Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate CA265_RS16340 CA265_RS16340 acetate--CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Pedo557:CA265_RS16340 Length = 631 Score = 149 bits (376), Expect = 3e-40 Identities = 148/549 (26%), Positives = 239/549 (43%), Gaps = 50/549 (9%) Query: 21 RYNAADDLIGRNLLAGRGGKTVYI-------DDAGSYTYDELALRVNRCGSALRTTLGLQ 73 + N ++ + R+L A G K + +++ +YTY L RV R + L+ G + Sbjct: 57 KLNITENCLDRHL-ATNGDKPAIVWEPNNPEEESVTYTYKMLHERVCRFANVLKRN-GAK 114 Query: 74 PKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQ--- 130 DR+ + + + L + G V I + + DS +V + + Sbjct: 115 KGDRICIYMPMVPELAIAVLACARIGAVHSVIFGGFSAKSIADRINDSKCKVVITADGSY 174 Query: 131 ------ELLPLFAPMLGKVPTLEHLVVAGGAG-------------EDSLAALLATGSEQF 171 L + L PT+E +V ED + + ++ Sbjct: 175 RGNKQIPLKDVIDDALIGCPTVEKCIVLTHIRTPVSMLKGRDVWWEDEVKHV----NDIC 230 Query: 172 EAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLF 231 EA +D F LY+SGSTG PKG VH + A + + G+V F A + Sbjct: 231 EAEEMDAEDMLFILYTSGSTGKPKGVVHTCGGYMVYAGYTFSNVFNYQPGEVYFCTADIG 290 Query: 232 FAYGLGNGLIFPLAVGATAVL---MAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANP 288 + G + PL+ GAT+VL + PTP+ ++ + +H+ + Y PT S+++ Sbjct: 291 WITGHSYIVYGPLSQGATSVLFEGIPTYPTPSRFWDIVEKHKVNTLYTAPTAIRSLMSYG 350 Query: 289 DCPKEGE--LRLRACTSAGEALPEDVGRRWQARFG---VDILDGIGSTEMLHIFLSNRAG 343 D P G+ +R S GE + E+ + + G I+D TE I +S A Sbjct: 351 DDPLNGKDLSSIRVLGSVGEPINEEAWHWFDEKIGHGKAPIVDTWWQTETGGIMISPIAT 410 Query: 344 DVHYGTSGK--PVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMY--WNNPEKTAAT 399 S P+PG + L+DE+G EI GV G L I P ++ + + E+ T Sbjct: 411 VTPTKPSFATLPLPGIQPILVDENGNEIEGNGVMGNLCIKFPWPGMLRTTYGDHERCKQT 470 Query: 400 FMGEWTR---SGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAV 456 + + +GD L +++GYY GR DD+L VSG + EVE+A+ H V+E+AV Sbjct: 471 YFSTYDNLYFTGDGCLRDEDGYYRITGRVDDVLNVSGHRIGTAEVENAINMHAGVVESAV 530 Query: 457 VGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTAT 516 VG+ + AF++ +G E + D+ V ++ P I FV LPKT + Sbjct: 531 VGYPHDVKGQGIYAFVIYPEMHGEAELSKKDILQTVTRVIGAIAKPDKILFVSGLPKTRS 590 Query: 517 GKIQRFKLR 525 GKI R LR Sbjct: 591 GKIMRRILR 599 Lambda K H 0.319 0.138 0.412 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: 893 Number of extensions: 47 Number of successful extensions: 6 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: 527 Length of database: 631 Length adjustment: 36 Effective length of query: 491 Effective length of database: 595 Effective search space: 292145 Effective search space used: 292145 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: 53 (25.0 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