Align 3-oxoadipate CoA-transferase subunit B; 3-oxoadipate:succinyl-CoA transferase subunit B; Beta-ketoadipate:succinyl-CoA transferase subunit B; EC 2.8.3.6 (characterized)
to candidate PfGW456L13_2532 3-oxoadipate CoA-transferase subunit B (EC 2.8.3.6); Glutaconate CoA-transferase subunit B (EC 2.8.3.12)
Query= SwissProt::Q8VPF2 (260 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2532 Length = 262 Score = 105 bits (263), Expect = 7e-28 Identities = 83/253 (32%), Positives = 127/253 (50%), Gaps = 11/253 (4%) Query: 4 YSTNEMMTVAAARRLK-NGAVCFVGIG-LPSKAANLARLTSSPDVVLIYESGPIGAKPTV 61 YS E+M AA+ + +G V GIG +P AA+LA LTS+P +++ + A+P Sbjct: 6 YSLAELMICAASEAWREDGEVLASGIGVIPRLAASLAMLTSNPQLLMTDSEAYMVAEP-- 63 Query: 62 LPLSIGDGELAETADTVVPTGEIF-RYWLQGGRIDVGFLGAAQVDRFGNINTTVIGDYNK 120 +PL G D+ + IF W GG+ +G Q+DRFG N + IGDY K Sbjct: 64 VPLGARKG-YEPKRDSWMGFSRIFDNVW--GGKRHA-LVGPTQIDRFGQANISCIGDYAK 119 Query: 121 PKVRLPGAGGAPEIAGSAKEVLIILKQSHRTFVD-KLAFITSVGHGEGGDHRKQLGLPGK 179 PK ++ G G P + S + + R FV+ ++ + SVG+ R L Sbjct: 120 PKAQMLGVRGFPGNSISHANSFCVPSHNRRLFVEGEVDMVASVGYNPARLARGW-SLNDI 178 Query: 180 GPVAIITDLCIMEPEAGSNEFIVTSLHPGVTREQVIENTGWAIRFAEQVKETAAPTEVEL 239 IITDLC+++ + + + SLHPGVT QV +NTG+ + + TAAPT +L Sbjct: 179 DIRLIITDLCVLDFQGPQRQMRIRSLHPGVTAAQVQDNTGFELHVPDDCPTTAAPTAEQL 238 Query: 240 EALRALEARTAAA 252 + ++ L+ A Sbjct: 239 QLIQRLDPHNLRA 251 Lambda K H 0.316 0.135 0.389 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: 177 Number of extensions: 12 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: 260 Length of database: 262 Length adjustment: 25 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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: 47 (22.7 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