Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate CCNA_01168 CCNA_01168 3-ketoacyl-CoA thiolase
Query= reanno::Marino:GFF2751 (415 letters) >FitnessBrowser__Caulo:CCNA_01168 Length = 399 Score = 546 bits (1406), Expect = e-160 Identities = 281/402 (69%), Positives = 319/402 (79%), Gaps = 6/402 (1%) Query: 10 AYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAGED 69 AYI D IRTPIGRYGG+LS VRADDL AIP+KAL R P LD + ID+++ G ANQAGED Sbjct: 4 AYICDGIRTPIGRYGGSLSKVRADDLAAIPLKALVARNPSLDLAAIDEIVLGSANQAGED 63 Query: 70 NRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMSRA 129 NR+VARM+LLLAG PV VPG T+NRLC SG++AVG AARAI +G L+IAGGVESMSRA Sbjct: 64 NRNVARMALLLAGYPVSVPGVTVNRLCASGLEAVGYAARAIASGHNDLVIAGGVESMSRA 123 Query: 130 PFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISREDQDA 189 PFVMGKADSAFSR AEIFDTTIGWRFVNP ++K YG+DSMPETAENVA D+G++REDQDA Sbjct: 124 PFVMGKADSAFSRSAEIFDTTIGWRFVNPAMRKLYGVDSMPETAENVATDYGVNREDQDA 183 Query: 190 FALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKLASLPTPFRE 249 FALRSQ R AAAQ G LA EITPV IP K P +VD DEHPRET++E LA L RE Sbjct: 184 FALRSQARAAAAQANGFLAGEITPVEIP-GKAGPTIVDRDEHPRETTMEALAKLKPIVRE 242 Query: 250 NGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPAPATR 309 GTVTAGNASGVNDGA AL++A DA+K++ L PRAR+ A+AGVEPR+MG GP PA R Sbjct: 243 GGTVTAGNASGVNDGAVALIIASEDAVKRHGLTPRARITGYASAGVEPRVMGIGPVPAVR 302 Query: 310 KVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLGMSGA 369 K++A GL + D DV+ELNEAFAAQ LAV R LGLPDD HVN NGGAIALGHPLG SGA Sbjct: 303 KLMAKTGLAIGDFDVVELNEAFAAQGLAVLRQLGLPDDGAHVNANGGAIALGHPLGASGA 362 Query: 370 RLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411 RLV TAL +LE GQ+ L T+CIGVGQG AL ER+ Sbjct: 363 RLVLTALRQLEA--IGGQR---GLATLCIGVGQGAALAFERV 399 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: 523 Number of extensions: 18 Number of successful extensions: 3 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: 399 Length adjustment: 31 Effective length of query: 384 Effective length of database: 368 Effective search space: 141312 Effective search space used: 141312 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