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 GFF3354 PGA1_c34070 long-chain-fatty-acid- CoA ligase IcfB
Query= SwissProt::Q9AJS8 (523 letters) >FitnessBrowser__Phaeo:GFF3354 Length = 500 Score = 188 bits (477), Expect = 5e-52 Identities = 147/482 (30%), Positives = 224/482 (46%), Gaps = 23/482 (4%) Query: 39 ITYRELDAATNRHGNALRAHGVGKGDRVLFLMDDSPELVAAYLGTLRIGAVAVALNVRLA 98 + Y EL A R AL + GV GDRV +D S + YLGT+ GA+ + LN Sbjct: 32 VGYGELFAGAERMAAALVSRGVAPGDRVAAQVDKSLAAIQLYLGTVMAGAIFLPLNPAYT 91 Query: 99 PRDVLYVIQDSACRLLYIDAEFLHLYQQIAGELEQPPQVVVRGDEAPAPAIIAFKHFLDG 158 +V Y I D+ R+ + + +AGE + + G+ + A +A H Sbjct: 92 EAEVAYFIGDATPRVFVCNPVRHESLRAVAGEATV---LTLDGEGQGSLADLAAGH---- 144 Query: 159 QAATLESVQVAPDDVAYWLYSSGTTGRPKAVMHAHRSVLIADRLEREYFGIKPGDRVFTT 218 A E ++ P D+A LY+SGTTGR K M +H ++ R+Y+ D + Sbjct: 145 --AGFEPIERKPSDLAAILYTSGTTGRSKGAMLSHENLYSNSLTLRDYWQFTAEDVLIHA 202 Query: 219 SKMFFGWSLGHSLMGGLQCGATVIVAPGWPDAERVMATAARHRPTILFSTPVMYRNLLRE 278 +F L + L GA V++ PG+ DAE ++A A T L P Y LL + Sbjct: 203 LPIFHTHGLFVATNVALLAGAQVVLLPGF-DAEAILA--AMPNATALMGVPTFYTRLLVD 259 Query: 279 GAGESAAMRDIRHFVSAGEKLPENIGQQWLDTFGIPITEGIGASETVFLFLCARP-DAYR 337 ++R F+S L +QW G I E G +ET + P D R Sbjct: 260 ARLTPDLAANMRLFISGSAPLLVETHEQWEARTGHRILERYGMTETNMS--TSNPYDGVR 317 Query: 338 I-GSCGKRVPWAEVRLLDELGNEITTPDTPGLIAIRMASQFVGYWKLPETTEKALR-DGW 395 + G+ G +P E R+ L N G++ +R + F GYW++PE T + LR DGW Sbjct: 318 VAGTVGPPLPGVEARVT--LDNAEIPLGEIGVLEVRGPNVFQGYWQMPEKTAEELRPDGW 375 Query: 396 YYPGDMFSFDADGFWYHNGRADDMLKISGQWVSPGEIESCASAVPGIAEAVVVAVPNDDG 455 + GD+ D++G+ GR D++ G V P E+E+ +PG+ E+ V+ VP+ D Sbjct: 376 FITGDLAKIDSNGYVTIVGREKDLVISGGFNVYPKEVETLIDDLPGVLESAVIGVPHPDF 435 Query: 456 LTRLTLFIVPEDPSASQQKLSEAWMTTLRGTLSIYKCPRTIQFLEELPRTATGKVQKYRL 515 + +VP + + A L L+ +K P+ I ++ELPR GKVQK L Sbjct: 436 GEAVVAVVVPTEEGTDAASIQAA----LSEHLAKFKQPKHIALMDELPRNTMGKVQKKAL 491 Query: 516 RD 517 R+ Sbjct: 492 RE 493 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: 619 Number of extensions: 33 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: 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