Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_012171496.1 AZC_RS15355 acetyl-CoA C-acyltransferase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000010525.1:WP_012171496.1 Length = 378 Score = 301 bits (772), Expect = 2e-86 Identities = 172/383 (44%), Positives = 237/383 (61%), Gaps = 24/383 (6%) Query: 19 GALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGEDNRNVARMATLLAGLP 78 G L+ VR DDLAA +REL+ R +++ E I+D+I+GCA E N+AR+ ++A LP Sbjct: 20 GDLARVRPDDLAAQVVRELIART-KVNPEDIEDLIVGCAFPEAEQGFNIARLIGMIAELP 78 Query: 79 QSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAPFVMGKAASAFSRQA 138 QSV+G T+NR CGS + ++ AA I G G+ I GVESMSR P + A Sbjct: 79 QSVAGVTVNRFCGSSMQSVHMAAGQILLGAGEAFICAGVESMSRVPMTGFNPMPNPALYA 138 Query: 139 EMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISREDQDSFALRSQQRTAKAQSS 198 + +G M +TAENVA +I+R DQ++FA+ SQ++ AKAQ+ Sbjct: 139 KNAAAYMG----------------MGDTAENVARKWQITRADQEAFAVESQRKAAKAQAE 182 Query: 199 GILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKAPFRANGVITAGNASGVND 258 G L +EIVP+ + K + D +RPETT + L GLK F NG +TAG +S + D Sbjct: 183 GKLKDEIVPIRINGK-----SVDADSCIRPETTADDLAGLKPAFDQNGTVTAGTSSPLTD 237 Query: 259 GAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPVPATRRVLERAGLSIHDMD 318 GA+A+++ SE A GL AR+ ++A AG P +MG+GPV ATR+ L RA + I D+D Sbjct: 238 GASAVLVCSEAYAEKHGLEVLARLRSVAVAGCAPEIMGIGPVDATRKALARANIKIEDVD 297 Query: 319 VIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRN 378 V+ELNEAFA+QA+ R+L + + +N +GGAIALGHPLG +GAR+ A+ L R Sbjct: 298 VVELNEAFASQAIACARDLNVKPET--LNIDGGAIALGHPLGATGARIVGKAASLLKREG 355 Query: 379 GRYALCTMCIGVGQGIAMILERV 401 GRYA+ T CIG GQGIA +LERV Sbjct: 356 GRYAVATQCIGGGQGIATVLERV 378 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: 443 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 401 Length of database: 378 Length adjustment: 30 Effective length of query: 371 Effective length of database: 348 Effective search space: 129108 Effective search space used: 129108 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