Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate RR42_RS25455 RR42_RS25455 acetyl-CoA acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >FitnessBrowser__Cup4G11:RR42_RS25455 Length = 394 Score = 317 bits (812), Expect = 4e-91 Identities = 178/402 (44%), Positives = 249/402 (61%), Gaps = 9/402 (2%) Query: 1 MSREVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQ 60 M+REV + VRT IG FGGSL + + A+ V+ + R QV + V G Q Sbjct: 1 MTREVVVVSGVRTAIGTFGGSLKDLSPTQMGAMVVREALAR-AQVSGDDVGHVVFGNVIQ 59 Query: 61 AGEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVES 120 + + R+A + G+ P +T+NRLC SG+ A+ +A + I G+A++ I GG ES Sbjct: 60 TEPRDMYLGRVAAVEGGVTIDAPALTVNRLCGSGLQAIVSAAQTILLGDADVAIGGGAES 119 Query: 121 MSRAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRA 180 MSRAPY+ A G ++ D + + L +G+ M TA+NVA +Y +SR Sbjct: 120 MSRAPYLAQSARW----GARMGDAKMLDMMLGALHDPFHGIH-MGVTAENVAKEYDISRV 174 Query: 181 DQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKP 240 QD AL S + A A AG+F ++I+PV +KG+KG+ D DEH+R D +E + KLKP Sbjct: 175 QQDEAALESHRRASAAIRAGHFKDQILPVTLKGRKGDVTFDTDEHVRHDAVMEDMTKLKP 234 Query: 241 VNGPDK-TVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGP 299 V + TVTAGNASG+ND + A++L +K GLK A+++ A AGV P+ MGIGP Sbjct: 235 VFVKENGTVTAGNASGLNDAAAAVVLMERAEAEKRGLKPMARLVSYAHAGVDPKTMGIGP 294 Query: 300 VPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPL 359 VPA +K LER L+VAD DVIE NEAFAAQ AVT+ LG+ D A+VNPNG I+LGHP+ Sbjct: 295 VPATKKALERAGLTVADLDVIEANEAFAAQACAVTKALGL--DPAKVNPNGSGISLGHPI 352 Query: 360 GASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401 GA+GA + + A+++L++ G+ L TMC+G GQG+A ERV Sbjct: 353 GATGALITVKALYELQRVQGRYALVTMCIGGGQGIAAIFERV 394 Lambda K H 0.317 0.134 0.379 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: 388 Number of extensions: 18 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: 401 Length of database: 394 Length adjustment: 31 Effective length of query: 370 Effective length of database: 363 Effective search space: 134310 Effective search space used: 134310 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 (21.6 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