Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_042117995.1 RHE_RS04635 malonyl-CoA synthase
Query= SwissProt::Q8GQN9 (527 letters) >NCBI__GCF_000092045.1:WP_042117995.1 Length = 504 Score = 186 bits (473), Expect = 1e-51 Identities = 146/478 (30%), Positives = 223/478 (46%), Gaps = 11/478 (2%) Query: 49 SYTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTL 108 ++TY + R A+ TLG++P DRV V V + +L ++ G V + +NT Sbjct: 27 TWTYGDAFALSGRIAGAM-DTLGIRPGDRVAVQVDKSAEALILYLACVRSGAVYLPLNTA 85 Query: 109 LTESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLATGS 168 T ++ +Y L D+ R+ VV+ + + + + A G+G SL L Sbjct: 86 YTLAELDYFLGDAEPRLVVVASGAREGVETIAKRHGAIVETLDADGSG--SLLDLARDEP 143 Query: 169 EQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAA 228 F A DD LY+SG+TG KG + H +L+ A L R + D + A Sbjct: 144 ADFVDASRAADDLAAILYTSGTTGRSKGAMLTHGNLLSNA-LTLRDYWRVTADDRLIHAL 202 Query: 229 KLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANP 288 +F +GL L GA+ L+++ + Q + GVPT Y +L +P Sbjct: 203 PIFHTHGLFVATNVTLLAGASMFLLSKFDADEVIS---LMPQATMLMGVPTFYVRLLQSP 259 Query: 289 DCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYG 348 KE ++R S L + +QAR G IL+ G TE + G G Sbjct: 260 RFGKEAAAKIRLFISGSAPLLAETHTEFQARTGHAILERYGMTETNMNTSNPYDGKRIAG 319 Query: 349 TSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGE-WTRS 407 T G P+PG +R+ D ++ G ++I GP+ YW PEKTAA F G+ + S Sbjct: 320 TVGLPLPGVTVRVTDPATGQVLPPEQTGMIEIKGPNVFKGYWRMPEKTAAEFTGDGFFIS 379 Query: 408 GDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIK 467 GD ++ +GY GR D++ G + P EVES + E V+E+AV+G D Sbjct: 380 GDLGKIDSDGYVHIVGRGKDLVISGGYNIYPKEVESEIDQIEGVVESAVIGVPHPDFGEG 439 Query: 468 PKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 A +V KPG E +T + A +++ LA YK P+ I F +DLP+ GK+Q+ LR Sbjct: 440 VTAVVVRKPGAALDE--KTIISA-LQDRLARYKQPKRIIFAEDLPRNTMGKVQKNILR 494 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: 681 Number of extensions: 38 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: 504 Length adjustment: 35 Effective length of query: 492 Effective length of database: 469 Effective search space: 230748 Effective search space used: 230748 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 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