Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_041642232.1 AZO_RS02365 acetyl-CoA C-acyltransferase
Query= BRENDA::Q8VCH0 (424 letters) >NCBI__GCF_000061505.1:WP_041642232.1 Length = 398 Score = 305 bits (782), Expect = 1e-87 Identities = 178/399 (44%), Positives = 250/399 (62%), Gaps = 12/399 (3%) Query: 31 LQASASDVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDVK-LKPEQLGDISVG 89 + D +V RTP+ + + G F+ PD++L+ VL AV+ V L ++GD+ G Sbjct: 1 MSTQIQDAYIVAAVRTPVAKRN-GAFRHVRPDDMLAHVLRAVVAQVPALDAGEIGDVITG 59 Query: 90 NVL-QPGAGAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMAC 148 + + G +ARI L+G+PE VP T+NR C+S LQAVA+ A IR G D+ +A Sbjct: 60 CAMPEAEQGMNVARIGLLLAGLPERVPGVTLNRFCASSLQAVADAANRIRLGEADVMIAA 119 Query: 149 GVESMTLSQR--GNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALAS 206 G ESM+ + GN +++ + ++ D MG+T+E VAE + VSR QDAFAL S Sbjct: 120 GTESMSAMPQIMGNKVSLNPEIFARQENIDIAYGMGLTAEKVAEEWKVSRADQDAFALQS 179 Query: 207 QQKAASAQSRGCFHAEIVPVTTTVLNDKGDKKTITVSQ-----DEGVRPSTTMQGLAKLK 261 Q+A++A + G F EI P T + G+ T+ +++ DEG R T++ LA+LK Sbjct: 180 HQRASAAIADGSFGDEIAPYTVRS-HLPGEGGTVRIAERIVDTDEGPRADATLEALARLK 238 Query: 262 PAFKDGGSTTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGP 321 P F GS TAGNSSQ+SDGA AVLL + + G+ L RSYAV GVPP VMGIGP Sbjct: 239 PVFAARGSVTAGNSSQMSDGAGAVLLMSETALQRYGVTPLARFRSYAVAGVPPRVMGIGP 298 Query: 322 AYAIPAALQKAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGC 381 AIP AL+ AGL ++ +D E+NEAFA+QA+ + LG+ +VNP GGAIALGHPLG Sbjct: 299 VEAIPRALRLAGLGLDALDRIELNEAFAAQALAVIRTLGLDPARVNPQGGAIALGHPLGA 358 Query: 382 TGARQVVTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 TGA + TL+ +++ G R +G+++MC+GTGMGAAA+FE Sbjct: 359 TGAIRTATLMRAMRQGGVR-HGMITMCVGTGMGAAAIFE 396 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: 448 Number of extensions: 21 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: 398 Length adjustment: 31 Effective length of query: 393 Effective length of database: 367 Effective search space: 144231 Effective search space used: 144231 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