Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate 3609948 Dshi_3330 Formyl-CoA transferase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Dino:3609948 Length = 411 Score = 300 bits (769), Expect = 4e-86 Identities = 161/405 (39%), Positives = 246/405 (60%), Gaps = 12/405 (2%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 G L ++V++L+ ++AGP G +LAD+GADVIKVE+P +GDD+R + PP D GE+ Sbjct: 7 GPLKGMKVIELAHIMAGPVCGMMLADMGADVIKVEKP-DGDDSRRFLPP---DINGES-- 60 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 A Y+ NR K+ ++++ P+ ++ L +D++IEN+++G + GL Y++L+ Sbjct: 61 --AAYMMMNRGKRGISLNLKDPDAVEVLHALLRDADVVIENYRMGTMEKLGLGYETLRKE 118 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 NP+LIYC I+GFG+TGPYA R G+D + QG+ GLMS+TG EG G PVK G ++DI Sbjct: 119 NPRLIYCEISGFGRTGPYAHRGGFDLIAQGMSGLMSITG--EGP-GRPPVKPGAPISDIT 175 Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241 +G+ + + AA AH G GQ +D +L + + Q+ TG AP+ G+AHP Sbjct: 176 SGIVAAMGVNAAYAHALRTGQGQRVDTSLFEAAITQTYWQSAIAFATGTAPEPEGSAHPI 235 Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301 PYQ F TADG + N + + EV + DDPRFATN+ R N + L+PL+ Sbjct: 236 NAPYQAFHTADGWINIGAANQKNWLRLLEVLEADELRDDPRFATNRDRRVNLSELVPLLE 295 Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361 +TT +W+ ++E+AG+P GP+ + ++ ADPQ +AR + +E H +AG+V + P Sbjct: 296 AHFETRTTQDWLVRMEEAGLPAGPVLTVPEMHADPQARAREMIVETEHPVAGRVQALGLP 355 Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 ++ SETP + PLLG+H+ VL LG D AV +G + Sbjct: 356 VKFSETPGAVQRPAPLLGQHSRAVLAD-LGYDADAVARLIASGAV 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: 479 Number of extensions: 20 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: 411 Length adjustment: 31 Effective length of query: 375 Effective length of database: 380 Effective search space: 142500 Effective search space used: 142500 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