Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Echvi_1071 Echvi_1071 acetyl-CoA acetyltransferases
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Cola:Echvi_1071 Length = 391 Score = 256 bits (653), Expect = 1e-72 Identities = 154/393 (39%), Positives = 223/393 (56%), Gaps = 5/393 (1%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQQG 61 +A I+ RT +GKA +G L I+ + G++ + V+D+++G A+ + Sbjct: 2 DAYIIKGYRTAVGKAKKGGFRFYRPDDLAVDVIKKLIADTPGLEAERVDDLIVGNAVPEA 61 Query: 62 ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121 G + R L A L G I+R C SGL+AIALA + + + GG ES+S Sbjct: 62 EQGMQMGRMISLMA-LGKVVPGFIINRYCGSGLEAIALATAKIKSGMADCIIAGGTESMS 120 Query: 122 LVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAAA 181 +V T A++ + + D Y++M TAE +AK Y ISRE D++++ S R +A Sbjct: 121 MVPMMGYKT--ALNWKIASEHPDYYLSMGLTAEELAKDYDISREDSDQFAVTSHERAISA 178 Query: 182 QQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGEGF 241 + G+F +EI PI + VD A+G + T+ DEGPRP T + L GLK +G Sbjct: 179 IKEGRFKEEIVPIEVEETFVD-ASGKRQTRTFTVDTDEGPRPGTNMDVLGGLKPAFKQGG 237 Query: 242 TITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPRL 301 +TAGN+SQ SDGA+ TV+MS++ L+P+ G +P MGIGP AVP+ Sbjct: 238 QVTAGNSSQTSDGAAFTVVMSERMVKELNLEPVARLVSYSVAGVDPRIMGIGPKEAVPKA 297 Query: 302 LKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARLAG 361 LK+ G+ + DI L ELNEAFA Q L L +DP +NVNGGA+++GHP G +GA+L Sbjct: 298 LKQAGMKMSDISLVELNEAFAAQALAVIRALDMDPNTVNVNGGAVALGHPLGCTGAKLTV 357 Query: 362 HALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 + E RRR KY +VT CVGGG G AG+ E++ Sbjct: 358 QMINELRRRNQKYGMVTACVGGGQGVAGVVELL 390 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: 411 Number of extensions: 16 Number of successful extensions: 3 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