Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate WP_012585922.1 C665_RS01455 CoA transferase
Query= SwissProt::Q9HAC7 (445 letters) >NCBI__GCF_000310185.1:WP_012585922.1 Length = 396 Score = 181 bits (458), Expect = 5e-50 Identities = 132/405 (32%), Positives = 190/405 (46%), Gaps = 14/405 (3%) Query: 38 PQSDMNNIKPLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVG 97 P S+ PL GV+ILDLTR+L GP AT +L D GAEVIKVE GAGD RT G G Sbjct: 3 PASNAPARAPLAGVRILDLTRLLPGPLATQHLADYGAEVIKVEDTGAGDYARTMGA-MGG 61 Query: 98 TESTYYLSVNRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDE 157 S +Y VNRNK+S+ +++K G + L DV VE + PG + +GLGY + E Sbjct: 62 DTSWFYQLVNRNKRSLRLDLKQEAGRALFLRLVESADVVVEGFRPGVMERLGLGYAVLAE 121 Query: 158 IAPHIIYCSITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDPVRPGVAMTDLATG- 216 P ++ CSI+GYGQTGP + RAG+D +G++ G G P + + DL G Sbjct: 122 RNPRVVLCSISGYGQTGPYALRAGHDINYLGYAGVLDQIGCAGGAPALSNLQIGDLLGGT 181 Query: 217 LYAYGAIMAGLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLI-GQKEAKRWGTAHGSI 275 + A I+ L ++G+G +D ++ + A + A L G + G + Sbjct: 182 MGAVMGILVALFDARRSGRGREVDVSMTDAAFAHMIFPLAEVLAHGGVRPRGEDLLTGGV 241 Query: 276 VPYQAFKTKDG-YIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKILS 334 Y ++T DG Y+ VGA + + +C L +LI T R EL I Sbjct: 242 PCYGVYETADGRYMAVGALEEKFWGLLCTTLGRADLIP-GHLATGADGARVRGELATIFR 300 Query: 335 ERFEEELTSKWLYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPA 394 R + E W+ +F+ P+ ++ +PQ+ G+V+E + G A Sbjct: 301 GRSQRE----WVEVFDPVDCCVTPVLRLEESLRDPQLRARGMVVE-----TNGLCHAGAA 351 Query: 395 VRYSKFKMSEARPPPLLGQHTTHILKEVLRYDDRAIGELLSAGVV 439 VR P P T + E L D + L AGVV Sbjct: 352 VRLGGMPPIPDAPAPACAGADTDAILEALGVDAEELARLRGAGVV 396 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: 418 Number of extensions: 20 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 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