Align 4-hydroxybenzoate--CoA/benzoate--CoA ligase; 4-hydroxybenzoyl-CoA synthetase; EC 6.2.1.25; EC 6.2.1.27 (characterized)
to candidate GFF2177 Psest_2220 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases
Query= SwissProt::Q53005 (539 letters) >FitnessBrowser__psRCH2:GFF2177 Length = 585 Score = 195 bits (495), Expect = 5e-54 Identities = 167/555 (30%), Positives = 251/555 (45%), Gaps = 38/555 (6%) Query: 1 MPLRDYNAAVDFVDRNVAEGRGGKIA--FID---PQRSLSYGELRDAVARVGPMLARLGV 55 +P N A + VDR+ A R G A F++ +R LSY +L+ R +LA+LGV Sbjct: 41 LPGGGLNLAHEAVDRHAAGPRAGYCALRFLERNGSRRELSYLQLKRQTNRFANVLAQLGV 100 Query: 56 EQENRIALVLKDTVDFPILFWGAIRAGIV---------PVLLNTRLTADQYRYLLEDSRS 106 + R+ ++ V+ + G ++ G V P L TRL LL S Sbjct: 101 ARGERLFVLCNRGVELYLGVLGGLKNGCVVSPLFAAFGPEPLETRLRLGDCSVLLT---S 157 Query: 107 RVVFASSEFLPVIEEAAADLPHLRTIIAVGDAPAPT-----LQLANLLATEQEGGAPAAT 161 +++ + LP L+ ++ ++ T L L +LLA E A T Sbjct: 158 EMLYRKK-----VARLRDRLPLLKHVLLYDESGGHTSIDGTLDLHDLLAAAGEEFKIAPT 212 Query: 162 CADDIAYWQYSSGTTGMPKGVMHVHSSPRVMAENAGRRIGYREDDVVFSAAKLFFAYGLG 221 AD + ++SGTTG PKG +HVH + + DD+ + +A + G Sbjct: 213 TADSPSLLHFTSGTTGTPKGALHVHGAALTHYVTGRYALDLHPDDIYWCSADPGWVTGTS 272 Query: 222 NAMFCPMGIGATSVLYPERPTADSVFDTLRLHQPTLLFAVPT-LYAAMLADPRSRTETLP 280 + P+ +G TSV+ A+ + L + ++ + PT + M A P Sbjct: 273 YGILAPLLLGVTSVVDCGEFDAERWYGILEKERISVWYTAPTAIRMLMKAGPELARRHFH 332 Query: 281 DRLRLCVSAGEPLPAQVGLNWRNRFGHDIVNGVGSTEMGHLFLTNLPHA-VEYGTSGVPV 339 +LR S GEPL + + G I + TE G + + N+P ++ G+ G P+ Sbjct: 333 PQLRFVASVGEPLNPEAVWWGKEVLGLPIHDNWWQTETGGIMIANIPAMPIKPGSMGKPL 392 Query: 340 DGYRLRLVGDRGQD-----VADDEIGELLVSGG--SSAAGYWNQRDKTRTTFVGEWTRTG 392 G +V G+D + DDEIGEL + Y Q ++ R F G+W +G Sbjct: 393 PGVEAAIVR-HGEDGNLTFLGDDEIGELALKQPWPGMFRTYLGQEERYRRCFAGDWYLSG 451 Query: 393 DKYHRRADGVYTYCGRTDDIFKVSGIWVSPFEIEQALMSHAKVLEAAVIPAEDTDGLIKP 452 D R ADG Y + GR+DD+ K +G + PFE+E ALM H+ V EAAVI D Sbjct: 452 DLARRDADGYYWFIGRSDDVIKSAGHLIGPFEVESALMEHSAVAEAAVIGKPDPLLGETV 511 Query: 453 KAFIVLASRGDIDPGALFDELKEHVKSAIGPWKYPRWIQIMDDLPKTSSGKLQRYLLREM 512 KAF+ L RG AL DEL H + +G P+ ++ + LP+T SGKL R LL+ Sbjct: 512 KAFVSL-KRGREASEALHDELIGHARKRLGAAVAPKELEFLASLPRTRSGKLMRRLLKAR 570 Query: 513 TLGGIEATESAPSEP 527 LG E S P Sbjct: 571 ELGLPEGDISTLENP 585 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: 831 Number of extensions: 48 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: 585 Length adjustment: 36 Effective length of query: 503 Effective length of database: 549 Effective search space: 276147 Effective search space used: 276147 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: 53 (25.0 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