Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate SM_b21089 SM_b21089 membrane-anchored racemase
Query= SwissProt::Q9HAC7 (445 letters) >FitnessBrowser__Smeli:SM_b21089 Length = 356 Score = 166 bits (420), Expect = 1e-45 Identities = 96/293 (32%), Positives = 165/293 (56%), Gaps = 12/293 (4%) Query: 47 PLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTW--GPPFVGTESTYYL 104 PL G+ ++D+++ L+GP+ ++ L DLGA VIK+ERP GD +R +G +ST + Sbjct: 8 PLSGLVVVDMSQFLSGPYCSLRLMDLGARVIKIERPDGGDLSRRLYLSDTEIGGDSTIFH 67 Query: 105 SVNRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIY 164 ++NR K+S+A+++K+ + +K L A DV ++N+ PG + +GL YE + I P I+Y Sbjct: 68 AINRAKESLAIDLKNEADLAALKRLLAQADVMIQNFRPGVIERLGLDYEAVRAINPRIVY 127 Query: 165 CSITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDPVRPGVAMTDLATGLYAYGAIM 224 SI+GYG+ GP +R G D +A + SG+M + G E PV G+A+ D+ G A I+ Sbjct: 128 ASISGYGEEGPWVKRPGQDLLAQSRSGVMWLNGDEGQGPVPFGLAIGDMLAGAAAAQGIL 187 Query: 225 AGLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYL-IGQKEAKR--WGTAHGSI-VPYQA 280 A L+++ +G G ++ +LL + V + +L G + KR + +AH + PY Sbjct: 188 AALVRRGISGNGSLVETSLLEALVDFQFEVLTTHLNDGGRLPKRSAFRSAHAYLAAPYGV 247 Query: 281 FKTKDGYIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKIL 333 + DGY+ + + K+ DL E+ + + Y+ + ++ IK L Sbjct: 248 YAASDGYLAIA------MTPIPKLADLLEIDELAPYRDDPSSWFTERDRIKAL 294 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: 363 Number of extensions: 15 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: 445 Length of database: 356 Length adjustment: 31 Effective length of query: 414 Effective length of database: 325 Effective search space: 134550 Effective search space used: 134550 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