Align 4-hydroxybenzoate--CoA/benzoate--CoA ligase; 4-hydroxybenzoyl-CoA synthetase; EC 6.2.1.25; EC 6.2.1.27 (characterized)
to candidate AZOBR_RS19340 AZOBR_RS19340 long-chain fatty acid--CoA ligase
Query= SwissProt::Q53005 (539 letters) >FitnessBrowser__azobra:AZOBR_RS19340 Length = 519 Score = 186 bits (471), Expect = 2e-51 Identities = 159/507 (31%), Positives = 243/507 (47%), Gaps = 31/507 (6%) Query: 26 AFIDPQRSLSYGELRDAVARVGPMLARLGVEQENRIALVLKDTVDFPILFWGAIRAGIVP 85 A I + ++++ EL V L GV + +R+A++L++++++ +GA++AG V Sbjct: 21 ALIAGENAVTFAELDRQSDAVACALQSAGVVRGDRVAVMLENSIEYVAGLFGALKAGAVY 80 Query: 86 VLLNTRLTADQYRYLLEDSRSRVVFASSEFLPVIEEAAADLPHLRTIIAVG---DAPAPT 142 V +N AD+ Y+L D+ R + A S + AA + HL T + VG A A Sbjct: 81 VPVNPSTKADKLAYILTDAGVRALIAPSALARQVVPAAGEASHLATTLWVGPAVPAGAGG 140 Query: 143 LQLANLLATE---QEGGAPAAT---CADDIAYWQYSSGTTGMPKGVMHVHSSPRVMAENA 196 L +++AT Q GG + D+A Y+SGTTG PKGVM H++ + Sbjct: 141 LSFTDIVATHPDPQSGGTKPQSRGLIDQDLAAILYTSGTTGRPKGVMLSHAALVNTTWSI 200 Query: 197 GRRIGYREDDVVFSAAKLFFAYGLGNAMFCPMGIGATSVLYPERPTADSVFDTLRL--HQ 254 + DDVV L F YGL + + +G T VL ER A R+ H+ Sbjct: 201 STYLENTPDDVVMCVLPLTFGYGL-SQILTGARVGFTVVL--ERSFAFPAETLARMVKHR 257 Query: 255 PTLLFAVPTLYAAMLADPRSRTETLPDRLRLCVSAGEPLPAQVGLNWRNRFGHDIVNGV- 313 T L VPT ++ +L +T L LR +A PLP R RF + Sbjct: 258 ITGLPGVPTFFSTLLGMEALKTADL-SSLRYLTNAAAPLPTAHIDRLRERFPDAAFYSMY 316 Query: 314 GSTE--MGHLFLTNLPHAVEYGTSGVPVDGYRLRLVGDRGQDVADDEIGELLVSGGSSAA 371 G TE +L + + G + +V + G A E+GEL+V G + Sbjct: 317 GMTECCTRICYLDPRDLGTKTASVGRAIPNCEAYVVDELGNRAAPGEVGELVVRGANVMR 376 Query: 372 GYWNQRDKT----RTTFVGE-WTRTGDKYHRRADGVYTYCGRTDDIFKVSGIWVSPFEIE 426 GYWN+ ++T R+ GE TGD + ADG + R DD+FK G VSP E+E Sbjct: 377 GYWNRPEETAKRLRSGPQGETLLYTGDLFTMDADGCLYFVSRKDDVFKCRGEKVSPKEVE 436 Query: 427 QALMSHAKVLEAAVIPAEDTDGLIKPKAFIVLASRGDIDPGALFDE--LKEHVKSAIGPW 484 AL V+EAAV+ D+ + KA++V + PGA E +++H + + Sbjct: 437 NALYELEAVVEAAVLGVPDSADGMAVKAYLV------VRPGATLTEMAIRQHCRGRLESH 490 Query: 485 KYPRWIQIMDDLPKTSSGKLQRYLLRE 511 P++I+I D+LPKT SGK++R +L E Sbjct: 491 LVPKFIEIRDELPKTESGKIKRAMLAE 517 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: 670 Number of extensions: 35 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: 539 Length of database: 519 Length adjustment: 35 Effective length of query: 504 Effective length of database: 484 Effective search space: 243936 Effective search space used: 243936 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