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 WP_013450480.1 CALNI_RS01735 acetyl-CoA C-acyltransferase
Query= SwissProt::P07871 (424 letters) >NCBI__GCF_000183405.1:WP_013450480.1 Length = 392 Score = 315 bits (806), Expect = 2e-90 Identities = 184/384 (47%), Positives = 240/384 (62%), Gaps = 23/384 (5%) Query: 50 RAGRGGFKDTTPDELLSAVLTAVLQDVKLKPECLGDISVGNVLQPGA-GAAMARIAQFLS 108 +A RG FKD PD+LL VL ++ ++ P+ + D+ +G G G ++R+A F++ Sbjct: 16 KAKRGKFKDLRPDDLLGKVLAETVKRSQVDPQLIEDVIIGCAFPEGEQGMNVSRVASFIA 75 Query: 109 GIPETVPLSAVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMTLSERG------NPG 162 G+P VP +NR CSSGLQ++A A + G D +A GVESMT+ G NPG Sbjct: 76 GLPIDVPAMTINRFCSSGLQSIAIAAERVMAGFADCIVAGGVESMTMIPMGGVKYSANPG 135 Query: 163 NISSRLLENEKARDCLIPMGITSENVAERFGISRQKQDAFALASQQKAASAQSKGCFRAE 222 IS K + MGIT+E VAE++GISR+ QD FAL S KA A +G F E Sbjct: 136 LIS-------KWPETYASMGITAELVAEKYGISREDQDQFALNSHMKAVKAIKEGKFADE 188 Query: 223 IVPVTT--TVLDDKGD----RKTITVSQDEGVRPSTTMEGLAKLKPAFKDGGSTTAGNSS 276 IVPV T +D KG+ ++ +T+ D+G R TT EGLAKLKP FK GS TAGNSS Sbjct: 189 IVPVEVEYTAVDPKGNIVKTKEVVTI--DDGAREDTTYEGLAKLKPVFKLNGSVTAGNSS 246 Query: 277 QVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPAALQKAGLTV 336 Q++DGAAA L+ + L + ++ GV P+IMGIGP +IP LQKAGLT Sbjct: 247 QMTDGAAACLVVSEDFLKRYNLKPMARFVGFSARGVEPEIMGIGPVKSIPVVLQKAGLTF 306 Query: 337 NDIDIFEINEAFASQALYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVVTLLNELKR 396 NDI + E+NEAFA+Q+L + LG+ E +N GGAIALGHPLGCTG + TLLNE+KR Sbjct: 307 NDIGLIELNEAFAAQSLAVIRNLGLNPEIINVNGGAIALGHPLGCTGTKLTATLLNEMKR 366 Query: 397 RGRRAYGVVSMCIGTGMGAAAVFE 420 R + YG+VSMCIG GMGAA +FE Sbjct: 367 RNVK-YGMVSMCIGGGMGAAGIFE 389 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: 450 Number of extensions: 16 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: 392 Length adjustment: 31 Effective length of query: 393 Effective length of database: 361 Effective search space: 141873 Effective search space used: 141873 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 24 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