Align Benzoyl-CoA oxygenase component B; Benzoyl-CoA 2,3-dioxygenase subunit B; Benzoyl-CoA dioxygenase oxygenase component; EC 1.14.13.208 (characterized)
to candidate RR42_RS07505 RR42_RS07505 benzoyl-CoA oxygenase
Query= SwissProt::Q9AIX7 (473 letters) >FitnessBrowser__Cup4G11:RR42_RS07505 Length = 474 Score = 708 bits (1828), Expect = 0.0 Identities = 334/472 (70%), Positives = 389/472 (82%) Query: 2 INYSERIPNNVNLNENKTLQRALEQWQPSFLNWWDDMGPENSSNYDVYLRTAVSVDPKGW 61 I+YS++IPNNVNL++++ LQRALE WQP+FL+WW DMGPE S +DVYLRTAVSVDP GW Sbjct: 3 IDYSQKIPNNVNLSDDRALQRALEHWQPAFLDWWRDMGPEGSHQHDVYLRTAVSVDPAGW 62 Query: 62 ADFGYVKMHDYRWGIFLAPQEGEKKITFGEHKGQDVWQEVPGEYRSTLRRIIVTQGDTEP 121 A F +VKM DYRWGIFL P + ++I FGEHKG+ WQEVPGE+R+ LRRIIVTQGDTEP Sbjct: 63 AHFDHVKMPDYRWGIFLQPADPARRIHFGEHKGEAAWQEVPGEHRANLRRIIVTQGDTEP 122 Query: 122 ASVEQQRHLGLTAPSLYDLRNLFQVNVEEGRHLWAMVYLLHAHFGRDGREEGEALLERRS 181 ASVEQQRHLG+T PSLYDLRNLFQVNVEEGRHLWAMVYLLH HFGRDGREE EALL RRS Sbjct: 123 ASVEQQRHLGMTCPSLYDLRNLFQVNVEEGRHLWAMVYLLHRHFGRDGREEAEALLGRRS 182 Query: 182 GDEDNPRILTAFNEKTPDWLSFFMFTFITDRDGKFQLASLAESAFDPLARTCKFMLTEEA 241 GDEDNPRIL AFNE+TPDWL+FFMFT TDRDGKFQL +LAES+FDPLART +FMLTEEA Sbjct: 183 GDEDNPRILGAFNERTPDWLAFFMFTHFTDRDGKFQLCALAESSFDPLARTTRFMLTEEA 242 Query: 242 HHLFVGESGIARVIQRTCEVMKELGTDDPAKLRAAGVIDLPTLQKYLNFHYSVTSDLYGA 301 HH+FVGESGI+RVIQRTCEVM+E DPA +RAAGVIDL T+Q+YLNFHYSVT DL+GA Sbjct: 243 HHMFVGESGISRVIQRTCEVMRERDIQDPADVRAAGVIDLDTIQRYLNFHYSVTIDLFGA 302 Query: 302 EISSNAATYYTNGLKGRFEEEKIGDDHKLQNSEYEVMDVAGDKILTRHVPALSALNERLR 361 + SSNAAT+Y+ GLKGRFEE K GDDH L+ Y ++DV ++ R VP L+ALNE LR Sbjct: 303 DQSSNAATFYSAGLKGRFEEGKRGDDHVLKGEVYRILDVTDGRLGEREVPMLNALNEVLR 362 Query: 362 DDWITDVQAGVDRWNRIPAKFGFDFRFTLPHKGFHRKIGMFADVHVSPDGRLISEAEWTH 421 DD++ D GV RWN++ K G R T+PHK F+RKIG A+VHVSP G L++EA+W Sbjct: 363 DDYVKDTLGGVARWNKVIEKHGIALRMTVPHKAFNRKIGSLANVHVSPAGELLTEAQWQA 422 Query: 422 QHKNWLPTESDRLYVHSLMGRCLEPGKFANWIAAPARGINNQPVNFEYVRFN 473 + WLPT DR +V SLMGR EPGK+ANWIA P G+N QP++FEYVRFN Sbjct: 423 GEREWLPTGEDRAFVASLMGRVTEPGKYANWIAPPVVGVNRQPMDFEYVRFN 474 Lambda K H 0.320 0.137 0.428 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: 851 Number of extensions: 19 Number of successful extensions: 1 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: 473 Length of database: 474 Length adjustment: 33 Effective length of query: 440 Effective length of database: 441 Effective search space: 194040 Effective search space used: 194040 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: 51 (24.3 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