Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Pf6N2E2_2289 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 Length = 383 Score = 244 bits (622), Expect = 4e-69 Identities = 158/399 (39%), Positives = 220/399 (55%), Gaps = 25/399 (6%) Query: 5 VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQQGAT 63 VIV RTP+G++ G T + H I ++R +DP EVEDV+ G Q Sbjct: 1 VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPNEVEDVIWGCVNQTLEQ 60 Query: 64 GGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLV 123 G NIAR A L +P T AG T+ R C S + A+ AA++++ ++ V GG E + V Sbjct: 61 GWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHV 120 Query: 124 QNDKMNTFHAVDP----ALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179 + H VDP +L A K M + TAE + K +GI+RE+QD + + S + Sbjct: 121 -----SMMHGVDPNPHMSLYAAKASGMMGL--TAEMLGKMHGITREQQDAFGVRSHQLAH 173 Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLK-AVRG 238 A GKF DEI P+ G + D DE RPETT E LA LK A Sbjct: 174 KATVEGKFKDEIIPMQGY-----DENGFLKLFDY----DETIRPETTLESLAALKPAFNP 224 Query: 239 EGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAV 298 +G T+TAG +SQ++DGAS ++MS + A G++P+ + R M G +P MG GPV A Sbjct: 225 KGGTVTAGTSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPAT 284 Query: 299 PRLLKRHGLSVDDIGLWELNEAFAVQVL-YCRDKLGIDP--EKLNVNGGAISVGHPYGMS 355 + LKR GL + DI +ELNEAFA Q L +D +D EK+N++GGAI++GHP+G S Sbjct: 285 QKALKRAGLGIADIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCS 344 Query: 356 GARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 GAR++G L ++ + V TMC+G G G A +FE V Sbjct: 345 GARISGTLLNVMKQNGGTFGVSTMCIGLGQGIATVFERV 383 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: 387 Number of extensions: 22 Number of successful extensions: 5 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: 383 Length adjustment: 30 Effective length of query: 365 Effective length of database: 353 Effective search space: 128845 Effective search space used: 128845 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