Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate WP_073038547.1 BUB04_RS08370 CaiB/BaiF CoA-transferase family protein
Query= SwissProt::Q9HAC7 (445 letters) >NCBI__GCF_900129305.1:WP_073038547.1 Length = 392 Score = 229 bits (583), Expect = 2e-64 Identities = 140/396 (35%), Positives = 218/396 (55%), Gaps = 10/396 (2%) Query: 47 PLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTESTYYLSV 106 P EG+++LDL+R+L GPF +M L DLGA+VIKVE P GD R W PP +G S +++ + Sbjct: 4 PFEGIRVLDLSRLLPGPFCSMLLADLGADVIKVEDPKVGDYIRWW-PPKIGANSGFHVVL 62 Query: 107 NRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIYCS 166 NRNK+S+ +N+K+P G + LAA DV +E + PG + +G+GY + E+ P IIYC+ Sbjct: 63 NRNKRSLTLNLKEPAGRDVFVRLAASADVVLEGFRPGVMDRLGVGYGALREVNPRIIYCA 122 Query: 167 ITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDPVRPGVAMTDLATG-LYAYGAIMA 225 ITGYGQ GP + RAG+D A+SG++ G GDPV PGV + DL G L A +I A Sbjct: 123 ITGYGQDGPRADRAGHDINYLALSGVLSYCG-RGGDPVVPGVQIGDLGGGALTAAFSIAA 181 Query: 226 GLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLI-GQKEAKRWGTAHGSIVPYQAFKTK 284 L + +TG+G ID ++ A +L G+ + + Y ++T+ Sbjct: 182 ALFWRERTGEGQMIDISMTDGAAAWNCLRWGKFLADGRVPEPGDDLLNHGLACYDVYRTR 241 Query: 285 DG-YIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKILSERFEEELTS 343 DG ++ +GA Q + C+++ P+ ++ ++KEL ++E F + + Sbjct: 242 DGRHMSLGALEPQFWKAFCRVMGRPDWDRPDYFQPG----PHQKELRDQVAEAFAGKTQA 297 Query: 344 KWLYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVRYSKFKMS 403 +W+ +FE P+ N+ V + + H +V+E+ H G G A ++SK Sbjct: 298 QWVRIFEAEDCCCEPVLNLAEVLDDEAMRHRRMVVELHHQAWGAYRQMGLAPKFSKTSGE 357 Query: 404 EARPPPLLGQHTTHILKEVLRYDDRAIGELLSAGVV 439 P LG+HT +L E YD+ AI +L + GVV Sbjct: 358 IRTHAPDLGEHTRDVLLEA-GYDEGAIEKLRAEGVV 392 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: 474 Number of extensions: 21 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: 392 Length adjustment: 32 Effective length of query: 413 Effective length of database: 360 Effective search space: 148680 Effective search space used: 148680 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 Apr 09 2024. 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