Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate GFF2241 PGA1_c22730 3-ketoacyl-CoA thiolase FadA
Query= BRENDA::Q8VCH0 (424 letters) >FitnessBrowser__Phaeo:GFF2241 Length = 394 Score = 276 bits (706), Expect = 8e-79 Identities = 166/397 (41%), Positives = 236/397 (59%), Gaps = 20/397 (5%) Query: 37 DVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDVKLKPEQLGDISVGNVLQPG- 95 + V+V RTPIG A +G + ++ + ++ + P + D+ +G+VL G Sbjct: 3 EAVIVSTARTPIGVAFKGALNNIKSPTMMGHAMQHAVERAGVDPGLIEDVVIGSVLTAGT 62 Query: 96 AGAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMTL 155 AG +AR++ +G+P TV T++RQCSSGL A+A A I ++ +A G E+++ Sbjct: 63 AGMNVARLSALAAGLPNTVAGQTIDRQCSSGLMAIATAAKQIIVDGQNVAVAGGQENISA 122 Query: 156 SQRGNHGNISSRLLENEK-------ARDCLIPMGITSENVAERFGVSRQKQDAFALASQQ 208 Q N + +EK + +PM +T+ENVA +G+SR QD +A SQ Sbjct: 123 LQ-----NAYLKWAGDEKDPNVIAQSEHAYMPMLMTAENVARTYGISRDVQDEYAALSQG 177 Query: 209 KAASAQSRGCFHAEIVPVTTT--VLNDKGDKKTI---TVSQDEGVRPSTTMQGLAKLKPA 263 + A AQ+ G F EIVP+T V N + ++T+ T+S+DEG RP TT + L L P Sbjct: 178 RTARAQAAGAFEDEIVPITAIKRVKNRETGEETVEEVTLSKDEGNRPGTTAETLGALNPV 237 Query: 264 FKDGGSTTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAY 323 +GG TAGN+SQ+SDGA+A +L AE+ GL LG+ R AV G P+ MG+GP + Sbjct: 238 V-EGGLITAGNASQLSDGASACVLMEGKMAEQQGLTPLGIYRGMAVAGNAPEEMGVGPIF 296 Query: 324 AIPAALQKAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTG 383 AIP L+ AGL + DI ++E+NEAFA Q +YC + LGI E N GGAI++GHP G TG Sbjct: 297 AIPKLLKNAGLRIEDIGLWELNEAFACQVLYCRDHLGIDPEIYNVNGGAISIGHPYGMTG 356 Query: 384 ARQVVTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 RQV L E +RRG + Y V SMC+G GMGAAA+FE Sbjct: 357 VRQVGHALIEGRRRGVK-YVVTSMCVGGGMGAAALFE 392 Lambda K H 0.317 0.133 0.377 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: 452 Number of extensions: 22 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: 424 Length of database: 394 Length adjustment: 31 Effective length of query: 393 Effective length of database: 363 Effective search space: 142659 Effective search space used: 142659 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