Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate BPHYT_RS07105 BPHYT_RS07105 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__BFirm:BPHYT_RS07105 Length = 401 Score = 315 bits (806), Expect = 2e-90 Identities = 179/406 (44%), Positives = 234/406 (57%), Gaps = 19/406 (4%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 GAL L+V+DLSRVL GP+ Q LAD GA VIK+E P NGD+TR WGPPF D Sbjct: 12 GALQGLKVIDLSRVLGGPYCTQALADHGAQVIKLEPP-NGDETRGWGPPFYGDT------ 64 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYD-SLKA 120 A Y+ NRNKQ + +D +R EG+ ++ +L +D+L+ENFK G L +G+DY+ L+ Sbjct: 65 -AWYFAGVNRNKQGIAVDLSREEGRAILWKLLEDADVLVENFKPGTLERWGMDYERDLRE 123 Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180 P+LI+C+++GFG GP GYD IQ + GLMS+ G +G +VG+ + D+ Sbjct: 124 RFPKLIHCAVSGFGPDGPLGGLPGYDAAIQAMTGLMSVNGERDGPA----TRVGLPVVDM 179 Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240 +TGL + A IL ALA R G GQ ID+AL D V+ L NY +G P+R GNAHP Sbjct: 180 VTGLNALAGILLALAERAKSGRGQSIDIALYDCGVSLLHPHLPNYFGSGRTPQRSGNAHP 239 Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300 NI PY + TA L VGND QF K G P+ ADDPR+ N+ R A+R L + Sbjct: 240 NITPYDSYRTATAPIFLAVGNDRQFAKLCAHLGAPELADDPRYVDNRSRCAHREPLKAAL 299 Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360 L AGVPCGP+ + V P RGL +E+ G+ AS Sbjct: 300 ESLLTAHECEPLAHALINAGVPCGPVQTVDVVARHPHTLHRGLVVEM-----GEYRGTAS 354 Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 PI+LS TP YR+APP LG T +VL + LG+D A E+GVL Sbjct: 355 PIKLSRTPATYRSAPPSLGADTRDVLDK-LGIDAATQQRLLESGVL 399 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: 515 Number of extensions: 33 Number of successful extensions: 7 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: 401 Length adjustment: 31 Effective length of query: 375 Effective length of database: 370 Effective search space: 138750 Effective search space used: 138750 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