Align 3-hydroxybenzoate--CoA/4-hydroxybenzoate--CoA ligase; 3-hydroxybenzoyl-CoA synthetase; EC 6.2.1.27; EC 6.2.1.37 (characterized)
to candidate Ac3H11_4064 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= SwissProt::Q9AJS8 (523 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4064 Length = 503 Score = 167 bits (423), Expect = 8e-46 Identities = 150/515 (29%), Positives = 228/515 (44%), Gaps = 36/515 (6%) Query: 20 RPLAQGLGEQTAMLCAERSI-TYRELDAATNRHGNALRA-HGVGKGDRVLFLMDDSPELV 77 R AQ Q A+L ++ + TY+ L A T LR HGV GDRV ++PE + Sbjct: 8 RRSAQLYPAQPAVLQGDQLLFTYQALGARTAALAACLRERHGVLPGDRVAIYAANAPEYL 67 Query: 78 AAYLGTLRIGAVAVALNVRLAPRDVLYVIQDSACRLLYIDAEFLHLYQQIAGELEQPPQV 137 A L GAV+V +N +L +++ YV+ DS R++ + ++ L Q AG P Sbjct: 68 EALHAILWAGAVSVPVNYKLHAKELAYVLTDSGARMVLV-SDALSAAAQEAGA--DPAHT 124 Query: 138 VVRGDEAPAPAIIAFKHFLDGQAATLESVQVAPDDVAYWLYSSGTTGRPKAVMHAHRSVL 197 +V G EA A+ A L APDD+A Y+SGTTGRPK VM HR++L Sbjct: 125 LVLGSEAYQAAV---------SHAPLPVCDRAPDDLASLFYTSGTTGRPKGVMQTHRNLL 175 Query: 198 IADRLEREYF----GIKPGDRVFTTSKMFFGWSLGHSLMGGLQCGATVIVAPGWPDAERV 253 YF I PGD + + M G L ++ L+ G V+ G + + Sbjct: 176 AMTAC---YFTDVDDILPGDAMVYAAPMSHGAGL-YNYAQVLRGGRHVVPLSGGFEPAEL 231 Query: 254 MATAARHRPTILFSTPVMYRNLLREGAGESAAMRDIRHFVSAGEKLPENIGQQWLDTFGI 313 + AA LF+ P M L+ A + + V G + + + L G Sbjct: 232 VQLAASVGQLTLFAAPTMVHRLVDHVRATGADVSGFKTIVYGGGPMYADDLRNALAVMGN 291 Query: 314 PITEGIGASETVFLFLCARPD----------AYRIGSCGKRVPWAEVRLLDELGNEITTP 363 + G E+ + A R+ S G EVR++D G + Sbjct: 292 RFVQIYGQGESPMTITALQRAQLADRDHPRWAERMVSVGVAQSLVEVRVVDAQGQPLPPG 351 Query: 364 DTPGLIAIRMASQFVGYWKLPETTEKALRDGWYYPGDMFSFDADGFWYHNGRADDMLKIS 423 +T G + +R + GYW PE T + LRDGW Y DM + DADGF R+ D++ Sbjct: 352 ET-GEVVVRGDTVMPGYWNNPEATAQTLRDGWLYTSDMGALDADGFLTLKDRSKDVIISG 410 Query: 424 GQWVSPGEIESCASAVPGIAEAVVVAVPNDDGLTRLTLFIVPEDPSASQQKLSEAWMTTL 483 G + P E+E P + E VV + + + ++V + A + +A Sbjct: 411 GSNIYPREVEEVLLLHPRVREVAVVGQRDAEWGEVVVAYLVAGEGGAVEDAALDALCLE- 469 Query: 484 RGTLSIYKCPRTIQFLEELPRTATGKVQKYRLRDM 518 ++ +K P+ +++E LP+ A GKV K LR+M Sbjct: 470 --HIARFKRPKEYRWVEGLPKNAYGKVLKTELREM 502 Lambda K H 0.321 0.137 0.417 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: 654 Number of extensions: 39 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: 523 Length of database: 503 Length adjustment: 35 Effective length of query: 488 Effective length of database: 468 Effective search space: 228384 Effective search space used: 228384 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