Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate BPHYT_RS09150 BPHYT_RS09150 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__BFirm:BPHYT_RS09150 Length = 393 Score = 323 bits (827), Expect = 7e-93 Identities = 183/404 (45%), Positives = 263/404 (65%), Gaps = 17/404 (4%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M DV I A RT +G+FGG+LA + A +L A ++A++E ++ +QV EV G A Sbjct: 1 MTDVVIVSAARTAVGKFGGSLAKIAAPELGATVIRAVLE-RAGLKPEQVSEVILGQVLTA 59 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 G +N AR A++ AGLP ++PG+T+N +C SG+ A+ A AI +G+ ++ +AGG E+M Sbjct: 60 GS-GQNPARQAVIKAGLPTAVPGMTINVVCGSGLKAVMLAANAIIAGDADIVVAGGQENM 118 Query: 121 SRAPFVMGKAESGYSR-NMKLEDTTIG---WRFINPLMKSQYGVDSMPETADNVADDYQV 176 S AP V+ + G+ + KL D+ I W N QY M TA+NVA +Y + Sbjct: 119 SAAPHVLPGSRDGFRMGDAKLIDSMIVDGLWDVYN-----QY---HMGVTAENVAKEYGI 170 Query: 177 SRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETI-VERDEHLRPETTLEALT 235 +R QDAFA SQ KA AAQ AG F +EIVPV I +KGE + DE +R T E+L Sbjct: 171 TREQQDAFAALSQNKAEAAQKAGRFDDEIVPVEIPQRKGEPLRFATDEFVRHGVTAESLA 230 Query: 236 KLKPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMG 295 LKP + +VTA NASG+NDGAAA+++ SA+ + GL P AR+ A+ G+ P+VMG Sbjct: 231 GLKPAFSKEGSVTAANASGLNDGAAAVLVMSAKKAEALGLKPLARIKAYATSGLDPKVMG 290 Query: 296 IGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALG 355 +GPVPA R+ ER G +D D++E+NEAFA+Q AV +++G D ++N NGGAIA+G Sbjct: 291 MGPVPASRRCLERAGWTPADLDLMEINEAFAAQACAVNQQMGW--DTSKINVNGGAIAIG 348 Query: 356 HPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399 HP+G SG R+++T LH+++K +KGLA++C+G G G+ALA+ER Sbjct: 349 HPIGASGCRILVTLLHEMQKRDAKKGLASLCIGGGMGVALALER 392 Lambda K H 0.318 0.134 0.383 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: 402 Number of extensions: 16 Number of successful extensions: 5 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: 400 Length of database: 393 Length adjustment: 31 Effective length of query: 369 Effective length of database: 362 Effective search space: 133578 Effective search space used: 133578 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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