Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_076582976.1 BB347_RS13070 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_001971705.1:WP_076582976.1 Length = 404 Score = 276 bits (707), Expect = 6e-79 Identities = 151/403 (37%), Positives = 228/403 (56%), Gaps = 14/403 (3%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L + VLDLS + G + +LA+ GA+V+K+E+PG GD R GPPF++ E+ Sbjct: 8 LEGVTVLDLSTFVTGGFCSAMLANQGAEVLKIEQPGYGDAIRHSGPPFIEG-------ES 60 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 YY + N K+S+ +D P + + EL ++DI I+NF+ G +DYD++ N Sbjct: 61 PYYWTVNYGKKSLELDLKNPRAKEALYELVEETDIFIQNFRPGTAERLEVDYDTIAQHNE 120 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +IY +I+ FGQTGP+ +RAGYD +IQG+GG+M +T G+EG PVK G+ +TD++T Sbjct: 121 DVIYLAISAFGQTGPWRERAGYDLLIQGMGGIMDVT----GEEGRQPVKTGLPMTDLITS 176 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 ++++ + AL R+ G G++ID+ +L+ + L QA + GN +R+G P + Sbjct: 177 MWASFGAMTALYRRERTGDGEYIDLGMLESTLPWLTKQA-GQVFAGNETRRMGTKDPVLA 235 Query: 244 PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQA 303 PYQ F T DG + + N+ + + E +P +D RF TN RV + L I Sbjct: 236 PYQTFETKDGFLNVCILNEKLWGELCEALERPDLPEDDRFETNADRVDHLDALEAEIEAT 295 Query: 304 TVFKTTAEWVTQL-EQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPI 362 KTT EW+ + E AGVP GP+ D+ + +PQ++ARG EL H G VP + P+ Sbjct: 296 LGTKTTDEWIEIIAEDAGVPAGPVYDVEEALTNPQIEARGTITELEHPELGTVPVIEHPL 355 Query: 363 RLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGV 405 + + APPLLGEH +V R LG EA + E GV Sbjct: 356 KFDRAETGFDRAPPLLGEHNRDVF-RDLGYTEAELDELAEEGV 397 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: 441 Number of extensions: 25 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: 404 Length adjustment: 31 Effective length of query: 375 Effective length of database: 373 Effective search space: 139875 Effective search space used: 139875 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 24 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