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 AZOBR_RS22375 AZOBR_RS22375 malonyl-CoA synthase
Query= SwissProt::Q9AJS8 (523 letters) >FitnessBrowser__azobra:AZOBR_RS22375 Length = 519 Score = 191 bits (484), Expect = 7e-53 Identities = 149/486 (30%), Positives = 239/486 (49%), Gaps = 19/486 (3%) Query: 37 RSITYRELDAATNRHGNALRAHGVGKGDRVLFLMDDSPELVAAYLGTLRIGAVAVALNVR 96 R++TY +L+A T R+ N L G+ KGDRV ++ S E + YL T+R G V + LN Sbjct: 36 RTVTYGDLEALTGRYANLLADLGLKKGDRVAVQVEKSVENIILYLATVRAGGVFLPLNPA 95 Query: 97 LAPRDVLYVIQDSACRLLYIDAEFLHLYQQIAGELEQPPQVVV-RGDEAPAPAIIAFKHF 155 +V Y + D+ + E +++A + + + + E P A Sbjct: 96 YTKAEVEYFLTDAEPHVFVARPESADALREVADKAKVAHLLTLGTHGEGTLPEQAA---- 151 Query: 156 LDGQAATLESVQVAPDDVAYWLYSSGTTGRPKAVMHAHRSVLIADRLEREYFGIKPGDRV 215 G+ +V DD+A LY+SGTTGR K M +HR++ +Y+G +P D + Sbjct: 152 --GKGTDFTTVPAEADDLAAILYTSGTTGRSKGAMMSHRNLGSNALTLHKYWGFQPDDVL 209 Query: 216 FTTSKMFFGWSLGHSLMGGLQCGATVIVAPGWPDAERVMATAARHRPTILFSTPVMYRNL 275 +F L + L G++++ P + DAE+VM R T++ P Y L Sbjct: 210 LHALPIFHTHGLFVATNCVLLNGSSMLFLPKF-DAEQVMGLLP--RATVMMGVPTFYTRL 266 Query: 276 LREGAGESAAMRDIRHFVSAGEKLPENIGQQWLDTFGIPITEGIGASETVFLFLCARP-D 334 L A +R FVS L + +++ G I E G +ET L + P D Sbjct: 267 LAHPGLTREATAHMRLFVSGSAPLLADTHKEFSARTGHAILERYGMTETG--MLTSNPLD 324 Query: 335 AYRI-GSCGKRVPWAEVRLLD-ELGNEITTPDTPGLIAIRMASQFVGYWKLPE-TTEKAL 391 RI G+ G +P VR+++ E G + T D G+I + + F GYW++PE TT++ Sbjct: 325 GDRIPGTVGFPLPEVSVRVVNPETGASLGT-DEIGIIEVAGPNVFSGYWRMPEKTTQEIK 383 Query: 392 RDGWYYPGDMFSFDADGFWYHNGRADDMLKISGQWVSPGEIESCASAVPGIAEAVVVAVP 451 DG++ GD+ D G+ + GRA D++ G V P E+E+ + G+ E+ VV VP Sbjct: 384 PDGFFITGDVGKVDGRGYVHIVGRAKDLIISGGFNVYPKEVETVIDGIDGVVESAVVGVP 443 Query: 452 NDDGLTRLTLFIVPEDPSASQQKLSEAWMTTLRGTLSIYKCPRTIQFLEELPRTATGKVQ 511 + D +T ++ + SA+ + A + + L+ +K P+ + F++ELPR A GKVQ Sbjct: 444 HPDFGEAVTAVVLRKPGSATPDE--AAVIAVCKEQLANFKVPKRVFFMDELPRNAMGKVQ 501 Query: 512 KYRLRD 517 K LRD Sbjct: 502 KNLLRD 507 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: 665 Number of extensions: 38 Number of successful extensions: 6 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: 519 Length adjustment: 35 Effective length of query: 488 Effective length of database: 484 Effective search space: 236192 Effective search space used: 236192 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