Align 4-hydroxybenzoate-CoA ligase (EC 6.2.1.27); 3-hydroxybenzoate-CoA ligase (EC 6.2.1.37) (characterized)
to candidate HSERO_RS19285 HSERO_RS19285 long-chain fatty acid--CoA ligase
Query= BRENDA::Q5P0J2 (493 letters) >FitnessBrowser__HerbieS:HSERO_RS19285 Length = 566 Score = 133 bits (335), Expect = 1e-35 Identities = 149/519 (28%), Positives = 215/519 (41%), Gaps = 57/519 (10%) Query: 17 AIECDDEKVSYAVLRDRVSRAAGAW-KTLGLQPGNRVIVFAPDSVDWVVAYLGAIWAGGV 75 A C + +SY L D +SRA G W + LGLQ G RV + P+ + + +A + AG Sbjct: 41 AYVCMGKYLSYREL-DSLSRALGGWLQGLGLQKGARVAIMMPNVLQYPIAIAAILRAGYT 99 Query: 76 AIGVNPRLSMNEFAPILNE-------------CEPRFVWCETEQARALVAE--------- 113 + VNP + E L + C + V T +VA Sbjct: 100 VVNVNPLYTARELEHQLKDSGAEAIFVLENFACTLQKVVAHTNIKHIVVASMGELLGALK 159 Query: 114 -------ARTVAEIVA----DGPGTSNWATHLAAAEAVAPLERATEDAALWIGTSGTTGV 162 R V ++V T + A A + + P+ +D A T GTTGV Sbjct: 160 GTLVNLVVRHVKKLVPAWSLPNAITFSQALSQARGKTLQPVTLTHDDIAFLQYTGGTTGV 219 Query: 163 PKGVVHAQRT----VTNAHSFACGILGL-TAADRLY--ASSKLFFAYALGNSLFAGLRVG 215 KG V R V A + L D+L + L+ +AL G R G Sbjct: 220 AKGAVLTHRNLVANVLQAEEWLTPALKAGKPIDQLVFVCALPLYHIFALTVCNMLGTREG 279 Query: 216 ATVILDRQWPTAERVEYMVEKYRPTLLFSVPTLYRKMLQTGVARRIAQYGIRHCVSAGEA 275 A +L + KY+ +V TLY +L R+ G R CV G A Sbjct: 280 ALNLLIPNPRDIPGFVKELAKYKVNTFPAVNTLYNALLNNADFARLDFSGYRCCVGGGMA 339 Query: 276 LPLAVRQDWREATGHTLISGYGTSETLCLMLFS----DDDSGLM-RPTPLTEVRHADDVD 330 + +V W++ TG +I GYG SET + + D+ +G + P P TE DD Sbjct: 340 VQKSVADKWKKLTGCPIIEGYGLSETSPIASANPCTIDEYTGTIGLPLPSTEFAILDDDG 399 Query: 331 PDV----PQRVWIRHSAVALGYWERPEAQADGFR-DGWFSPGDMFLRHADGRLEYTGRND 385 V P + IR V GYW+RP+ A DG+F GD+ + G + R Sbjct: 400 QPVPLGQPGEIAIRGPQVMPGYWQRPDETAKVMTPDGFFKTGDIGVMDERGYTKIVDRKK 459 Query: 386 DMLKIAGQWVSTLWVEQSLASVCGETLHQIASVGVSSADGLTALAV-LAVASPERRSEAR 444 DM+ ++G V VE +A G + + A VGV D T AV L V ++ A Sbjct: 460 DMILVSGFNVYPNEVEGVVAQHPG--VLECACVGV--PDEHTGEAVKLFVVRKDKTLSAA 515 Query: 445 QRMDEGIATLPGHRRPRWVHWLDELPLTPTGKLQRGRLR 483 Q MD G+++P+++ + DELP T GK+ R LR Sbjct: 516 QLMDYCKEQFTGYKKPKYIEFRDELPKTNVGKILRRELR 554 Lambda K H 0.320 0.133 0.414 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: 594 Number of extensions: 30 Number of successful extensions: 6 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: 493 Length of database: 566 Length adjustment: 35 Effective length of query: 458 Effective length of database: 531 Effective search space: 243198 Effective search space used: 243198 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