Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate SM_b20589 SM_b20589 beta-ketoadipyl CoA thiolase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Smeli:SM_b20589 Length = 400 Score = 240 bits (612), Expect = 6e-68 Identities = 163/413 (39%), Positives = 225/413 (54%), Gaps = 32/413 (7%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59 M EA I RTPIG+ + G+L + L ++ + R +D + V+DV+ G A Q Sbjct: 1 MREAYICDYIRTPIGR-FGGSLASVRADDLGAIPLKALMDRNRSVDWEAVDDVIFGCANQ 59 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G NIAR +LL AGLPV GTTI+R C SG+ A+ AAR++ E+ + GG ES Sbjct: 60 AGEDNRNIARMSLLLAGLPVAVPGTTINRLCGSGMDAVIAAARAIKCGEAELMIAGGVES 119 Query: 120 ISLVQ----------------NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGIS 163 +S D + V+P ++A G +M +T E VA+ Y +S Sbjct: 120 MSRAPFVLPKAESAFSRNAEIYDTTIGWRFVNPLMKAQYG--VDSMPETGENVAEDYKVS 177 Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223 RE QD ++L SQ + AAAQ G+ EI ++ + + G + + +DE PR Sbjct: 178 REDQDAFALRSQAKAAAAQANGRLASEIVAVT-----IPQRKGG----PVVIDRDEHPRA 228 Query: 224 ETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSY 283 TT E LAGLK EG T+TAGNAS ++DGA+A +I S++ A GL+P+ G S Sbjct: 229 -TTIEALAGLKTPFREGGTVTAGNASGVNDGAAALIIASEEAARKHGLRPMARILGGASA 287 Query: 284 GCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNV 341 G P MG+GPV A RL+ R G + D + ELNEAFA Q L LGI D ++N Sbjct: 288 GVPPRIMGMGPVPASQRLMTRLGATQDRFDVIELNEAFASQGLAVLRALGIADDDPRVNR 347 Query: 342 NGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 NGGAI++GHP GMSGAR+ G A +E + ++ TMC+G G G A E V Sbjct: 348 NGGAIALGHPLGMSGARITGTAALELAETGGRTSLSTMCIGVGQGIAVALERV 400 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: 425 Number of extensions: 26 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: 400 Length adjustment: 31 Effective length of query: 364 Effective length of database: 369 Effective search space: 134316 Effective search space used: 134316 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