Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate PP_2137 PP_2137 beta-ketoadipyl CoA thiolase, beta component
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Putida:PP_2137 Length = 391 Score = 246 bits (629), Expect = 6e-70 Identities = 161/401 (40%), Positives = 222/401 (55%), Gaps = 25/401 (6%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAG-IDPKEVEDVVMGAAMQQG 61 + VIV RTP+G++ G T + H I ++R G +DPKEVEDV+ G Q Sbjct: 7 DVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNGKVDPKEVEDVIWGCVNQTL 66 Query: 62 ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121 G NIAR A L +P T+A T+ R C S + A+ AA++++ ++ V GG E + Sbjct: 67 EQGWNIARMASLMTPIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMG 126 Query: 122 LVQNDKMNTFHAVDP----ALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRR 177 V + H VDP +L A K M + TAE + K +GI+RE+QD + L S + Sbjct: 127 HV-----SMMHGVDPNPHLSLHAAKASGMMGL--TAEMLGKMHGITREQQDLFGLRSHQL 179 Query: 178 TAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLK-AV 236 A GKF DEI P+ G + D DE RPETT EGLA LK A Sbjct: 180 AHKATVEGKFKDEIIPMQGY-----DENGFLKVFDF----DETIRPETTLEGLASLKPAF 230 Query: 237 RGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVF 296 +G T+TAG +SQ++DGAS ++MS + A G++PL + R M G +P MG GPV Sbjct: 231 NPKGGTVTAGTSSQITDGASCMIVMSGQRAMDLGIQPLAVIRSMAVAGVDPAIMGYGPVP 290 Query: 297 AVPRLLKRHGLSVDDIGLWELNEAFAVQVL-YCRDKLGID--PEKLNVNGGAISVGHPYG 353 + + LKR GL++ DI ELNEAFA Q L +D +D EK+N++GGAI++GHP+G Sbjct: 291 STQKALKRAGLTMADIDFIELNEAFAAQALPVLKDLKVLDKMDEKVNLHGGAIALGHPFG 350 Query: 354 MSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 SGAR++G L ++ V TMCVG G G +FE V Sbjct: 351 CSGARISGTLLNVMKQNGGTLGVATMCVGLGQGITTVFERV 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: 395 Number of extensions: 27 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: 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