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_011384976.1 AMB_RS13060 acetyl-CoA C-acyltransferase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000009985.1:WP_011384976.1 Length = 398 Score = 434 bits (1117), Expect = e-126 Identities = 229/401 (57%), Positives = 290/401 (72%), Gaps = 3/401 (0%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 M +A+I DG+R+PIGR+GG L+ VR+DDLAA +R L+ R+ E ++DVILGC NQA Sbjct: 1 MLDAYIYDGLRSPIGRHGGGLAPVRSDDLAAEVIRALVARSS-FKPEDVEDVILGCTNQA 59 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 GED+RNVAR A LLAGLP V+G T+NRLC SGL A+ AAR++ G+GDL +AGGVESM Sbjct: 60 GEDSRNVARHAALLAGLPVEVAGQTVNRLCASGLAAVLDAARSVTCGEGDLYLAGGVESM 119 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180 +RAPFV+ K SA+SR A +FDTTIG RF NP + + FG SMPETA+N+A L +SRE Sbjct: 120 TRAPFVLAKGDSAWSRDARIFDTTIGARFANPKVVKSFGGHSMPETADNIAHDLGLSREA 179 Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240 D+FA SQ + AKA++ G EI P+ + +KG T + DEH RP+T L L LK Sbjct: 180 SDAFAAASQAKYAKAKAEGFYEGEIHPITIAGRKG-DTIVAEDEHPRPQTDLAALTKLK- 237 Query: 241 PFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPV 300 P GV+TAGNASG+NDGAAAL I S G+ P ARIVA A AGV PR+MGLGPV Sbjct: 238 PLFEGGVVTAGNASGINDGAAALFIGSRAAGEKAGIAPIARIVAGAAAGVPPRVMGLGPV 297 Query: 301 PATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLG 360 PA + L RA LS+ D+D+IE+NEAFA Q LG + +LG+ D +NPNGGAIA+GHPLG Sbjct: 298 PAITKALARAKLSLKDLDLIEINEAFAVQVLGCVTQLGVAADDSRLNPNGGAIAIGHPLG 357 Query: 361 MSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 SGARLAL A+ +L R GR+A+ ++CIGVG G+A ++ERV Sbjct: 358 CSGARLALTAARQLQRTGGRHAVVSLCIGVGHGLAAVIERV 398 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: 524 Number of extensions: 14 Number of successful extensions: 4 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: 398 Length adjustment: 31 Effective length of query: 370 Effective length of database: 367 Effective search space: 135790 Effective search space used: 135790 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