Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate RR42_RS29900 RR42_RS29900 CoA-transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Cup4G11:RR42_RS29900 Length = 407 Score = 436 bits (1122), Expect = e-127 Identities = 208/405 (51%), Positives = 273/405 (67%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 G L+ ++VLDLSR+LAGPW+ Q+L+DLGADV+KVERPG GDDTRAWGPPFL G T Sbjct: 3 GPLAGIKVLDLSRILAGPWSTQLLSDLGADVMKVERPGTGDDTRAWGPPFLTREDGTTTE 62 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 E+AY+L ANR K+S+T+D + GQ L+ EL D+ +EN+K G + YGLD+ +L I Sbjct: 63 ESAYFLCANRGKRSITLDVSSKVGQDLLHELVKDCDVFVENYKFGDMQRYGLDFKTLSEI 122 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 NP+L+YCSITGFGQTGPY KRAGYDF++Q +GGLMS+TG +G G GP K GV ++D++ Sbjct: 123 NPRLVYCSITGFGQTGPYRKRAGYDFVVQAMGGLMSITGERDGVPGGGPQKCGVPISDLM 182 Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241 TG+Y++ AI++AL R G GQ+IDM+LLD QVA LANQA NYL G+ P+R GNAHPN Sbjct: 183 TGMYASVAIVSALFERVGSGRGQYIDMSLLDTQVAWLANQASNYLVGGSHPRRWGNAHPN 242 Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301 + PYQ FP +DG I+ VGND QFR E G DD R+ N R+ NR L+ ++ Sbjct: 243 LAPYQSFPASDGSLIVAVGNDRQFRAMCEALGLINLPDDDRYRRNADRLKNRESLVEVLS 302 Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361 + W+ LE GVPCGPI + + DP ++AR + LPH PQVA+P Sbjct: 303 ARFEEEERDTWLKLLESVGVPCGPIQSIPEALEDPHIRAREMVFSLPHSSGASAPQVANP 362 Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 I+ S + ++Y APP LGEHT +L+ LG + A R G + Sbjct: 363 IKFSRSSIDYLRAPPALGEHTETILKNELGKSVEQIEAMRRDGTI 407 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: 537 Number of extensions: 19 Number of successful extensions: 1 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: 407 Length adjustment: 31 Effective length of query: 375 Effective length of database: 376 Effective search space: 141000 Effective search space used: 141000 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