Align 3-ketoacyl-CoA thiolase B, peroxisomal; Acetyl-CoA acyltransferase B; Beta-ketothiolase B; Peroxisomal 3-oxoacyl-CoA thiolase B; EC 2.3.1.155; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate Ac3H11_1916 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= SwissProt::P07871 (424 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1916 Length = 399 Score = 303 bits (775), Expect = 8e-87 Identities = 184/397 (46%), Positives = 244/397 (61%), Gaps = 10/397 (2%) Query: 32 QASASDVVVVHGRRTPIGRAGRGGFKDTTPDELL-SAVLTAVLQDVKLKPECLGDISVGN 90 Q D +V RTPIGR+GRG FK+T PD+LL +A+ +A+LQ L P+ + D +G Sbjct: 3 QKQVQDAYIVAATRTPIGRSGRGYFKNTRPDDLLVAAIKSAMLQVPTLDPKAIEDAIIGC 62 Query: 91 VLQPGA-GAAMARIAQFLSGIPETVPLSAVNRQCSSGLQAVANIAGGIRNGSYDIGMACG 149 G G MARIA L+ V VNR C+SG+ A+ A IR G D+ +A G Sbjct: 63 SFPEGEQGMNMARIAVGLA-FNHPVGGVTVNRFCASGITALQMAADRIRVGEADVLIAGG 121 Query: 150 VESMTLSERG-NPGNISSRLLENEKARDCLIPMGITSENVAERFGISRQKQDAFALASQQ 208 ESM+L G N + ++ + ++ MG+T+E VA+++ ISR+ QDAFAL S Sbjct: 122 AESMSLVPMGGNKPSFNAEVFARDEDVGIAYGMGLTAEKVAQQWKISREAQDAFALESHL 181 Query: 209 KAASAQSKGCFRAEIVPV-----TTTVLDDKGDRKTITVSQDEGVRPSTTMEGLAKLKPA 263 +A AQ G F EI P + + + K TVS DEG RP T++EGLAKLKP Sbjct: 182 RAIKAQKAGEFTDEITPFEVVERSPNLATGEVVEKRRTVSLDEGPRPDTSLEGLAKLKPV 241 Query: 264 FKDGGSTTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAY 323 F GS TAGNSSQ SDGA A+++A ++ GL L SYA GVPP+IMGIGP Sbjct: 242 FAARGSVTAGNSSQTSDGAGALIVASEKAVKQFGLTPLARFVSYAARGVPPEIMGIGPIE 301 Query: 324 AIPAALQKAGLTVNDIDIFEINEAFASQALYCVEKLGIPAEKVNPLGGAIALGHPLGCTG 383 AIPAAL+ AGL +DI +E+NEAFA+Q+L + LG+ VNP+GGAIALGHPLG TG Sbjct: 302 AIPAALRYAGLKSDDIGWYELNEAFAAQSLAVINTLGLNPANVNPMGGAIALGHPLGATG 361 Query: 384 ARQVVTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 A + T+++ L RR + YG+V+MC+GTG GAA + E Sbjct: 362 AIRAATVVHAL-RRHKLKYGMVTMCVGTGQGAAGIIE 397 Lambda K H 0.316 0.133 0.378 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: 451 Number of extensions: 24 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: 424 Length of database: 399 Length adjustment: 31 Effective length of query: 393 Effective length of database: 368 Effective search space: 144624 Effective search space used: 144624 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