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_036834007.1 N784_RS08140 acetyl-CoA C-acyltransferase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000775615.1:WP_036834007.1 Length = 399 Score = 434 bits (1116), Expect = e-126 Identities = 230/400 (57%), Positives = 288/400 (72%), Gaps = 4/400 (1%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 M E I D +RTPIGRY GAL VR DDLAA ++ LL RNP + I++V+ G ANQA Sbjct: 1 MIEVAIVDALRTPIGRYRGALKDVRPDDLAAHVIQGLLERNPNVPIHEIEEVVFGNANQA 60 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 GEDNRNVARMA LLAGLP V+GTTINRLCGSGLDA+ +AARAI AG+GD+ IAGG ESM Sbjct: 61 GEDNRNVARMAALLAGLPVEVAGTTINRLCGSGLDAVNYAARAIMAGEGDIFIAGGTESM 120 Query: 121 SRAPFVMGKAASAFSR-QAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRE 179 +RAP+VM K+ ++F R +++DTTIGWRFVN +A +GTDSMPETAENVA+ ISRE Sbjct: 121 TRAPYVMAKSETSFQRGNPQLYDTTIGWRFVNDKLANMYGTDSMPETAENVAKRYGISRE 180 Query: 180 DQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLK 239 QD FA SQQ+ A +GI +E +PV + ++KG T I DEH RP TTL++L LK Sbjct: 181 AQDQFAYESQQKAKVAMETGIFEQETIPVTVTDRKGKETVIYEDEHPRPNTTLDKLSQLK 240 Query: 240 APFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGP 299 P + G ITAGNASGVNDGA+AL++ S A G+ P A+AG+EP +MGLGP Sbjct: 241 -PLFSGGTITAGNASGVNDGASALLLMSLNKARELGVKPLVTYHVSASAGLEPNVMGLGP 299 Query: 300 VPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPL 359 + AT++ L R+ L+I + ++ELNEAFA+Q+L ++EL L D VN NGGAIA GHPL Sbjct: 300 IYATKKALSRSKLTIKHIGLVELNEAFASQSLQCIKELEL--DTNIVNVNGGAIAFGHPL 357 Query: 360 GMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILE 399 G SGAR+ +E+ RRN +Y L TMC+GVGQGIA I+E Sbjct: 358 GASGARILTTLIYEMKRRNVQYGLATMCVGVGQGIATIVE 397 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: 456 Number of extensions: 9 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: 399 Length adjustment: 31 Effective length of query: 370 Effective length of database: 368 Effective search space: 136160 Effective search space used: 136160 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