Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate WP_086509474.1 BZY95_RS08305 CoA transferase
Query= SwissProt::Q9HAC7 (445 letters) >NCBI__GCF_002151265.1:WP_086509474.1 Length = 380 Score = 214 bits (546), Expect = 3e-60 Identities = 126/387 (32%), Positives = 204/387 (52%), Gaps = 20/387 (5%) Query: 46 KPLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTESTYYLS 105 K LEG+ +++ + GP A M LGDLGA VIKVE PG GD R + G S +Y + Sbjct: 3 KVLEGITVIEQGTFITGPAAGMLLGDLGANVIKVEMPGKGDPFRAFKG---GLYSPHYQT 59 Query: 106 VNRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIYC 165 NRNK+SIA+N K+P+ + L DV+++N+ PG +G G E + E+ P +IYC Sbjct: 60 YNRNKRSIALNTKEPEDLATFDALIRDADVYIQNFRPGTAERLGAGEERLRELNPRLIYC 119 Query: 166 SITGYGQTGPISQRAGYDAVASAVSGLMH-ITGPENGDPVRPGVAMTDLATGLYAYGAIM 224 +I+G+G GP + R YD VA A SG + + PEN P G AM D +G YA I+ Sbjct: 120 AISGFGNDGPYAGRPSYDTVAQAASGFLKLLVNPEN--PRVVGPAMADALSGFYAAYGIL 177 Query: 225 AGLIQKYKTGKGLFIDCNLLSSQV-----ACLSHIAANYLIGQKEAKRWGTAHGSIVPYQ 279 L+++ +TG+G +D ++L + A +++ N ++G + ++ Sbjct: 178 GALVERGRTGQGRRVDVSMLEAMCHFNLDAFTHYLSENEIMGPYSRPQVSQSY------- 230 Query: 280 AFKTKDG-YIVVGAGNNQQF-ATVCKILDLPELIDNSKYKTNHLRVHNRKELIKILSERF 337 + DG ++ + + ++F + ++ PEL+ + ++ T R+ +++++I++L + F Sbjct: 231 VMECADGKWVALHMSSPEKFWQGLANAMEYPELLQDERFATREGRIDHQEQMIEVLKQVF 290 Query: 338 EEELTSKWLYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVRY 397 ++W E VP+ P+ + V +PQV H L + EHPTVG V Y Sbjct: 291 RRHDRTEWCRRLEAEDVPHAPMYDTDEVLEDPQVKHLQLEVSTEHPTVGTFRTLRSPVSY 350 Query: 398 SKFKMSEARPPPLLGQHTTHILKEVLR 424 K E PP+L +H IL EV R Sbjct: 351 DGVKPLEVTAPPVLDEHREEILAEVKR 377 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: 405 Number of extensions: 24 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: 380 Length adjustment: 31 Effective length of query: 414 Effective length of database: 349 Effective search space: 144486 Effective search space used: 144486 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 24 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