Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_058857116.1 AS188_RS00055 long-chain fatty acid--CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >NCBI__GCF_001482365.1:WP_058857116.1 Length = 568 Score = 179 bits (453), Expect = 3e-49 Identities = 161/512 (31%), Positives = 227/512 (44%), Gaps = 47/512 (9%) Query: 51 TYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLT 110 +Y L +V R LR LG+ DRV + + + F ++ G V + N L T Sbjct: 59 SYARLGEQVERAAEGLRR-LGVAAGDRVAIVLPNCPQHIVAFYAVLRLGAVVVEHNPLYT 117 Query: 111 ESDYEYMLTDSAARVAVVSQ----------ELLPLFAPMLGKVP------TLEHLVVAGG 154 + + D ARVA+V E L L A + V T L + Sbjct: 118 APELRHQFEDHGARVAIVWDRAADRIRSLPEDLRLDAVVAVDVTQAMPRRTRAALRLPLP 177 Query: 155 AGEDSLAALLA-----------TGSEQFEAAPTRPDDHCFWL--YSSGSTGAPKGTVHIH 201 A S A L +E A RP H L Y+SG+TG PKG + H Sbjct: 178 AARASRAQLTGPAPGTIPWRRLVAAEPLAADHPRPTAHDLALLQYTSGTTGLPKGAMLTH 237 Query: 202 SDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAA 261 +L A L + L E +VV LF A+GL G+ F +++GA VL PT A Sbjct: 238 RNLESNA-LMGQHWLHSGEDEVVHGVLPLFHAFGLTLGVTFAMSLGARLVLF---PTVRA 293 Query: 262 --VFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRA---CTSAGEALPEDVGRRW 316 V + LRR +P + VP +Y +L D +E LR S LP + RW Sbjct: 294 DLVLKALRRSRPTVLPAVPPVYEKLL---DAAEERGADLRGIAVAVSGAMTLPVPLVERW 350 Query: 317 QARFGVDILDGIGSTEMLHIFLSNRAGDVHY-GTSGKPVPGYRLRLIDEDGAEITTAGVA 375 + G +++G G TE + N D G+ G P P +RL+D + E G Sbjct: 351 ERATGGMLVEGYGLTECSPLVACNPLNDSRRAGSIGVPFPSTEIRLVDPETLEDVPRGHE 410 Query: 376 GELQISGPSSAVMYWNNPEKTAATFMGE-WTRSGDKYLVNDEGYYVYAGRSDDMLKVSGI 434 GEL + GP YW PE+TA + + W R+GD V+D+G+ R +++ G Sbjct: 411 GELWVRGPQVFRGYWKRPEETARVLVEDGWLRTGDVVTVDDDGFLRVVDRIKEVIITGGF 470 Query: 435 YVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKN 494 V+P EVE+AL H+ V +AAVVG +D A +VL PG E L+ H Sbjct: 471 NVAPTEVETALKLHDDVADAAVVGLDDGRGGEAVVAAVVLAPGAVLDEQA---LREHCYG 527 Query: 495 LLAPYKYPRWIEFVDDLPKTATGKIQRFKLRS 526 + YK PR I V+DLP+T GK R ++R+ Sbjct: 528 KVTRYKVPRRIVAVEDLPRTMLGKTLRREVRA 559 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: 795 Number of extensions: 56 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 527 Length of database: 568 Length adjustment: 36 Effective length of query: 491 Effective length of database: 532 Effective search space: 261212 Effective search space used: 261212 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 24 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