Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_073037622.1 BUB04_RS05220 CaiB/BaiF CoA-transferase family protein
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_900129305.1:WP_073037622.1 Length = 400 Score = 453 bits (1165), Expect = e-132 Identities = 232/404 (57%), Positives = 287/404 (71%), Gaps = 12/404 (2%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 LS ++VLDLSRVLAGP+ +L D+GADVIKVERPG GDDTR WGPP E EA Sbjct: 7 LSDVKVLDLSRVLAGPYCSMMLGDMGADVIKVERPGAGDDTRHWGPP-------EAGGEA 59 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 AYYL NRNK+S+T+D + EG+ ++R LAA+SDILIEN+KVG L GL Y LK +NP Sbjct: 60 AYYLCVNRNKRSITVDLKKEEGREIIRRLAAQSDILIENYKVGTLPKMGLGYVDLKKLNP 119 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +LIYCSITGFGQ GPY + GYDFMIQG+GG+MS+TG P+G P+KVGVA+ DI G Sbjct: 120 RLIYCSITGFGQNGPYKDKPGYDFMIQGMGGVMSITGDPDGP----PMKVGVAIVDITAG 175 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 L++ +AILAAL HRD G GQ+ID+ALLD VA LAN NYL +G P+R GNAHPNIV Sbjct: 176 LFACSAILAALRHRDRTGRGQYIDIALLDAVVAWLANVGSNYLVSGELPRRYGNAHPNIV 235 Query: 244 PYQDFPTADGDFI-LTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQ 302 PY+ F T DG +I L VGND Q++ F +AG A DPRFATN RV +R LIPL+ + Sbjct: 236 PYEPFKTRDGTYIALAVGNDRQWQDFCRLAGLDHLAHDPRFATNPQRVIHRDELIPLVAE 295 Query: 303 ATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPI 362 A + KT +W+ +L++ +PCGPIN L +VF+DPQV+AR + E+PH AG V VASP+ Sbjct: 296 AMLKKTADQWLEELDKLKIPCGPINTLDRVFSDPQVKAREMVAEVPHPTAGSVKLVASPM 355 Query: 363 RLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 + SETP PPLLGEHT EVL LG + + RE GV+ Sbjct: 356 KFSETPCGIDRHPPLLGEHTDEVLHAELGYGDEEIARLRELGVV 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: 579 Number of extensions: 25 Number of successful extensions: 4 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: 400 Length adjustment: 31 Effective length of query: 375 Effective length of database: 369 Effective search space: 138375 Effective search space used: 138375 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 Apr 09 2024. 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