Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate RR42_RS32705 RR42_RS32705 CoA-transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Cup4G11:RR42_RS32705 Length = 405 Score = 406 bits (1044), Expect = e-118 Identities = 202/403 (50%), Positives = 271/403 (67%), Gaps = 2/403 (0%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L ++VLDL+RV+AGPWA Q LAD+GA V K+E+PG+GDDTR GP FL DA+G T ++ Sbjct: 5 LDGIKVLDLTRVVAGPWATQNLADMGATVYKIEKPGDGDDTRKMGP-FLNDAQGAATNDS 63 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 A+YL+ NR KQS+TID ++PEG LVR+LAA+ D+++EN+K G L YGLDY+S++A+ P Sbjct: 64 AFYLACNRGKQSLTIDISQPEGAELVRQLAARCDVVVENYKAGSLKKYGLDYESIRAVRP 123 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +IYCS+TGFG GPYA R YDF++QG+ GLMS G+P+G G P++ + +TDILTG Sbjct: 124 DVIYCSVTGFGPDGPYAARPAYDFILQGMAGLMSTCGQPDGSPGGEPMRTAIPITDILTG 183 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 LY+T ++L AL HR G GQ+ID A+LD VA + A+ Y TG P+R GN++P Sbjct: 184 LYATVSLLGALYHRQATGEGQYIDAAMLDASVAVNGHLALGYQMTGKLPRRAGNSNPVAA 243 Query: 244 PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQA 303 P + F DG I+ GN+GQF ++ G P+ A DPR+ N RVANR L I + Sbjct: 244 PSEVFACRDGHLIIASGNNGQFAALCKLLGIPELAADPRYTQNANRVANRDALRETIAER 303 Query: 304 TVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPIR 363 A+ + LE+AGVP GPIN+L +VF D QV+ RGL ++LPH VP + SP+R Sbjct: 304 VATWNAADLLASLERAGVPGGPINELDEVFEDAQVKHRGLLVQLPHGRGVDVPSLRSPMR 363 Query: 364 LSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 S TPV R PP+LGEHT L+ LGL + V R G+L Sbjct: 364 FSATPVAMR-CPPMLGEHTDAALRAELGLSDGDVAGLRARGIL 405 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: 549 Number of extensions: 21 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: 406 Length of database: 405 Length adjustment: 31 Effective length of query: 375 Effective length of database: 374 Effective search space: 140250 Effective search space used: 140250 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