Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_089322819.1 CHB58_RS03975 acetate--CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >NCBI__GCF_900188395.1:WP_089322819.1 Length = 631 Score = 155 bits (391), Expect = 5e-42 Identities = 145/545 (26%), Positives = 236/545 (43%), Gaps = 48/545 (8%) Query: 23 NAADDLIGRNLLAGRGGKTVYI--DDAGS---YTYDELALRVNRCGSALRTTLGLQPKDR 77 N + + R++ GR K + D+ G+ TY L VN+ +AL+ G++ DR Sbjct: 79 NITVNALDRHVKNGRKNKVAFFWEDEFGNEKVVTYGSLYTLVNKLANALKNA-GIKKGDR 137 Query: 78 VLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQ------- 130 V++ + ++ L + G V + + + + D+ A++ + + Sbjct: 138 VVIYMPLVVEQVAAMLACARIGAVHSVVYAGFSVPALRHRIEDAQAKMVITADMTIRRGR 197 Query: 131 --ELLPLFAPMLGKVPTLEHLVVAG---------GAGEDSLAALLATGSEQFEAAPTRPD 179 L + + + +E +VV G E + E + Sbjct: 198 AIPLKQIVDEAVRGLDNVEKVVVLRRLKPKVDLIGEKEIDFYEFIKDADTYCEPEVMDSE 257 Query: 180 DHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNG 239 D F LY+SGSTG PKG +H + + + ++E D+ + A + G Sbjct: 258 DPLFMLYTSGSTGKPKGVIHTTGGYMVGTYYSMKTVFDLKEDDIYWCTADPGWITGHSYI 317 Query: 240 LIFPLAVGATAVLMAERPTPAAV---FERLRRHQPDIFYGVPT-LYASMLANPDCPKEGE 295 + PL GAT VL P + + ++ IFY PT + M A P++ + Sbjct: 318 VYGPLVAGATQVLAEGAPNYPDFGRWWSLIEKYGVTIFYTAPTAIRMFMRAGEHWPEKYD 377 Query: 296 LR-LRACTSAGEALPEDVGRRWQARFGV------DILDGIGSTEMLHIFLSNRAG-DVHY 347 L LR S GE + + W F V I+D TE + ++ G + Sbjct: 378 LSSLRLLGSVGEPINPEA---WMWYFRVIGKERCPIVDTWWQTETGAVMITTIDGLPMKP 434 Query: 348 GTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWTR- 406 G +GKPVPG ++D++G + G L + P ++M K + W Sbjct: 435 GRAGKPVPGVVADVVDKEGNPVEP-NKGGFLVVRNPWPSMM--RTIHKNKEKYESYWNTI 491 Query: 407 -----SGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWED 461 +GD +++GY + GR+DD++ VSG + +EVESAL++H +V EAAV+G D Sbjct: 492 PGCYFAGDVATKDEDGYIMILGRADDVINVSGHRIGTMEVESALVSHPSVAEAAVIGKPD 551 Query: 462 EDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQR 521 + KAF++LK G E L LK HV+ L P IEFVD LPKT +GKI R Sbjct: 552 PVKGERIKAFVILKEGESPSEELVNSLKKHVRTELGALAVPSEIEFVDKLPKTRSGKIMR 611 Query: 522 FKLRS 526 L++ Sbjct: 612 RVLKA 616 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: 879 Number of extensions: 61 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: 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 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