Align 4-hydroxybenzoate--CoA/benzoate--CoA ligase; 4-hydroxybenzoyl-CoA synthetase; EC 6.2.1.25; EC 6.2.1.27 (characterized)
to candidate Dsui_2069 Dsui_2069 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
Query= SwissProt::Q53005 (539 letters) >FitnessBrowser__PS:Dsui_2069 Length = 529 Score = 165 bits (417), Expect = 5e-45 Identities = 148/499 (29%), Positives = 218/499 (43%), Gaps = 27/499 (5%) Query: 31 QRSLSYGELRDAVARVGPMLARLGVEQENRIALVLKDTVDFPILFWGAIRAGIVPVLLNT 90 +R +Y +L V R L LGV++ + +A L +T F A R G V +N Sbjct: 38 RRVWTYAQLNAEVNRHAHALLALGVQKGDVVAAFLYNTPAFVFSLLAAARVGAVFNPINY 97 Query: 91 RLTADQYRYLLEDSRSRVVFASSEFLPVIEEAAAD-LPHLRTIIAVGDA-PA-PTLQLAN 147 RL A + ++LED +++V+ E V+E+A +P I A DA PA T +L Sbjct: 98 RLAAQELAFILEDGQAKVLLFEKEGCEVVEKAREHGVPTAHWIYADSDAAPAFATARLDQ 157 Query: 148 LLATEQEGGAPAATCADDIAYWQYSSGTTGMPKGVMHVHSSPRVMAENAGRRIGYREDDV 207 L+ + P +D Y+SGTTG PKGV+H H S + + +DV Sbjct: 158 LVRHQPATLPPVIVEENDNCILMYTSGTTGRPKGVLHTHRSKLAHNAMMHQAMTLSREDV 217 Query: 208 VFSAAKLFFAYGLGNAMFCPMGIGATSVLYPERPTADSVFDTLRLHQPTLLFAVPTLYAA 267 + A L L + + +GAT VL R A + + + T FA PT+ Sbjct: 218 GLAVAPLNHTAELHTSFLPRLQLGATQVLL-RRFDAGEAWRLTEVEKVTHFFAAPTMVTL 276 Query: 268 MLADPRSRTETLPDRLRLCVSAGEPLPAQVGLNWRNRFGHDIVNGVGSTEMGHLFLTNLP 327 +L P + L LRL G + + W + G +V G+TEMG P Sbjct: 277 LLHHPDVASRDLSS-LRLVEYGGASMAPHLIREWDKKVGAGLVQIYGTTEMGPCMSVLYP 335 Query: 328 HAV--EYGTSGVPVDGYRLRLV--------GDRGQDVADDEIGELLVSGGSSAAGYWNQR 377 H G++G+P + L + D A DE+GE+LV G GY N+ Sbjct: 336 HEQLSHAGSAGLPSLNHDLLVARVKADGSPSDPADLAAPDEVGEILVRGPCMMGGYLNRP 395 Query: 378 DKTRTTFVGEWTRTGDKYHRRADGVYTYCGRTDDIFKVSGIWVSPFEIEQALMSHAKVLE 437 + W TGD +G R D + V P E+E AL+ H VLE Sbjct: 396 EANARALAFGWYHTGDLGSLDKEGYLWIRDRIDHMINSGAENVYPREVEDALVEHPGVLE 455 Query: 438 AAVI-PAEDTDGLIKPKAFIVLASRGDIDPGA-LFDELKEHV---KSAIGPWKYPRWIQI 492 AV+ +DT G V+A+ PGA L E +H + +K PR Sbjct: 456 VAVVGEPDDTWGQ-------VVAAHVVAKPGATLTQEALDHFLLEGDRLAHYKRPRRYHF 508 Query: 493 MDDLPKTSSGKLQRYLLRE 511 ++ LPKT+SGK+Q++LLR+ Sbjct: 509 IEALPKTTSGKIQKHLLRQ 527 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: 715 Number of extensions: 36 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: 539 Length of database: 529 Length adjustment: 35 Effective length of query: 504 Effective length of database: 494 Effective search space: 248976 Effective search space used: 248976 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