Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate PP_3393 PP_3393 CAIB/BAIF family protein
Query= SwissProt::Q9HAC7 (445 letters) >FitnessBrowser__Putida:PP_3393 Length = 396 Score = 194 bits (492), Expect = 5e-54 Identities = 116/394 (29%), Positives = 209/394 (53%), Gaps = 9/394 (2%) Query: 47 PLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTESTYYLSV 106 PL+G+++++++ ++ GP M LGDLGAEVIK+E P GD TR +G + ++ + Sbjct: 5 PLDGIRVVEISHMVMGPTCGMILGDLGAEVIKIE-PVRGDGTRR----LLGAGAGFFRTF 59 Query: 107 NRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIYCS 166 NRNK+ IAV+++ P+G + + +L DVF+EN+ PG++ +GLGY+ + + P +IY S Sbjct: 60 NRNKQCIAVDVETPEGREAVLQLIDTADVFIENFKPGRMQKLGLGYDALCQRNPGLIYAS 119 Query: 167 ITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDPVRPGVAMTDLATGLYAYGAIMAG 226 G+ +GP R D V ++GL ++TGP G P+R G ++ D+ G++ ++A Sbjct: 120 HKGF-LSGPYDNRLALDEVVQMMAGLAYMTGPV-GRPLRAGSSVNDIMGGMFGAIGVLAA 177 Query: 227 LIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLIGQKEAKRWGTAHGSIVPYQAFKTKDG 286 L +++ TG+G + L + V + Y++ + A + Y F G Sbjct: 178 LNERHSTGRGREVQSALYENCVLLAAQHMQQYVVTGEAAAPMPNRISAWAIYDVFTFAGG 237 Query: 287 -YIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKILSERFEEELTSKW 345 + V A Q+ +C++L L+D+ +N+ RV R L+ L+E F + Sbjct: 238 EQMFVAATGEGQWHALCRVLGQTALLDDPTLGSNNDRVLQRPRLLAHLAEVFAPLDAGQL 297 Query: 346 LYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVRYSKFKMSEA 405 E +G+P+ PI + +F +P +L +G + E++ +P + ++ Sbjct: 298 ALQLEANGIPFAPIRRPEELFEDPHLLQSGGMAELQLEDGSHTPMPLLPLSLDGQRLQPR 357 Query: 406 RPPPLLGQHTTHILKEVLRYDDRAIGELLSAGVV 439 R +G+HT +++E L Y D I +L +AGV+ Sbjct: 358 RAIARIGEHTRQVMRE-LGYSDAHIAQLCAAGVL 390 Lambda K H 0.318 0.137 0.410 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: 450 Number of extensions: 23 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: 445 Length of database: 396 Length adjustment: 32 Effective length of query: 413 Effective length of database: 364 Effective search space: 150332 Effective search space used: 150332 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 (21.7 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