Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate N515DRAFT_3223 N515DRAFT_3223 Crotonobetainyl-CoA:carnitine CoA-transferase CaiB
Query= SwissProt::Q9HAC7 (445 letters) >FitnessBrowser__Dyella79:N515DRAFT_3223 Length = 384 Score = 191 bits (485), Expect = 3e-53 Identities = 114/373 (30%), Positives = 194/373 (52%), Gaps = 8/373 (2%) Query: 47 PLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTESTYYLSV 106 PL G+++LDL+ +AGP+ L D GA+V+K+E PG GD+ R + P + +ES +L V Sbjct: 15 PLHGIRVLDLSAYIAGPYGCTLLADQGADVLKIEPPG-GDNLRQY-PSTLPSESRAFLGV 72 Query: 107 NRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIYCS 166 NR+K+ + +++K+P ++ L DV V N+ P +G+ ++ + I P +IYC+ Sbjct: 73 NRSKRGMVLDLKNPADHAVLLRLVRDADVLVHNFRPNVPKRLGIDFDQLTAINPRLIYCA 132 Query: 167 ITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDP-VRPGVAMTDLATGLYAYGAIMA 225 +TGYG++GP+ +AGYD V ++G+ + G G P + G + A L A G + + Sbjct: 133 VTGYGESGPMRDKAGYDQVLQTMTGMCALQGKRGGPPEIIYGSVVDYYAAALLAAG-VSS 191 Query: 226 GLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLIGQKEAKRWGTAHGSIVPYQAFKTKD 285 L ++ ++G G F+ +LL A L+ +A + E+ G S T D Sbjct: 192 ALYERERSGLGQFVGVSLLR---AALTMQSARLIWADGESLDIGRDMRSGGVTGIHPTAD 248 Query: 286 GYIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKILSERFEEELTSKW 345 G+I + A + + +C+ L L ++ +Y T R + E++ L E W Sbjct: 249 GHIYISANTPRFWRALCEKTGLHALAEDPRYDTVRKRAEHAAEILPQLHEALAARPAMAW 308 Query: 346 LYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVRYSKFKMSEA 405 LF G VP ++++F PQVL G+V +EHP VG+ ++++ + E Sbjct: 309 EALF-GDEVPSAAARRIEDMFEHPQVLAEGIVGTIEHPVVGRYHGVAQSIKFGRTPGPEP 367 Query: 406 RPPPLLGQHTTHI 418 P+LGQHT + Sbjct: 368 FAAPMLGQHTDEV 380 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: 429 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: 384 Length adjustment: 31 Effective length of query: 414 Effective length of database: 353 Effective search space: 146142 Effective search space used: 146142 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