Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate BWI76_RS13135 BWI76_RS13135 3-oxoadipyl-CoA thiolase
Query= SwissProt::Q0AVM3 (396 letters) >FitnessBrowser__Koxy:BWI76_RS13135 Length = 401 Score = 331 bits (849), Expect = 2e-95 Identities = 184/402 (45%), Positives = 260/402 (64%), Gaps = 14/402 (3%) Query: 3 REVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAG 61 R+ + RTP+G +GG L + + L AI + E + R ID+VI GC QAG Sbjct: 2 RDAFICDGIRTPIGRYGGALASMRADDLAAIPLRELLSRNPKFDPASIDDVILGCANQAG 61 Query: 62 L-GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMD 120 +NVA + AG P V T+N++CGSGL A+ AA+ IKAG+AD+++AGG E+M Sbjct: 62 EDNRNVAHMATLLAGYPHTVPGTTVNRLCGSGLDAIGFAARAIKAGEADLMIAGGVESMS 121 Query: 121 KAPFILPNARWGYRMSMPKGDLIDEMV-WGGLTDV----FNGYHMGITAENINDMYGITR 175 +APF++ A Y+ + +L D + W + + F M TAEN+ ++ I+R Sbjct: 122 RAPFVMGKASAAYQR---QAELFDTTIGWRFVNPLMQQRFGTDSMPETAENVAELLNISR 178 Query: 176 EEQDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGDI--VFDTDEHPR-KSTPEAMAK 232 +QDAF +RSQ +A+A G EIVPV I G KG + V++ DEHPR ++T E +++ Sbjct: 179 ADQDAFAYRSQQRSARAQRDGILAQEIVPVPIIGGKGAVSTVYE-DEHPRAETTLEQLSR 237 Query: 233 LAPAFKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGL 292 L F+KGG VTAGNASG+ND AAA+I+ S ++A G+ P A++V+ A+ GV+P +MGL Sbjct: 238 LKTPFRKGGVVTAGNASGVNDGAAALIIASSQQAIAQGLTPRARIVAMATAGVEPKLMGL 297 Query: 293 GPIPASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGH 352 GP+PA RK LE+AGL+I D+DLIE NEAFAAQ++ V R LG AD VN NGGAIA+GH Sbjct: 298 GPVPAVRKVLERAGLSIKDMDLIELNEAFAAQALGVLRQLGLADDAPHVNPNGGAIALGH 357 Query: 353 PIGSSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 P+G SGAR+ ++ E+Q+R + L T+CIG G G A+I+E Sbjct: 358 PLGMSGARLALSASLELQRRSGRYALCTMCIGVGQGIAMILE 399 Lambda K H 0.317 0.135 0.387 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: 448 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: 396 Length of database: 401 Length adjustment: 31 Effective length of query: 365 Effective length of database: 370 Effective search space: 135050 Effective search space used: 135050 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