Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate BPHYT_RS09150 BPHYT_RS09150 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__BFirm:BPHYT_RS09150 Length = 393 Score = 321 bits (822), Expect = 3e-92 Identities = 184/401 (45%), Positives = 256/401 (63%), Gaps = 10/401 (2%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M + +I+ A RT +G++ G+LA + A +LGA ++A++ R L V +VI G A Sbjct: 1 MTDVVIVSAARTAVGKFGGSLAKIAAPELGATVIRAVLER-AGLKPEQVSEVILGQVLTA 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 G +N AR A + AGLP +VPG T+N +CGSGL AV AA A+ G+A +++AGG E+M Sbjct: 60 GS-GQNPARQAVIKAGLPTAVPGMTINVVCGSGLKAVMLAANAIIAGDADIVVAGGQENM 118 Query: 121 SRAPFVMGKSEQAFGRS-AEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRA 179 S AP V+ S F A++ D+ I + Q G+ TAENVA ++ I+R Sbjct: 119 SAAPHVLPGSRDGFRMGDAKLIDSMIVDGLWDVYNQYHMGV-----TAENVAKEYGITRE 173 Query: 180 DQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLG 239 QDAFA SQ+KA AA GR EIV VEI QRKG DE R T E LA L Sbjct: 174 QQDAFAALSQNKAEAAQKAGRFDDEIVPVEIPQRKGEPLRFATDEFVRHGVTAESLAGLK 233 Query: 240 TPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGP 299 F + GSVTA NASG+NDGA A+L+ S++ A+ GLK AR+ AT+G++P++MG+GP Sbjct: 234 PAFSKEGSVTAANASGLNDGAAAVLVMSAKKAEALGLKPLARIKAYATSGLDPKVMGMGP 293 Query: 300 VPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPL 359 VPA+R+ LE G AD+D++E+NEAFAAQ AV +++G D ++N NGGAIA+GHP+ Sbjct: 294 VPASRRCLERAGWTPADLDLMEINEAFAAQACAVNQQMGW--DTSKINVNGGAIAIGHPI 351 Query: 360 GMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400 G SG R++ T LHE+++R + L ++CIG G G+AL +ER Sbjct: 352 GASGCRILVTLLHEMQKRDAKKGLASLCIGGGMGVALALER 392 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: 421 Number of extensions: 17 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: 393 Length adjustment: 31 Effective length of query: 370 Effective length of database: 362 Effective search space: 133940 Effective search space used: 133940 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