEAFAAQ+L +++LGL D +N NGGAIAL Sbjct: 282 YGPVPATQKALARAGITVNDLDVIELNEAFAAQSLPCVKDLGLLDVVEDKINLNGGAIAL 341 Query: 356 GHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 GHPLG SGAR++ + + ++ L TMCIG+GQGIA + ERV Sbjct: 342 GHPLGCSGARISTTLINLMEHKDATLGLATMCIGLGQGIATVFERV 387 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: 428 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: 387 Length adjustment: 31 Effective length of query: 370 Effective length of database: 356 Effective search space: 131720 Effective search space used: 131720 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