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 CCNA_02483 CCNA_02483 4-coumarate--CoA ligase
Query= SwissProt::Q9AJS8 (523 letters) >FitnessBrowser__Caulo:CCNA_02483 Length = 496 Score = 155 bits (393), Expect = 2e-42 Identities = 152/528 (28%), Positives = 229/528 (43%), Gaps = 54/528 (10%) Query: 11 MNAADEIIGRPLAQGLGEQTAMLCAERSITYRELDAATNRHGNALRAHGVGKGDRVLFLM 70 M D + + Q G L R TY ELDA R LR GVG+GDR+ L Sbjct: 1 MTPIDHVAFQARLQPGGLAAVELANGRRWTYAELDADIARAVGVLRRRGVGEGDRLAVLA 60 Query: 71 DDSPELVAAYLGTLRIGAVAVALNVRLAPRDVLYVIQDSACRLLYIDAEFLHLYQQIAGE 130 + LV +L R+GA+ LN RL+ ++ +I+D+ Sbjct: 61 KNQVLLVILHLACARLGAMFAPLNWRLSASELHALIEDA--------------------- 99 Query: 131 LEQPPQVVVRGDEAPAPAIIAFKHFLDGQAATLESVQVAPDDVA--------YWLYSSGT 182 P ++V D+ A + LD A ++ PD A LY+SGT Sbjct: 100 ---DPAMIVGDDQLAAAGLDGVD--LDVLRAEIDCAD--PDTRARADRERPSLILYTSGT 152 Query: 183 TGRPKAVMHAHRSVLIADRLEREYFGIKPGDRVFTT-SKMFFGWSLGHSLMGGLQCGATV 241 +GRPK + + R+ L + G + VF + MF L S+ L G + Sbjct: 153 SGRPKGALLSERN-LDQTAINFGRLGKVTHESVFLVDAPMFHIIGLITSIRPVLMHGGAI 211 Query: 242 IVAPGWPDAERVMATAARHRPTI----LFSTPVMYRNLLREGAGESAAMRDIRHFVSAGE 297 +V+ G+ A + PT+ F P M L R+ A +++A+R + + G Sbjct: 212 LVSDGFEPARTLGRLGD---PTLGITHYFCVPQMAAMLRRQPAFDASALRRLTAIFTGGA 268 Query: 298 KLPENIGQQWLDTFGIPITEGIGASETVFLFLCARPDAY---RIGSCGKRVPWAEVRLLD 354 P + WL GIP+ +G G SE +F R GS G +P R++D Sbjct: 269 PHPAPDIRAWLAE-GIPMVDGYGMSEAGTVFGMPADATLIDARAGSAGLCMPPVFTRIVD 327 Query: 355 ELGNEITTPDTPGLIAIRMASQFVGYWKLPETTEKAL-RDGWYYPGDMFSFDADGFWYHN 413 E + P PG + ++ + F GYW+ PE T +A DGW+ GD+ DA+G+ + Sbjct: 328 EQDRDCP-PGVPGELLLKGDNVFRGYWRRPEDTARAFTEDGWFRTGDIALADAEGYHWLV 386 Query: 414 GRADDMLKISGQWVSPGEIESCASAVPGIAEAVVVAVPNDDGLTRLTLFIVPEDPSASQQ 473 R DM G+ V P EIE+ + P I E VV VP+ L + + + Sbjct: 387 DRKKDMFISGGENVYPAEIEAALADHPAILECAVVGVPDPRWGEVGHLVVTCREGAVLDL 446 Query: 474 KLSEAWMTTLRGTLSIYKCPRTIQFLEELPRTATGKVQKYRLRDMLQA 521 L ++ L L+ YK P+ + + LPRTA+GK+QK LR+ L A Sbjct: 447 ALI---LSHLEDRLARYKLPKALTLVAALPRTASGKIQKTVLRERLLA 491 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: 664 Number of extensions: 40 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 523 Length of database: 496 Length adjustment: 34 Effective length of query: 489 Effective length of database: 462 Effective search space: 225918 Effective search space used: 225918 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