Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate PfGW456L13_3635 L-carnitine dehydratase/bile acid-inducible protein F
Query= SwissProt::Q9HAC7 (445 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3635 Length = 409 Score = 315 bits (808), Expect = 1e-90 Identities = 169/399 (42%), Positives = 247/399 (61%), Gaps = 5/399 (1%) Query: 45 IKPLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTESTYYL 104 ++ ++GVKI+DL+R L+GPF TM L DLGA+VIK+E GD +RTWGP F STYYL Sbjct: 1 MQAMQGVKIVDLSRALSGPFCTMVLADLGADVIKIEPGPTGDMSRTWGP-FDRGVSTYYL 59 Query: 105 SVNRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIY 164 S NRNK+ + ++++ P+G+ I++L DV +EN+ PG L +MGLGYE + P ++ Sbjct: 60 SCNRNKRGMCIDLRTPEGLTTIQQLIDDADVVIENFKPGTLESMGLGYEVLSARNPRLVL 119 Query: 165 CSITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDPVRPGVAMTDLATGLYAYGAIM 224 SI +G GP+S G+D +A SGLM +TG +GDP R G A+ DL +G++ A++ Sbjct: 120 GSINAFGADGPMSSWPGFDQIAQGYSGLMSLTGFVDGDPTRTGTAIGDLTSGMWLVTAVL 179 Query: 225 AGLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLIGQKEAKRWGTAHGSIVPYQAFKTK 284 A L+++ +TG+G + +LL+S V LS YL +R G AH I PY F+TK Sbjct: 180 AALLERERTGRGQHVSTSLLASLVGLLSVHGQRYLSLGDVPRRTGNAHSVIAPYGVFQTK 239 Query: 285 DGYIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKILSERFEEELTSK 344 DG + + + + +C +LDLPEL D+S++ TN RV R EL +IL R + + Sbjct: 240 DGPLNLAPITSAMWGRLCILLDLPELPDDSRFATNEARVERRDELREILESRLKTRSKRE 299 Query: 345 WLYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKI-SVPGPAVRYSKFKMS 403 W LF +G+P GPIN + VF +PQVLH+ L + HPT+G + V P + +S Sbjct: 300 WTSLFVDAGLPAGPINTLDEVFDDPQVLHSQLTETLTHPTLGALRQVVTPVFCANDSVVS 359 Query: 404 EARPPPLLGQHTTHILKEVLRYDDRAIGELLSAGVVDQH 442 RPPPLLG+HT +L+E +D +I LL+A +V Q+ Sbjct: 360 --RPPPLLGEHTVEVLREA-GFDAASINALLAAKIVFQN 395 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: 501 Number of extensions: 18 Number of successful extensions: 3 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: 409 Length adjustment: 32 Effective length of query: 413 Effective length of database: 377 Effective search space: 155701 Effective search space used: 155701 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: 51 (24.3 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