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 H281DRAFT_00374 H281DRAFT_00374 benzoyl-CoA oxygenase, component B
Query= SwissProt::Q9AIX7 (473 letters) >FitnessBrowser__Burk376:H281DRAFT_00374 Length = 475 Score = 728 bits (1878), Expect = 0.0 Identities = 343/472 (72%), Positives = 397/472 (84%) Query: 2 INYSERIPNNVNLNENKTLQRALEQWQPSFLNWWDDMGPENSSNYDVYLRTAVSVDPKGW 61 INYSE+IPNNVNL +++ LQRALEQWQP+FL+WW DMGPE S YDVYLRTAVSVD GW Sbjct: 4 INYSEKIPNNVNLADDRALQRALEQWQPNFLSWWGDMGPEGSHGYDVYLRTAVSVDAGGW 63 Query: 62 ADFGYVKMHDYRWGIFLAPQEGEKKITFGEHKGQDVWQEVPGEYRSTLRRIIVTQGDTEP 121 A F +VKM DYRWGIFL P + ++KI FGEHKG+ WQ+VPGE+R+ LRRIIVTQGDTEP Sbjct: 64 AHFDHVKMPDYRWGIFLTPGDQDRKIHFGEHKGEAAWQDVPGEHRANLRRIIVTQGDTEP 123 Query: 122 ASVEQQRHLGLTAPSLYDLRNLFQVNVEEGRHLWAMVYLLHAHFGRDGREEGEALLERRS 181 ASVEQQRHLGLTAPS+YDLRNLFQVNVEEGRHLWAMVYLLH +FGRDGREE EALL RRS Sbjct: 124 ASVEQQRHLGLTAPSMYDLRNLFQVNVEEGRHLWAMVYLLHRYFGRDGREEAEALLGRRS 183 Query: 182 GDEDNPRILTAFNEKTPDWLSFFMFTFITDRDGKFQLASLAESAFDPLARTCKFMLTEEA 241 GD+DNPRIL AFNEKTPDWL+F+MFT+ TDRDGKFQL++LAES FDPLART KFMLTEEA Sbjct: 184 GDDDNPRILGAFNEKTPDWLAFYMFTYFTDRDGKFQLSALAESGFDPLARTTKFMLTEEA 243 Query: 242 HHLFVGESGIARVIQRTCEVMKELGTDDPAKLRAAGVIDLPTLQKYLNFHYSVTSDLYGA 301 HH+FVGESG++RVIQRT +VM ELGTDD A++RAAGVIDLPT+Q+YLNFHYSVT DL+GA Sbjct: 244 HHMFVGESGVSRVIQRTAQVMNELGTDDVARIRAAGVIDLPTIQRYLNFHYSVTIDLFGA 303 Query: 302 EISSNAATYYTNGLKGRFEEEKIGDDHKLQNSEYEVMDVAGDKILTRHVPALSALNERLR 361 + SSNAAT+Y++GLKGR+EE K DDH+L Y+++DV K++ R VP L+A+NE LR Sbjct: 304 DHSSNAATFYSSGLKGRYEEGKRDDDHQLNGQSYKLLDVQDGKLVEREVPMLNAMNEVLR 363 Query: 362 DDWITDVQAGVDRWNRIPAKFGFDFRFTLPHKGFHRKIGMFADVHVSPDGRLISEAEWTH 421 DD+I D AGV RWN++ K G DFR T+PHK F+R+IG FA VSPDGR+I EAEW Sbjct: 364 DDYIKDSVAGVGRWNKVLEKAGIDFRMTVPHKAFNRQIGTFAGTRVSPDGRVIGEAEWAA 423 Query: 422 QHKNWLPTESDRLYVHSLMGRCLEPGKFANWIAAPARGINNQPVNFEYVRFN 473 WL T DR +V SLMGR EPGKFANWIA PA G+N QPV+FEYVRFN Sbjct: 424 NEAKWLATPEDRAFVASLMGRVTEPGKFANWIAPPAMGVNRQPVDFEYVRFN 475 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: 849 Number of extensions: 29 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: 475 Length adjustment: 33 Effective length of query: 440 Effective length of database: 442 Effective search space: 194480 Effective search space used: 194480 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