Align Butyrate--acetoacetate CoA-transferase subunit B; Short=Coat B; EC 2.8.3.9 (characterized, see rationale)
to candidate RR42_RS06560 RR42_RS06560 succinyl-CoA:3-ketoacid-CoA transferase
Query= uniprot:P23673 (221 letters) >FitnessBrowser__Cup4G11:RR42_RS06560 Length = 212 Score = 202 bits (515), Expect = 3e-57 Identities = 100/208 (48%), Positives = 142/208 (68%), Gaps = 5/208 (2%) Query: 9 KEIIAKRVARELKNGQLVNLGVGLPTMVADYIPKNFKITFQSENGIVGMGASPKINEADK 68 ++ +A R A EL++G VNLG+GLPT+VA+++P+ ++ QSENG++G+G P E D Sbjct: 5 RDEMAARAASELQDGFYVNLGIGLPTLVANHVPQGMEVWLQSENGLLGIGPFPTEAEVDA 64 Query: 69 DVVNAGGDYTTVLPDGTFFDSSVSFSLIRGGHVDVTVLGALQVDEKGNIANWIVPGKMLS 128 D++NAG T LP + F S+ SF++IRGGH+++ +LGA+QV EKG++ANW++PGKM+ Sbjct: 65 DMINAGKQTVTTLPGSSIFSSADSFAMIRGGHINLAILGAMQVSEKGDLANWMIPGKMVK 124 Query: 129 GMGGAMDLVNGAKKVIIAMRHTNKGQP-----KILKKCTLPLTAKSQANLIVTELGVIEV 183 GMGGAMDLV G +V++ M HT K + KIL C LPLT N I+T+LGVI+V Sbjct: 125 GMGGAMDLVAGVGRVVVLMEHTAKKKDGGEDIKILASCALPLTGVGVVNRIITDLGVIDV 184 Query: 184 INDGLLLTEINKNTTIDEIRSLTAADLL 211 GL L E + +EI+S T A LL Sbjct: 185 TEAGLKLVETAPGVSREEIQSKTGAPLL 212 Lambda K H 0.316 0.136 0.376 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: 182 Number of extensions: 8 Number of successful extensions: 2 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: 221 Length of database: 212 Length adjustment: 22 Effective length of query: 199 Effective length of database: 190 Effective search space: 37810 Effective search space used: 37810 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: 45 (21.9 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