GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxB in Cupriavidus basilensis 4G11

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 RR42_RS07505 RR42_RS07505 benzoyl-CoA oxygenase

Query= SwissProt::Q9AIX7
         (473 letters)



>FitnessBrowser__Cup4G11:RR42_RS07505
          Length = 474

 Score =  708 bits (1828), Expect = 0.0
 Identities = 334/472 (70%), Positives = 389/472 (82%)

Query: 2   INYSERIPNNVNLNENKTLQRALEQWQPSFLNWWDDMGPENSSNYDVYLRTAVSVDPKGW 61
           I+YS++IPNNVNL++++ LQRALE WQP+FL+WW DMGPE S  +DVYLRTAVSVDP GW
Sbjct: 3   IDYSQKIPNNVNLSDDRALQRALEHWQPAFLDWWRDMGPEGSHQHDVYLRTAVSVDPAGW 62

Query: 62  ADFGYVKMHDYRWGIFLAPQEGEKKITFGEHKGQDVWQEVPGEYRSTLRRIIVTQGDTEP 121
           A F +VKM DYRWGIFL P +  ++I FGEHKG+  WQEVPGE+R+ LRRIIVTQGDTEP
Sbjct: 63  AHFDHVKMPDYRWGIFLQPADPARRIHFGEHKGEAAWQEVPGEHRANLRRIIVTQGDTEP 122

Query: 122 ASVEQQRHLGLTAPSLYDLRNLFQVNVEEGRHLWAMVYLLHAHFGRDGREEGEALLERRS 181
           ASVEQQRHLG+T PSLYDLRNLFQVNVEEGRHLWAMVYLLH HFGRDGREE EALL RRS
Sbjct: 123 ASVEQQRHLGMTCPSLYDLRNLFQVNVEEGRHLWAMVYLLHRHFGRDGREEAEALLGRRS 182

Query: 182 GDEDNPRILTAFNEKTPDWLSFFMFTFITDRDGKFQLASLAESAFDPLARTCKFMLTEEA 241
           GDEDNPRIL AFNE+TPDWL+FFMFT  TDRDGKFQL +LAES+FDPLART +FMLTEEA
Sbjct: 183 GDEDNPRILGAFNERTPDWLAFFMFTHFTDRDGKFQLCALAESSFDPLARTTRFMLTEEA 242

Query: 242 HHLFVGESGIARVIQRTCEVMKELGTDDPAKLRAAGVIDLPTLQKYLNFHYSVTSDLYGA 301
           HH+FVGESGI+RVIQRTCEVM+E    DPA +RAAGVIDL T+Q+YLNFHYSVT DL+GA
Sbjct: 243 HHMFVGESGISRVIQRTCEVMRERDIQDPADVRAAGVIDLDTIQRYLNFHYSVTIDLFGA 302

Query: 302 EISSNAATYYTNGLKGRFEEEKIGDDHKLQNSEYEVMDVAGDKILTRHVPALSALNERLR 361
           + SSNAAT+Y+ GLKGRFEE K GDDH L+   Y ++DV   ++  R VP L+ALNE LR
Sbjct: 303 DQSSNAATFYSAGLKGRFEEGKRGDDHVLKGEVYRILDVTDGRLGEREVPMLNALNEVLR 362

Query: 362 DDWITDVQAGVDRWNRIPAKFGFDFRFTLPHKGFHRKIGMFADVHVSPDGRLISEAEWTH 421
           DD++ D   GV RWN++  K G   R T+PHK F+RKIG  A+VHVSP G L++EA+W  
Sbjct: 363 DDYVKDTLGGVARWNKVIEKHGIALRMTVPHKAFNRKIGSLANVHVSPAGELLTEAQWQA 422

Query: 422 QHKNWLPTESDRLYVHSLMGRCLEPGKFANWIAAPARGINNQPVNFEYVRFN 473
             + WLPT  DR +V SLMGR  EPGK+ANWIA P  G+N QP++FEYVRFN
Sbjct: 423 GEREWLPTGEDRAFVASLMGRVTEPGKYANWIAPPVVGVNRQPMDFEYVRFN 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: 851
Number of extensions: 19
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: 474
Length adjustment: 33
Effective length of query: 440
Effective length of database: 441
Effective search space:   194040
Effective search space used:   194040
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