Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate H281DRAFT_00857 H281DRAFT_00857 acetyl-CoA acetyltransferase /3-ketoacyl-CoA thiolase
Query= reanno::Marino:GFF2751 (415 letters) >FitnessBrowser__Burk376:H281DRAFT_00857 Length = 394 Score = 299 bits (765), Expect = 1e-85 Identities = 181/409 (44%), Positives = 243/409 (59%), Gaps = 22/409 (5%) Query: 8 KDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAG 67 +D +V +RT IG +GG+L DLGA ++ R ++ ++ V++G Sbjct: 3 RDVVVVSGVRTAIGGFGGSLKDFPPTDLGARVVREALAR-ANVSGDEVGHVVFGNVVHTE 61 Query: 68 EDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMS 127 + +AR++ + G+ P T+NRLCGSG+ A+ SAA+++ G+ + I GG E+MS Sbjct: 62 PKDMYLARVAAINGGVAQHTPALTVNRLCGSGLQAIVSAAQSVLLGDADIAIGGGAENMS 121 Query: 128 RAPFVMGKADSAFSRK---AEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISR 184 RAP+ M A F ++ A + D +G L + M TAENVA + +SR Sbjct: 122 RAPYSMPAA--RFGQRMGDARLVDMMVG------ALNDPFQSIHMGVTAENVARKYDVSR 173 Query: 185 EDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPR-ETSLEKLASL 243 E QDA AL S +R A A G +I P+TIP +K D V DTDEH R S E + L Sbjct: 174 EAQDALALESHRRAANAITSGYFKEQILPITIPSKKGDT-VFDTDEHARMNASAEDFSKL 232 Query: 244 PTPF-RENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGF 302 F +ENGTVTAGNASG+ND A A++L +Q +KP AR+V+ A AGV+P MG Sbjct: 233 KPVFAKENGTVTAGNASGINDAAAAVVLMERSVAEQRGIKPLARLVSYAHAGVDPAYMGI 292 Query: 303 GPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGH 362 GP PA+RK L AGL +AD+DVIE NEAFAAQA AV+++LG D VNPNG I+LGH Sbjct: 293 GPVPASRKALERAGLTVADLDVIEANEAFAAQACAVSKELGF--DPAKVNPNGSGISLGH 350 Query: 363 PLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411 P+G +GA + AL EL+R RYAL TMCIG GQGIA I ER+ Sbjct: 351 PIGATGALITVKALYELQR-----IGGRYALVTMCIGGGQGIAAIFERI 394 Lambda K H 0.318 0.133 0.382 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: 417 Number of extensions: 19 Number of successful extensions: 6 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: 415 Length of database: 394 Length adjustment: 31 Effective length of query: 384 Effective length of database: 363 Effective search space: 139392 Effective search space used: 139392 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