GapMind for catabolism of small carbon sources

 

Aligments for a candidate for boxB in Magnetospirillum magneticum AMB-1

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)



>lcl|NCBI__GCF_000009985.1:WP_011382622.1 AMB_RS00890 benzoyl-CoA
           2,3-epoxidase subunit BoxB
          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.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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