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 WP_011382622.1 AMB_RS00890 benzoyl-CoA 2,3-epoxidase subunit BoxB
Query= SwissProt::Q9AIX7 (473 letters) >NCBI__GCF_000009985.1:WP_011382622.1 Length = 473 Score = 687 bits (1774), Expect = 0.0 Identities = 323/472 (68%), Positives = 384/472 (81%), Gaps = 4/472 (0%) Query: 2 INYSERIPNNVNLNENKTLQRALEQWQPSFLNWWDDMGPENSSNYDVYLRTAVSVDPKGW 61 INY+E+IPNNVNL+E++ LQRALE WQP +++WW +MGPE +S ++YLRTA+S +P GW Sbjct: 4 INYAEKIPNNVNLSEDRKLQRALESWQPHYIDWWKEMGPEGTSTSEIYLRTAISAEPDGW 63 Query: 62 ADFGYVKMHDYRWGIFLAPQEGEKKITFGEHKGQDVWQEVPGEYRSTLRRIIVTQGDTEP 121 A FG+VKM DYRWGIFLAP E ++K+ FG HKG+D WQEVPGEYRS LRR+I QGDTEP Sbjct: 64 AQFGHVKMEDYRWGIFLAPPEKDRKVNFGAHKGEDAWQEVPGEYRSMLRRLITVQGDTEP 123 Query: 122 ASVEQQRHLGLTAPSLYDLRNLFQVNVEEGRHLWAMVYLLHAHFGRDGREEGEALLERRS 181 ASVEQQR LG PSLYDLRNLFQVNVEEGRHLWAMVYLLHAHFG+DGREE E +L RRS Sbjct: 124 ASVEQQRLLGKCCPSLYDLRNLFQVNVEEGRHLWAMVYLLHAHFGKDGREEAEEMLARRS 183 Query: 182 GDEDNPRILTAFNEKTPDWLSFFMFTFITDRDGKFQLASLAESAFDPLARTCKFMLTEEA 241 GD D PRIL AFNEKT DWL+FFMFTFITDRDGK+QL +LAES FDPL+R+C+FMLTEEA Sbjct: 184 GDADKPRILGAFNEKTADWLAFFMFTFITDRDGKYQLCALAESGFDPLSRSCRFMLTEEA 243 Query: 242 HHLFVGESGIARVIQRTCEVMKELGTDDPAKLRAAGVIDLPTLQKYLNFHYSVTSDLYGA 301 HH+FVGESG+ R+I+R C+VMKE T+D +R GVIDLPT+Q+YLNFHYSVTSDLYGA Sbjct: 244 HHMFVGESGVGRIIERACQVMKENRTED---VRKFGVIDLPTIQRYLNFHYSVTSDLYGA 300 Query: 302 EISSNAATYYTNGLKGRFEEEKIGDDHKLQNSEYEVMDVAGDKILTRHVPALSALNERLR 361 E+S+NAAT Y GLKGR+EE KIGDDH+L+++ Y V+ VPAL+ALNERLR Sbjct: 301 EVSTNAATSYNMGLKGRYEETKIGDDHQLEHTTYSVLHPVNGGFQAVEVPALNALNERLR 360 Query: 362 DDWITDVQAGVDRWNRIPAKFGFDFRFTLPHKGFHRKIGMFADVHVSPDGRLISEAEWTH 421 DW DV GV+RWN+I AK G DF+ TLPH F+R IG F+D+ V P G++IS E+ Sbjct: 361 LDWAEDVAKGVERWNKIIAKHGIDFKLTLPHLAFNRAIGHFSDIAVDPSGKVISTEEFAR 420 Query: 422 QHKNWLPTESDRLYVHSLMGRCL-EPGKFANWIAAPARGINNQPVNFEYVRF 472 + WLP+ESD YV SLMG + +PGKFANWIA PARGINNQPV+F+YVRF Sbjct: 421 RRDEWLPSESDLAYVLSLMGGAVTQPGKFANWIAPPARGINNQPVDFDYVRF 472 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: 809 Number of extensions: 23 Number of successful extensions: 3 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: 473 Length adjustment: 33 Effective length of query: 440 Effective length of database: 440 Effective search space: 193600 Effective search space used: 193600 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