Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate GFF2615 Psest_2666 Predicted acyl-CoA transferases/carnitine dehydratase
Query= SwissProt::Q9HAC7 (445 letters) >FitnessBrowser__psRCH2:GFF2615 Length = 401 Score = 219 bits (559), Expect = 9e-62 Identities = 131/397 (32%), Positives = 210/397 (52%), Gaps = 7/397 (1%) Query: 46 KPLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTESTYYLS 105 +PL+G+ ++ L +A PF T L DLGA VIKVERPGAGD R + G S +++ Sbjct: 9 RPLDGITVVSLEHAIAAPFCTRQLADLGARVIKVERPGAGDFARGYDERVDGLAS-HFVW 67 Query: 106 VNRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIYC 165 NR+K+S+ +++K +++ +L A DV V+N PG + MGL ++ + E P +I C Sbjct: 68 TNRSKESLTLDVKQDAAARVLDQLLAGADVLVQNLAPGAAARMGLSFDALHERFPRLIVC 127 Query: 166 SITGYGQTGPISQRAGYDAVASAVSGLMHIT-GPENGDPVRPGVAMTDLATGLYAYGAIM 224 I+GYG+ GP Q+ YD + + G + +T GP + + G ++ D+A G+YAY ++ Sbjct: 128 DISGYGEGGPYEQKKAYDLLIQSEGGFLSVTGGPGETEMAKAGCSIADIAAGMYAYTGVL 187 Query: 225 AGLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLIGQKEAKRWGTAHGSIVPYQAFKTK 284 + L+ + KTG+G +D ++L S V + + G R G AH +I PY F T Sbjct: 188 SALMLRDKTGEGSRVDVSMLESLVEWMGYPLYYAYKGATPPPRAGAAHATIYPYGPFPTG 247 Query: 285 D-GYIVVGAGNNQQFATVC-KILDLPELIDNSKYKTNHLRVHNRKELIKILSERFEEELT 342 D G +++G N +++ C K+L PEL + ++ +N R +R EL ++ E F Sbjct: 248 DGGTVMLGLQNEREWLAFCDKVLLQPELAQDERFSSNARRSEHRTELRALIVEAFSRLSA 307 Query: 343 SKWLYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVRYSKFKM 402 + + + + + +N+M V+A PQ+ E++ P G++ P R S F Sbjct: 308 EEVIARLDAAPIANAHVNDMAGVWAHPQLKARQRWSEVDSP-AGRLPALLPPGRNSAF-A 365 Query: 403 SEARPPPLLGQHTTHILKEVLRYDDRAIGELLSAGVV 439 P P LGQHT +L E L Y I L G V Sbjct: 366 PRMDPIPALGQHTDSLLAE-LGYAPGDIQRLHEQGAV 401 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: 458 Number of extensions: 22 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: 401 Length adjustment: 32 Effective length of query: 413 Effective length of database: 369 Effective search space: 152397 Effective search space used: 152397 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