Align 4-hydroxybenzoate--CoA/benzoate--CoA ligase; 4-hydroxybenzoyl-CoA synthetase; EC 6.2.1.25; EC 6.2.1.27 (characterized)
to candidate GFF944 HP15_923 acetyl-coA synthetase/AMP-(fatty) acid ligase
Query= SwissProt::Q53005 (539 letters) >FitnessBrowser__Marino:GFF944 Length = 549 Score = 188 bits (478), Expect = 4e-52 Identities = 149/491 (30%), Positives = 238/491 (48%), Gaps = 24/491 (4%) Query: 33 SLSYGELRDAVARVGPMLARLGVEQENRIALVLKDTVDFPILFWGAIRAGIVPVLLNTRL 92 +L++ EL++A AR L G+ + +R+A +L T + I+ G +RAG V L T Sbjct: 61 TLTFAELKEASARFANYLKSQGIGKGDRVAALLPRTPELLIVIAGTLRAGAVYQPLFTAF 120 Query: 93 TADQYRYLLEDSRSRVVFASSEFLPVIEEAAADLPHLRTIIAVGDAPAPTLQLANLLATE 152 + Y E + +++V + E P + + P + + A P + LA + Sbjct: 121 GSGAIEYRFERASTKLVVTNPENYPKLNDVKVCPPVVGVNASEIGADIPDFE--ETLAAQ 178 Query: 153 QEGGAPAATCADDIAYWQYSSGTTGMPKGVMHVHSSPRVMAENAGRRIGYREDDVVFSAA 212 P DD ++SGT G KGV + I ++ D ++ A Sbjct: 179 SSDFEPVMIKGDDPFLQMFTSGTVGKSKGVAVPAKALLAFYVYMKYAIDLQDGDRFWNVA 238 Query: 213 KLFFAYGLGNAMFCPMGIGATSVLYPERPTADSVFDTLRLHQPTLLFAVPTLYAAMLADP 272 +AYGL A+ P+ +G + P T +S +D +R ++ T L A PT Y + A+ Sbjct: 239 DPGWAYGLYYAVVGPLLMGHATHFNPGGFTPESTYDMIRKYKITNLAAAPTAYRLLKAND 298 Query: 273 RSRTETLPDRLRLCVSAGEPLPAQVGLNW-RNRFGHDIVNGVGSTEMGHLFLT--NLPHA 329 E LR+ SAGEPL +V +NW RNR + + G TE G L H Sbjct: 299 HVLPEGENLGLRVASSAGEPLNPEV-VNWIRNRHYCPVKDHYGQTETGMTCCNFHGLAHP 357 Query: 330 VEYGTSGVPVDGYRLRLVGDRGQDVADDEIGELLVSGGSSAA----GY-WNQRDKTRTTF 384 V G+ G G+++ + ++ + V + E+G+L V +S GY W ++D F Sbjct: 358 VREGSMGYASPGHKVVALNEKNEVVGEGEVGQLAVDVKASPLFHFDGYTWGEKD----PF 413 Query: 385 VGEWTRTGDKYHRRADGVYTYCGRTDDIFKVSGIWVSPFEIEQALMSHAKVLEAAVI--P 442 V + TGD +G +++ GR DDI +G V P ++E L+ HA V E+ V+ P Sbjct: 414 VNGYYLTGDMVINHGNGNFSFSGRDDDIITTAGYRVGPADVESTLLEHAAVAESGVVGKP 473 Query: 443 AEDTDGLIKPKAFIVLASRGDI---DPGALFDELKEHVKSAIGPWKYPRWIQIMDDLPKT 499 E +I KA++V+ +GD D AL DEL+E V+ + +PR I+ +D+LPKT Sbjct: 474 DEKRGSII--KAYVVI--KGDYALGDEQALKDELQELVRRRLSTHAFPREIEFVDELPKT 529 Query: 500 SSGKLQRYLLR 510 SGK+QR++LR Sbjct: 530 PSGKIQRFVLR 540 Lambda K H 0.320 0.138 0.415 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: 714 Number of extensions: 28 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: 539 Length of database: 549 Length adjustment: 35 Effective length of query: 504 Effective length of database: 514 Effective search space: 259056 Effective search space used: 259056 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 (21.8 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