Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate CA265_RS17585 CA265_RS17585 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Pedo557:CA265_RS17585 Length = 391 Score = 238 bits (607), Expect = 2e-67 Identities = 153/398 (38%), Positives = 214/398 (53%), Gaps = 14/398 (3%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQQG 61 EA I++ RT +GKA RG T L I V +D ++++DV++G A + Sbjct: 2 EAYIIAGYRTAVGKAPRGVFRFTRADDLAAEVIRALVASVPNLDNEQIDDVIVGNATPEA 61 Query: 62 ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121 G NI R L G T++R CASGL IA A + + + GG E +S Sbjct: 62 EQGLNIGRMISLMGLDTDKVPGVTVNRYCASGLDTIATAVAKIKAGMADCIIAGGVEVMS 121 Query: 122 LVQNDKMNTFHAVDPALEAIKG--DVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179 + P E K D Y M TAE VAK Y +SRE QD +SL+S + Sbjct: 122 GMPFGGWKLV----PNAEVAKNNPDWYWGMGLTAEAVAKEYNVSREDQDAFSLKSHEKAI 177 Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239 A + G D I PI+ +D A + + DEGPR +TT + LA LK V Sbjct: 178 HAIKNGHLKDGILPITVNENYLD-ANLKKKTRSYVVDTDEGPRADTTLDKLAKLKPVFDA 236 Query: 240 GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCE---PDEMGIGPVF 296 ++TAGN+SQ SDGA+ +++S+K +P+ +VSYG P MGIGP+ Sbjct: 237 VGSVTAGNSSQTSDGAAFVLVVSEKKMKELNAEPIA---RLVSYGIAGVPPRIMGIGPIE 293 Query: 297 AVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSG 356 A+P+ LK+ GL +DI L ELNEAFA Q L L ++P+ +NVNGGAI++GHP G +G Sbjct: 294 AIPKALKQAGLKKEDIDLIELNEAFASQSLAVIRTLDLNPDVINVNGGAIALGHPLGCTG 353 Query: 357 ARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 A+L + E +R+ KY +VTMCVG G G+AG+FE++ Sbjct: 354 AKLTVQIMNELKRQNKKYGMVTMCVGTGQGAAGIFELL 391 Lambda K H 0.316 0.134 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: 406 Number of extensions: 14 Number of successful extensions: 4 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: 395 Length of database: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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