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 WP_011383961.1 AMB_RS07835 acyl-CoA synthetase AMP-fatty acid ligase
Query= SwissProt::Q9AJS8 (523 letters) >NCBI__GCF_000009985.1:WP_011383961.1 Length = 500 Score = 478 bits (1231), Expect = e-139 Identities = 236/507 (46%), Positives = 333/507 (65%), Gaps = 10/507 (1%) Query: 11 MNAADEIIGRPLAQGLGEQTAMLCAERSITYRELDAATNRHGNALRAHGVGKGDRVLFLM 70 MNAADEI+G L G GE A++C E+++TY +L+ R GNA+ A GV + VL L+ Sbjct: 1 MNAADEILGPSLGSGRGESLAIICGEQTLTYDQLNRLACRFGNAMLAAGVQRQQPVLLLL 60 Query: 71 DDSPELVAAYLGTLRIGAVAVALNVRLAPRDVLYVIQDSACRLLYIDAEFLHLYQQIAGE 130 DD PELVAAYLG ++ G VAVALN RL+P+D+ + + DS LL + L + Sbjct: 61 DDGPELVAAYLGAMKAGLVAVALNTRLSPKDLSHALGDSGAPLLLAETALKDLAAESLA- 119 Query: 131 LEQPPQVVVRGDEAPAPAIIAFKHFLDGQAATLESVQVAPDDVAYWLYSSGTTGRPKAVM 190 L +V DE A FL+G + L S + P+D+A W+Y+SGTTG+PK + Sbjct: 120 LAHASARMVTTDELDA--------FLEGASDQLVSADMGPEDMALWMYTSGTTGQPKGAV 171 Query: 191 HAHRSVLIADRLEREYFGIKPGDRVFTTSKMFFGWSLGHSLMGGLQCGATVIVAPGWPDA 250 H H S+ + +R RE G+ PGDR+F+TSK+FF + LGH L+G L+CG T+++ GWPDA Sbjct: 172 HVHGSIPLGERHVRENLGLLPGDRIFSTSKLFFAYPLGHCLIGALRCGGTLVLHRGWPDA 231 Query: 251 ERVMATAARHRPTILFSTPVMYRNLLREGAGESAAMRDIRHFVSAGEKLPENIGQQWLDT 310 AR RP ++ S P +YR +L++G G S A R++R +VSAGE LP ++ ++W++ Sbjct: 232 TAAAEVIARTRPKLVLSVPSLYRIMLKDGVGSSPAFREVRTWVSAGENLPADLCRRWMEE 291 Query: 311 FGIPITEGIGASETVFLFLCARPDAYRIGSCGKRVPWAEVRLLDELGNEITTPDTPGLIA 370 G + EGIGA+E +FLF+ + P A + G+CG+ +PWAE +L G I PDTPG + Sbjct: 292 TGGLMLEGIGATEALFLFIASTPTAMKPGACGRPLPWAEAQLRSPSGEVIAAPDTPGDLW 351 Query: 371 IRMASQFVGYWKLPETTEKALRDGWYYPGDMFSFDADGFWYHNGRADDMLKISGQWVSPG 430 +RM S F Y P+ T++ L+DGW+ GD+FSFDA+G+W GR+DDM+K+SGQWVSP Sbjct: 352 VRMDSLFRRYHNRPDVTQRVLKDGWWKTGDVFSFDAEGWWSPQGRSDDMIKVSGQWVSPS 411 Query: 431 EIESCASAVPGIAEAVVVAVPNDDGLTRLTLFIVPEDPSASQQKLSEAWMTTLRGTLSIY 490 E+E A VPG+A+AV V +PN+DGL RL L+ V E + L + TLR L+IY Sbjct: 412 EVEEAALMVPGVADAVAVGIPNEDGLVRLVLYAVAE-AGEHEPLLETRIVETLRSKLAIY 470 Query: 491 KCPRTIQFLEELPRTATGKVQKYRLRD 517 KCPR ++FLE +PRTATGKVQ+++LR+ Sbjct: 471 KCPRNVRFLETIPRTATGKVQRFKLRE 497 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: 795 Number of extensions: 30 Number of successful extensions: 3 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: 500 Length adjustment: 35 Effective length of query: 488 Effective length of database: 465 Effective search space: 226920 Effective search space used: 226920 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