Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate PfGW456L13_4548 L-carnitine dehydratase/bile acid-inducible protein F (EC 2.8.3.16)
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4548 Length = 397 Score = 221 bits (562), Expect = 4e-62 Identities = 142/407 (34%), Positives = 219/407 (53%), Gaps = 19/407 (4%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 LS ++V+++ ++A P+A ++LA+ GA+VIK+E G GD R W + T Sbjct: 5 LSAIKVIEIGTLIAAPFAARMLAEFGAEVIKIEAMGQGDPLRKW-------RKLHEGTSL 57 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 +YL + RNK+S+ ++ PEG LV++LA +D+LIEN + G L GL +D L A+NP Sbjct: 58 WWYLQS-RNKKSLALNLKSPEGIELVKQLATSADVLIENLRPGALEKLGLGWDVLHALNP 116 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 L I+G+GQTGPY R G+ + + +GG+ TG P G+ P +VGV+L D L Sbjct: 117 NLTLVRISGYGQTGPYRDRPGFGAIGEAMGGIRYTTGTP----GSPPARVGVSLGDSLAS 172 Query: 184 LYST-AAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNI 242 L++ A+++ L + GGGQ +D++L + + + Y G+ +R G A P I Sbjct: 173 LHAVIGALMSLLRVKTGQGGGQIVDVSLAESVFNVMESLVPEYDMLGHVRERSGGALPGI 232 Query: 243 VPYQDFPTADGDFILTVGN-DGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301 P + TADG +++ GN D +++ + G+ A+ P FA N R A +L I Sbjct: 233 APSNTYLTADGAYVVIAGNSDPIYKRLMQTIGRADLAEAPEFAHNDGRAAKSNLLDAAIT 292 Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAM--ELPHLLAGKVPQVA 359 T E + LE A VP G I +A + ADP QAR + + ELP K+P + Sbjct: 293 HWTSSLPIDEVLAALEAAEVPAGRIYSVADIVADPHYQARDMLLNAELPGGATVKMPGIV 352 Query: 360 SPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 +LSETP + P LG+HT +L + LGL + + GV+ Sbjct: 353 P--KLSETPGGVNWSGPGLGQHTDGILAQ-LGLTAMDIERLKVEGVV 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: 437 Number of extensions: 24 Number of successful extensions: 5 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: 397 Length adjustment: 31 Effective length of query: 375 Effective length of database: 366 Effective search space: 137250 Effective search space used: 137250 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