Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate GFF3565 PS417_18255 AMP-binding protein
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__WCS417:GFF3565 Length = 546 Score = 166 bits (421), Expect = 2e-45 Identities = 155/511 (30%), Positives = 223/511 (43%), Gaps = 61/511 (11%) Query: 47 AGSYTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAIN 106 A +T+ EL R G+ LR G++P +RV + ++ LG + G V + Sbjct: 55 ATHHTFSELQAHAARFGNFLREQ-GVKPGERVAGLMPRTVELLIAILGTWRIGAVYQPLF 113 Query: 107 TLLTESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLAT 166 T E L S AR V P L V ++V G Sbjct: 114 TAFGPKAIEQRLGCSEARWIVTDAHN----RPKLDDVIDCPRIIVTG------------- 156 Query: 167 GSEQFEAAPTRPDDHCFW-----------------------LYSSGSTGAPKGTVHIHSD 203 A P PDD+ FW + +SG+TG P + + Sbjct: 157 ------AGPRNPDDYDFWTVLDRQQADCVPELLDASAPFLLMCTSGTTG-PAKPLEVPLS 209 Query: 204 LIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVF 263 I + Y R + +RE D ++ A +AYGL + PLA G + + Sbjct: 210 AILAFKGYMRDSIDLREDDHFWNLADPGWAYGLYYAVTGPLACGRATLFYDGPFAVDSTC 269 Query: 264 ERLRRHQPDIFYGVPTLYASMLANPDCPKEGEL-RLRACTSAGEALPEDVGRRWQARFGV 322 + ++ G PT Y ++A + RLR +SAGE L V R + GV Sbjct: 270 RIIAKYAITNLAGSPTAYRLLIAAGAAFADTVRGRLRVISSAGEPLNPQVIRWFADELGV 329 Query: 323 DILDGIGSTEMLHIFLSNRAG---DVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQ 379 I D G TE + + L N G V G++G VPGYR+ ++D+ E+ G G L Sbjct: 330 VIHDHYGQTE-IGMVLCNHHGLRHPVREGSAGYAVPGYRIVVLDDAHRELPP-GRPGVLA 387 Query: 380 ISGPSSAVM----YWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIY 435 + S + Y+ P + F+ + SGD +ND+G + GR+DD++ SG Sbjct: 388 VDRERSPLCWFEGYFGMPTQA---FVDRYYLSGDIVELNDDGSISFVGRNDDVITTSGYR 444 Query: 436 VSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNL 495 V P +VESALI H AV+EAAV+G D KAF+VL L L+ HV+ Sbjct: 445 VGPFDVESALIEHPAVVEAAVIGKPDPQRTELIKAFVVLNSQSLPSTELAEVLRLHVRQR 504 Query: 496 LAPYKYPRWIEFVDDLPKTATGKIQRFKLRS 526 LA + YPR IEFV+ LPKT +GK+QRF LR+ Sbjct: 505 LAAHAYPREIEFVEHLPKTPSGKLQRFILRN 535 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: 761 Number of extensions: 33 Number of successful extensions: 5 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: 546 Length adjustment: 35 Effective length of query: 492 Effective length of database: 511 Effective search space: 251412 Effective search space used: 251412 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: 52 (24.6 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