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 N515DRAFT_2688 N515DRAFT_2688 acetyl-CoA acyltransferase
Query= SwissProt::P07871 (424 letters) >FitnessBrowser__Dyella79:N515DRAFT_2688 Length = 401 Score = 319 bits (817), Expect = 1e-91 Identities = 189/400 (47%), Positives = 260/400 (65%), Gaps = 23/400 (5%) Query: 37 DVVVVHGRRTPIGRAGRGGFKDTTPDELLSAVLTAVL-QDVKLKPECLGDISVGNVL-QP 94 D +V RTP+G+A RG F++T PD++L+ V+ AV+ Q + +GD+ VG + + Sbjct: 7 DAYIVAATRTPVGKAPRGVFRNTRPDDMLAHVIRAVMAQAPGIDAHRIGDVIVGCAMPEA 66 Query: 95 GAGAAMARIAQFLSGIPETVPLSAVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154 G +ARI L+G+P+TVP VNR CSSG+QA+A A IR G D+ +A G ESM+ Sbjct: 67 EQGMNVARIGLLLAGLPDTVPGVTVNRFCSSGVQAIAQAADRIRLGEADLMIAAGTESMS 126 Query: 155 LSER-GNPGNISSRLLENEKARDCLIPMGITSENVAERFGISRQKQDAFALASQQKAASA 213 + G+ ++ + +NE MGIT+ENVA+++ ISR++QD FA AS ++A +A Sbjct: 127 MVPMMGHKVAMNPGIFDNEHI-GIAYGMGITAENVAKQWKISREEQDTFAAASHERALAA 185 Query: 214 QSKGCFRAEIVPVTTTVLDD----------KGDRKTITVSQDEGVRPSTTMEGLAKLKPA 263 G F+ EI P LDD K D + I DEG RP +T+E L KLKP Sbjct: 186 IKAGEFKDEITPFK---LDDHYPDLATRSIKTDSRLIDT--DEGPRPGSTVEVLGKLKPV 240 Query: 264 FKDG---GSTTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIG 320 F++G GS TAGNSSQ SDGA AVLLA + +E GL + SY+V GV PDIMGIG Sbjct: 241 FRNGQFGGSVTAGNSSQTSDGAGAVLLASEAAIKEYGLTPIARFVSYSVAGVRPDIMGIG 300 Query: 321 PAYAIPAALQKAGLTVNDIDIFEINEAFASQALYCVEKLGIPAEKVNPLGGAIALGHPLG 380 P AIP AL++AG+T + +D E+NEAFA+Q+L ++ LG+ K+NPLGGAIALGHPLG Sbjct: 301 PKEAIPKALKQAGMTQDQLDWIELNEAFAAQSLAVIKDLGLDPSKINPLGGAIALGHPLG 360 Query: 381 CTGARQVVTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 TGA + TL++ ++RR ++ YG+V+MCIGTGMGAA +FE Sbjct: 361 ATGAIRAATLVHGMRRR-KQKYGMVTMCIGTGMGAAGIFE 399 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: 437 Number of extensions: 20 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 424 Length of database: 401 Length adjustment: 31 Effective length of query: 393 Effective length of database: 370 Effective search space: 145410 Effective search space used: 145410 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 Apr 09 2024. 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