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_029134685.1 A3GO_RS0118600 benzoyl-CoA 2,3-epoxidase subunit BoxB
Query= SwissProt::Q9AIX7 (473 letters) >NCBI__GCF_000428045.1:WP_029134685.1 Length = 481 Score = 625 bits (1611), Expect = 0.0 Identities = 294/472 (62%), Positives = 367/472 (77%), Gaps = 3/472 (0%) Query: 2 INYSERIPNNVNLNENKTLQRALEQWQPSFLNWWDDMGPENSSNYDVYLRTAVSVDPKGW 61 +NY+++IPNNVNL+E++ LQRA+E+WQP F++WW MGP+ + +VYLRTAV DPKGW Sbjct: 7 VNYADKIPNNVNLSEDRRLQRAMEKWQPEFIDWWKSMGPDGFQDAEVYLRTAVGADPKGW 66 Query: 62 ADFGYVKMHDYRWGIFLAPQEGEKKITFGEHKGQDVWQEVPGEYRSTLRRIIVTQGDTEP 121 A F YVKM +YRWGI LA +E + I FG+HKG+ WQEVPGEYRS L+R+IV QGDTEP Sbjct: 67 AVFDYVKMPEYRWGILLAAKEEGRVIPFGKHKGEPAWQEVPGEYRSMLKRLIVIQGDTEP 126 Query: 122 ASVEQQRHLGLTAPSLYDLRNLFQVNVEEGRHLWAMVYLLHAHFGRDGREEGEALLERRS 181 ASVEQQR+LG T PSLYDLRNLFQVNVEEGRHLWAM YLL +FG+DGREE EALL+RRS Sbjct: 127 ASVEQQRYLGKTCPSLYDLRNLFQVNVEEGRHLWAMAYLLQKYFGKDGREEAEALLDRRS 186 Query: 182 GDEDNPRILTAFNEKTPDWLSFFMFTFITDRDGKFQLASLAESAFDPLARTCKFMLTEEA 241 GDED PRIL AFNEKTPDWLSFFMFTF TDRDGK QL SLA+S FDPLARTC+FMLTEEA Sbjct: 187 GDEDKPRILGAFNEKTPDWLSFFMFTFFTDRDGKMQLESLAQSGFDPLARTCRFMLTEEA 246 Query: 242 HHLFVGESGIARVIQRTCEVMKELGTDDPAK---LRAAGVIDLPTLQKYLNFHYSVTSDL 298 HH+FVGESG++RVI++T E M+E G DP + +RA GV+DLPTLQ+ +NFH+SVT DL Sbjct: 247 HHMFVGESGVSRVIRKTLERMQEAGITDPNEVDAVRALGVVDLPTLQRKVNFHFSVTLDL 306 Query: 299 YGAEISSNAATYYTNGLKGRFEEEKIGDDHKLQNSEYEVMDVAGDKILTRHVPALSALNE 358 +GAE+S+NAA + G+KGRF E++I DDH+L N Y V+ ++ AL+A+N Sbjct: 307 FGAEVSTNAANAFNAGIKGRFREDRIEDDHQLLNDTYPVLRHVDGELKVVEETALNAINA 366 Query: 359 RLRDDWITDVQAGVDRWNRIPAKFGFDFRFTLPHKGFHRKIGMFADVHVSPDGRLISEAE 418 RL DD+ITD AGV RWN++ G DF ++PHK F+R++G FAD+HV P+G L+S Sbjct: 367 RLLDDYITDATAGVKRWNKLFEGSGVDFEISVPHKAFNRRVGEFADLHVDPEGNLLSAEA 426 Query: 419 WTHQHKNWLPTESDRLYVHSLMGRCLEPGKFANWIAAPARGINNQPVNFEYV 470 W + WLP+++D Y+ SLM E GK+A+WIA P GI+ +P +FEYV Sbjct: 427 WQEKSAQWLPSQADEDYLLSLMKPVTEKGKYADWIAPPKVGIDKKPGDFEYV 478 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: 2 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: 481 Length adjustment: 33 Effective length of query: 440 Effective length of database: 448 Effective search space: 197120 Effective search space used: 197120 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 24 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