Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate 3609737 Dshi_3120 L-carnitine dehydratase/bile acid-inducible protein F (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Dino:3609737 Length = 396 Score = 227 bits (578), Expect = 5e-64 Identities = 142/403 (35%), Positives = 209/403 (51%), Gaps = 17/403 (4%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L+ +RVLDL+ VLAGP+ G LA +GA+VIKVERPG+GD R G ++A + Sbjct: 11 LTGVRVLDLTNVLAGPYCGYQLALMGAEVIKVERPGSGDLARQLGADPARNAANMGIS-- 68 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 +L+ N K+SVT+D P+G+ L+R L A +D+L+ENF+ G + GL YD L+ NP Sbjct: 69 --FLAQNAQKRSVTLDLKHPQGKALLRRLVAGADVLVENFRPGVMDRLGLGYDVLRLDNP 126 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +L+YC+I+GFGQ GP YD ++QG+ G+MS+TG PE P +VG + D G Sbjct: 127 ELVYCAISGFGQDGPRKDDPAYDQIVQGVSGVMSITGAPE----TAPCRVGYPVADTFGG 182 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 + + AI AAL R G +D+++ + ++ + NYL G AP GN + Sbjct: 183 MTAAFAIAAALNARPR---GAFLDVSMTEALLSSMGWVVSNYLIGGVAPAPHGNENTTSA 239 Query: 244 PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQA 303 P F TAD + D Q+ A G P +AT + R A+R L + + Sbjct: 240 PSGTFATADQPINIAANRDSQWESLARHLGLEALLRHPDYATREARKAHRDALRAELERV 299 Query: 304 TVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPIR 363 + +WV +L GVP G + + + A+ GL E+ L ++P +P R Sbjct: 300 LTTRAARDWVAELNALGVPAGQVMTVPEALAEQS----GLIAEVA-LAEERLPLAGAPCR 354 Query: 364 LSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 + PP LG T VL LG+ A + A R GV+ Sbjct: 355 VDGRRPVPDAPPPTLGADTERVLAE-LGVPGAEIAALRAEGVI 396 Lambda K H 0.319 0.137 0.408 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: 459 Number of extensions: 25 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: 406 Length of database: 396 Length adjustment: 31 Effective length of query: 375 Effective length of database: 365 Effective search space: 136875 Effective search space used: 136875 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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