Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate GFF2916 PS417_14920 CoA-transferase
Query= SwissProt::Q9HAC7 (445 letters) >FitnessBrowser__WCS417:GFF2916 Length = 397 Score = 215 bits (548), Expect = 2e-60 Identities = 133/401 (33%), Positives = 211/401 (52%), Gaps = 7/401 (1%) Query: 42 MNNIKPLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTEST 101 M N +PL+G+ ++ L +A PF T L DLGA VIKVERPGAGD R + G S Sbjct: 1 MTNPRPLDGITVVSLEHAIAAPFCTRQLADLGARVIKVERPGAGDFARGYDERVRGLAS- 59 Query: 102 YYLSVNRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPH 161 +++ NR+K+S+ +++K + I+ L A DV V+N PG + MGL +E + E P Sbjct: 60 HFVWTNRSKESLTLDLKQEEAGTILDTLLADADVLVQNLAPGAAARMGLSFEALHERFPR 119 Query: 162 IIYCSITGYGQTGPISQRAGYDAVASAVSGLMHIT-GPENGDPVRPGVAMTDLATGLYAY 220 +I C I+GYG+ GP ++ YD + + G + +T GP + G ++ D++ G+YAY Sbjct: 120 LIVCDISGYGEGGPYEKKKAYDLLIQSEGGFLSVTGGPGEDQMAKAGCSIADISAGMYAY 179 Query: 221 GAIMAGLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLIGQKEAKRWGTAHGSIVPYQA 280 I++ L+ + KTGKG ID ++L S V + + G + R G AH +I PY Sbjct: 180 SGILSALLLRGKTGKGSRIDVSMLESLVEWMGYPMYYAFDGAPQPPRAGAAHSTIYPYGP 239 Query: 281 FKTKD-GYIVVGAGNNQQFATVC-KILDLPELIDNSKYKTNHLRVHNRKELIKILSERFE 338 F T D G +++G N +++A C K+L P L + ++ N R NR+ L +I+ + F Sbjct: 240 FPTGDGGTVMLGLQNEREWAAFCDKVLLTPALATDERFSANFKRSANREVLRQIIVDSFA 299 Query: 339 EELTSKWLYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVRYS 398 + + E + + +N+M+ V+ PQ+ ++ P G + P R + Sbjct: 300 QLDAEAVIQRLESAQIASARVNDMQGVWDHPQLKARDSWRAVDSP-AGPLPALLPPARNA 358 Query: 399 KFKMSEARPPPLLGQHTTHILKEVLRYDDRAIGELLSAGVV 439 F P LGQH+ IL + L Y AI L + GV+ Sbjct: 359 AF-TPRMDGVPGLGQHSQGIL-DGLGYSTDAIDGLRARGVI 397 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: 444 Number of extensions: 22 Number of successful extensions: 4 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: 397 Length adjustment: 32 Effective length of query: 413 Effective length of database: 365 Effective search space: 150745 Effective search space used: 150745 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