Align 4-hydroxybenzoate--CoA/benzoate--CoA ligase; 4-hydroxybenzoyl-CoA synthetase; EC 6.2.1.25; EC 6.2.1.27 (characterized)
to candidate BPHYT_RS21775 BPHYT_RS21775 long-chain fatty acid--CoA ligase
Query= SwissProt::Q53005 (539 letters) >FitnessBrowser__BFirm:BPHYT_RS21775 Length = 553 Score = 182 bits (463), Expect = 2e-50 Identities = 151/516 (29%), Positives = 240/516 (46%), Gaps = 48/516 (9%) Query: 34 LSYGELRDAVARVGPMLARLGVEQENRIALVLKDTVDFPILFWGAIRAGIVPVLLNTRLT 93 L++ ELRD + G++ I++ + + + L A+ +G+V LN Sbjct: 43 LTFRELRDDCRALEARFREAGLQPGEVISVFMGNGIQTARLLLAAMYSGLVANPLNLLCQ 102 Query: 94 ADQYRYLLEDSRSRVVFASSEFLPVIEEAAADL--------------------------- 126 Q RY+++ S +R++FA+S+ VI A A+L Sbjct: 103 PSQVRYIVDHSDTRMIFAASDTHAVIGAAVAELRAAGLTREIALIQTEPDDAEPPSLAKH 162 Query: 127 -PHLRTIIAVG----DAPAPTLQLANLLATEQEGGAPA-ATCADDIAYWQYSSGTTGMPK 180 P L A G APAP L ++ A A ADD+A Y+SGTTG PK Sbjct: 163 EPALVEAAAHGASGATAPAPALAKRSVAPRPVTSRATAYEPTADDVALLMYTSGTTGTPK 222 Query: 181 GVMHVHSSPRVMAENAGRRIGYREDDVVFSAAKLFFAYGLGNAMFCPMGIGATSVLYPER 240 GV+ H + A N DD V ++ L+ GL + P+ G ++V+ R Sbjct: 223 GVLLTHRNLVANARNISAEHRLASDDRVLASLPLYHINGLVVTLLAPLFHGGSAVM-TSR 281 Query: 241 PTADSVFDTLRLHQPTLLFAVPTLYAAMLADPRSRTETLPDRLRLCVSAGEPLPAQVGLN 300 +A + + + LH T + VPT+ A +L + T L L+ C SA LPA Sbjct: 282 FSARTFWRDVALHACTWINVVPTIVAYLLNADEACTYDL-SALKFCRSASAALPADHHRA 340 Query: 301 WRNRFGHDIVNGVGSTEMGHLFLTNLPHAVE---YGTSGVPVDGYRLRLVGDRGQDVADD 357 + RFG ++ +G TE +N P+ +E G+ G+P G +++ G++ A + Sbjct: 341 FEARFGIGVIETMGMTETAAPVFSN-PYEMERRRVGSIGLP-SGGEAKVIDREGRECAAN 398 Query: 358 EIGELLVSGGSSAAGYWNQRDKTRTTFVGE-WTRTGDKYHRRADGVYTYCGRTDDIFKVS 416 E GEL++ G GY+ + ++T F + W RTGD +R ADG + GR ++ Sbjct: 399 ECGELVLRGEQVMGGYYKRPEETAAAFTSDGWLRTGDLGYRDADGYFYINGRAKELIIKG 458 Query: 417 GIWVSPFEIEQALMSHAKVLEAAVIPAEDTDGLIKPKAFIV---LASRGDIDPGALFDEL 473 G ++P EI++AL+ H VL+AA + D AF+V RG DP +L Sbjct: 459 GENIAPREIDEALLRHPDVLDAAAVGVPDPAYGQDIVAFVVPRMSDGRGAPDPA----DL 514 Query: 474 KEHVKSAIGPWKYPRWIQIMDDLPKTSSGKLQRYLL 509 +EH +G +K P+ + +D+LP+ SGK+QR L Sbjct: 515 REHCLRELGRYKTPKEFRFVDELPRGPSGKVQRLKL 550 Lambda K H 0.320 0.138 0.415 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: 721 Number of extensions: 43 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: 539 Length of database: 553 Length adjustment: 35 Effective length of query: 504 Effective length of database: 518 Effective search space: 261072 Effective search space used: 261072 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