GapMind for catabolism of small carbon sources

 

Alignments 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)



>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.

Links

Downloads

Related tools

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 (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:

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. 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