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 Ac3H11_3084 Benzoyl-CoA oxygenase component B
Query= SwissProt::Q9AIX7 (473 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3084 Length = 475 Score = 719 bits (1855), Expect = 0.0 Identities = 335/471 (71%), Positives = 396/471 (84%) Query: 2 INYSERIPNNVNLNENKTLQRALEQWQPSFLNWWDDMGPENSSNYDVYLRTAVSVDPKGW 61 INYSE+IPNNVNL E++TLQRALE WQP+F+NWWDD+GPE S+NYDVYLRTAVSVDP GW Sbjct: 4 INYSEKIPNNVNLGEDRTLQRALEGWQPNFINWWDDVGPEGSTNYDVYLRTAVSVDPNGW 63 Query: 62 ADFGYVKMHDYRWGIFLAPQEGEKKITFGEHKGQDVWQEVPGEYRSTLRRIIVTQGDTEP 121 A FG+VKM DYRWGIFL P + ++I FG+HKG+ WQ+VPGE+R+ LRRIIVTQGDTEP Sbjct: 64 AQFGHVKMRDYRWGIFLNPGDANREIHFGDHKGEKAWQDVPGEHRANLRRIIVTQGDTEP 123 Query: 122 ASVEQQRHLGLTAPSLYDLRNLFQVNVEEGRHLWAMVYLLHAHFGRDGREEGEALLERRS 181 ASVEQQRHLGLTAPS+YDLRNLFQ+NVEEGRHLWAMVYLLH HFGRDGREE EALL+R S Sbjct: 124 ASVEQQRHLGLTAPSMYDLRNLFQINVEEGRHLWAMVYLLHKHFGRDGREEAEALLQRTS 183 Query: 182 GDEDNPRILTAFNEKTPDWLSFFMFTFITDRDGKFQLASLAESAFDPLARTCKFMLTEEA 241 GD+DNPRIL AFNEKTPDWL+FFMFT+ TDRDGKFQL++LAESAFDPLART KFMLTEEA Sbjct: 184 GDQDNPRILGAFNEKTPDWLAFFMFTYFTDRDGKFQLSALAESAFDPLARTTKFMLTEEA 243 Query: 242 HHLFVGESGIARVIQRTCEVMKELGTDDPAKLRAAGVIDLPTLQKYLNFHYSVTSDLYGA 301 HH+FVGESG++RV+ RT +VM +L TDDPAK+RAAG IDL T+Q+YLNFHYSVT DL+GA Sbjct: 244 HHMFVGESGVSRVLSRTAQVMNDLKTDDPAKVRAAGAIDLGTIQRYLNFHYSVTIDLFGA 303 Query: 302 EISSNAATYYTNGLKGRFEEEKIGDDHKLQNSEYEVMDVAGDKILTRHVPALSALNERLR 361 + SSNAAT+Y++GLKGR+EE K DDH L+ Y+V++V ++ + VP L+ALNE LR Sbjct: 304 DQSSNAATFYSSGLKGRYEEGKRSDDHILKGQTYKVLEVVNGQLQEKDVPMLNALNEVLR 363 Query: 362 DDWITDVQAGVDRWNRIPAKFGFDFRFTLPHKGFHRKIGMFADVHVSPDGRLISEAEWTH 421 DD+I D AGV RWN++ K G R +PHK F+R+IG A + +SPDGR++SEAEWT Sbjct: 364 DDFIKDSMAGVGRWNKVLEKAGIPTRLAVPHKAFNRQIGALAGIKMSPDGRVVSEAEWTA 423 Query: 422 QHKNWLPTESDRLYVHSLMGRCLEPGKFANWIAAPARGINNQPVNFEYVRF 472 + WLPT D +V SLMGR +EPGKFA WIA P GIN QPV+FEYVRF Sbjct: 424 RKAEWLPTPEDFAFVASLMGRVVEPGKFAGWIAPPVMGINRQPVDFEYVRF 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: 841 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