Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_011385246.1 AMB_RS14445 benzoate-CoA ligase family protein
Query= SwissProt::Q8GQN9 (527 letters) >NCBI__GCF_000009985.1:WP_011385246.1 Length = 528 Score = 607 bits (1565), Expect = e-178 Identities = 310/522 (59%), Positives = 383/522 (73%), Gaps = 5/522 (0%) Query: 9 HSNTPPAIKIPERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRT 68 ++++ A+ IP YNAA I R++ GR K +ID GS+TY +L +VNR G+AL++ Sbjct: 5 NASSEHALDIPRDYNAATWFIDRHIKDGRSAKVAFIDADGSHTYAQLGEKVNRAGNALKS 64 Query: 69 TLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVV 128 LGL ++R+ + +LD +DFP+ F GAIK G+VPI +NTLLT DY YML+DS ARV V+ Sbjct: 65 -LGLHMENRIAMIMLDTVDFPSVFWGAIKAGIVPIPLNTLLTTGDYGYMLSDSRARVLVI 123 Query: 129 SQELLPLFAPMLGKVPTLEHLVVAG--GAGEDSLAALLATGSEQFEAAPTRPDDHCFWLY 186 S+EL P+L +P LEH+V++G G L+ ++A + + A T DD FWLY Sbjct: 124 SEELFDKVEPILPDLPLLEHVVISGKNAHGHTLLSDMMAAAEPKLKTAETTRDDVAFWLY 183 Query: 187 SSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAV 246 SSGSTGAPKG VH+ DL TA Y + +LGI E DV FSAAKLFFAYGLGNG+ F L V Sbjct: 184 SSGSTGAPKGAVHLQRDLPATAVHYGQQVLGITEDDVTFSAAKLFFAYGLGNGMTFSLHV 243 Query: 247 GATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKE-GELRLRACTSAG 305 GAT+VL+ +RPTP AV + L+ HQP IFYGVPTLY ++LA+P +E RLRAC SAG Sbjct: 244 GATSVLLKDRPTPEAVMKILKDHQPTIFYGVPTLYGTILADPQYRRETASTRLRACVSAG 303 Query: 306 EALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDED 365 EALPEDVGRRW+ RFG ILDG+GSTEMLHIFLSNR G+V YGTSGK VPGY L+++ +D Sbjct: 304 EALPEDVGRRWEERFGAAILDGLGSTEMLHIFLSNRHGEVRYGTSGKAVPGYDLKIVADD 363 Query: 366 GAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRS 425 G E+ G GEL + GPSSA YWN EK+ TF GEWT +GDKY V+D+GYY YAGR Sbjct: 364 GHELPQ-GEMGELVVRGPSSATAYWNQREKSLKTFRGEWTHTGDKYFVDDDGYYRYAGRG 422 Query: 426 DDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALR 485 DDMLKV GI+VSP EVE+ALI+HE VLEAAVVG D + L+KPKAF+VL PG E L+ Sbjct: 423 DDMLKVGGIWVSPFEVEAALISHEMVLEAAVVGEADSEGLVKPKAFVVLAPGETGSEVLK 482 Query: 486 TDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLRSA 527 L+A+VK LAPYKYPRWIEFV+ LPKTATGKIQRFKLR + Sbjct: 483 EQLQAYVKAKLAPYKYPRWIEFVEALPKTATGKIQRFKLRGS 524 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: 854 Number of extensions: 28 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: 528 Length adjustment: 35 Effective length of query: 492 Effective length of database: 493 Effective search space: 242556 Effective search space used: 242556 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