Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate RR42_RS07610 RR42_RS07610 acetyl-CoA acetyltransferase
Query= reanno::Marino:GFF2751 (415 letters) >FitnessBrowser__Cup4G11:RR42_RS07610 Length = 393 Score = 316 bits (809), Expect = 9e-91 Identities = 186/409 (45%), Positives = 259/409 (63%), Gaps = 22/409 (5%) Query: 7 LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66 + D IV A RT +G++GG+L+ + A +LGAI IKA ER + ++ +V+ G A Sbjct: 1 MTDIVIVSAARTAVGKFGGSLAKIPAPELGAIVIKAALER-AGVKPEQVSEVIMGQVLTA 59 Query: 67 GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126 G ++ AR + L AGLPV VP TIN++CGSG+ AV AA AI G+ ++++AGG E+M Sbjct: 60 GS-GQNPARQAALKAGLPVMVPAMTINKVCGSGLKAVMLAANAIAAGDAEIVVAGGQENM 118 Query: 127 SRAPFVM-GKADSAFSRKAEIFDTTIG---WRFVNPVLKKQYGIDSMPETAENVAADFGI 182 S AP V+ G D A++ D+ I W N QY M TAENVA ++GI Sbjct: 119 SAAPHVLPGSRDGFRMGDAKLIDSMIVDGLWDVYN-----QY---HMGVTAENVAKEYGI 170 Query: 183 SREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRE-TSLEKLA 241 +RE QDAFA SQ + AAQK G+ EI PV IP+RK DP++ TDE R + + LA Sbjct: 171 TREAQDAFAAGSQNKAEAAQKAGKFDEEIVPVPIPQRKGDPVMFATDEFVRHGVTQDALA 230 Query: 242 SLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMG 301 L F + G+VTA NASG+NDGA A+++ A K+ L P A + A TAGV+P++MG Sbjct: 231 GLKPAFDKAGSVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIRAYGTAGVDPKVMG 290 Query: 302 FGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALG 361 GP PA+++ L+ AG + ++D++E+NEAFAAQALAV + +G D VN NGGAIA+G Sbjct: 291 MGPVPASKRCLSRAGWSVEELDLMEINEAFAAQALAVHKQMGW--DTSKVNVNGGAIAIG 348 Query: 362 HPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIER 410 HP+G SG R++ T L+E++RR A L ++CIG G G+AL +ER Sbjct: 349 HPIGASGCRILVTLLHEMKRR-----DAHKGLASLCIGGGMGVALAVER 392 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: 427 Number of extensions: 20 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: 393 Length adjustment: 31 Effective length of query: 384 Effective length of database: 362 Effective search space: 139008 Effective search space used: 139008 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