Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate CA265_RS08550 CA265_RS08550 carnitine dehydratase
Query= SwissProt::Q9HAC7 (445 letters) >FitnessBrowser__Pedo557:CA265_RS08550 Length = 383 Score = 195 bits (495), Expect = 2e-54 Identities = 125/385 (32%), Positives = 196/385 (50%), Gaps = 17/385 (4%) Query: 46 KPLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPP--FVGTESTYY 103 +PLEG+ +L+ + LAGP A + L DLGA VIK+ERP GD R FV +S + Sbjct: 3 RPLEGLLVLEFCQFLAGPSAGLKLADLGARVIKIERPKTGDACRQLSIKNLFVDEDSLLF 62 Query: 104 LSVNRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHII 163 ++NRNK+S A ++K+P+ ++ +K+L + DV N+ PG + +GL Y+ + I P I+ Sbjct: 63 HTINRNKESYAADLKNPEDLEKLKKLISKADVMTHNFRPGVMEKIGLDYQTVQNINPKIV 122 Query: 164 YCSITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDPVRPGVAMTDLATGLYAYGAI 223 Y +TGYG GP + G D + +VSGL ++G + PV G++++D+ G + I Sbjct: 123 YGVVTGYGNEGPWKNKPGQDLLVQSVSGLTFLSGVDVDGPVPFGLSVSDIMCGNHLVQGI 182 Query: 224 MAGLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYL-IGQKEAKR---WGTAHGSI-VPY 278 MA LI++ KT K + ++ +LL S + + YL G K R G+AH + PY Sbjct: 183 MAALIKRAKTNKSVLVEVSLLESILDVQFEVLTTYLNDGGKLPDRSGAKGSAHAYLSAPY 242 Query: 279 QAFKTKDGYIVVGAGNNQQFATV--CKILDLPELIDNSKYKTNHLRVHNRKELIKILSER 336 ++T DGYI + GN + C I DL Y NR +LI L+ Sbjct: 243 GMYETADGYIAMAMGNLPNICAIINCDITDL--------YVEAGSAFENRDQLIVRLAAT 294 Query: 337 FEEELTSKWLYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVR 396 F++E T W+ L E G+ + N + A + E+ I +R Sbjct: 295 FKKENTKTWVELLENHGIWCAEVLNYQKATALSTYKKLDIAQELNLDGGKTIKTTVSPIR 354 Query: 397 YSKFKMSEARPPPLLGQHTTHILKE 421 + K+ ++ P LG +T+ I KE Sbjct: 355 LDREKLFASKAAPKLGGNTSDINKE 379 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: 384 Number of extensions: 20 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: 383 Length adjustment: 31 Effective length of query: 414 Effective length of database: 352 Effective search space: 145728 Effective search space used: 145728 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