Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_086509762.1 BZY95_RS09850 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_002151265.1:WP_086509762.1 Length = 402 Score = 432 bits (1112), Expect = e-126 Identities = 236/402 (58%), Positives = 283/402 (70%), Gaps = 3/402 (0%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M +A I D +RTP GR+ G+LA+VR DDL LKAL+AR+ A ++V+ GC NQA Sbjct: 1 MQDAYIFDGLRTPFGRHGGSLAAVRPDDLLGHVLKALVARNG-FAAEAYEEVLAGCTNQA 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 GED+RNVAR A LLAGLPV V T+NRLCGSGL AV AARA R GE L LAGGVESM Sbjct: 60 GEDSRNVARHAGLLAGLPVEVAAQTVNRLCGSGLAAVIDAARATRLGEGELFLAGGVESM 119 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180 SRAP+V+GK+E F R+ ++DT IG RF N + + +G SMPETA+NVA I R Sbjct: 120 SRAPYVLGKAESPFARNQPLYDTVIGSRFPNPWLAREYGSHSMPETADNVAHDLGIGRDA 179 Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQ-RKGPAKIVEHDEHPRGDTTLEQLAKLG 239 D FA RSQ A A+A G E++AVE+ Q RK P V+ DEHPR T ++LA+LG Sbjct: 180 SDVFAARSQAHYAEALARGFYDDELLAVEVPQGRKQPPLTVDRDEHPRPGTDADKLARLG 239 Query: 240 TPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGP 299 P +GG VTAGNASG+NDGA AL++ S A +R G+ RAR+V A AGV PR+MG+GP Sbjct: 240 -PLFEGGVVTAGNASGLNDGAAALIVGSLAAGERAGMAPRARIVASAVAGVPPRVMGLGP 298 Query: 300 VPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPL 359 VPA+RK LE GL LA MD IE+NEAFA Q L ++LGL DD R+N NGGAIA+GHPL Sbjct: 299 VPASRKALERAGLNLAQMDAIEINEAFAVQVLGCTQQLGLDPDDSRLNANGGAIAIGHPL 358 Query: 360 GMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 G SG RL TAL +LE GRYAL TMCIGVGQGIA IIER+ Sbjct: 359 GASGTRLALTALRQLEAGGGRYALVTMCIGVGQGIACIIERM 400 Lambda K H 0.319 0.134 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: 552 Number of extensions: 30 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: 402 Length adjustment: 31 Effective length of query: 370 Effective length of database: 371 Effective search space: 137270 Effective search space used: 137270 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