GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxA in Magnetospirillum magneticum AMB-1

Align Benzoyl-CoA oxygenase component A; Benzoyl-CoA 2,3-dioxygenase subunit A; Benzoyl-CoA dioxygenase reductase component; EC 1.14.13.208 (characterized)
to candidate WP_011382623.1 AMB_RS00895 benzoyl-CoA 2,3-epoxidase subunit BoxA

Query= SwissProt::Q9AIX6
         (414 letters)



>NCBI__GCF_000009985.1:WP_011382623.1
          Length = 393

 Score =  479 bits (1232), Expect = e-140
 Identities = 238/409 (58%), Positives = 284/409 (69%), Gaps = 22/409 (5%)

Query: 10  LARQHLIDPEICIRCNTCEEICPVDAITHDSRNYVVKFETCNGCLACISPCPTGAIDSWR 69
           L RQHLIDP +CIRCNTCEE CPVDAITHD  NYVV ++ C GC  C+SPCPTGAID+W 
Sbjct: 3   LKRQHLIDPVVCIRCNTCEEACPVDAITHDGTNYVVSYDKCTGCRTCVSPCPTGAIDNWL 62

Query: 70  NVDKATPHSLADQYSWDYLPDTTELDQFEATVMGAAEL----PAEVQQITEVATAGQGGP 125
            VD+  P S+ DQ+ W+ LP          T  G AE     P EV  +   ATA  G  
Sbjct: 63  LVDQ--PWSIDDQFGWEELP-------LGQTGPGPAEPAPLPPGEVSDLLAAATATTGPS 113

Query: 126 AMAPWSASHPYVNLYTPANPITATVTGNYRLTAEDASSDIHHIVLDFGTTPFPVLEGQSI 185
              P SA+ PY NLY+   P+TA V GN R+T E   SDIHH+VLDF    FP LEGQSI
Sbjct: 114 VPPPASAAKPYFNLYSRDTPVTARVAGNMRITGEGTDSDIHHVVLDFSHNAFPFLEGQSI 173

Query: 186 GIIPPGVDEKGKPHLLRMYSVASPRDGERPHYNNLSLTVKRVVEDHEGNPTRGVASNYVC 245
           GI+PPG D KG+ H +R+YS+ASPR+GER   NNL+LTVKRV          GV SNYVC
Sbjct: 174 GIVPPGTDAKGRAHNIRLYSIASPREGERSGCNNLALTVKRVAG--------GVGSNYVC 225

Query: 246 DLKKGDKVQVTGPYGSTYLMPNHPGSSIMMICTGTGSAPMRAMTERRRRRMDRKEGGELV 305
           DLKKGD+V+V GP+G  +LMP+ P ++I+MICTGTGSAP RA TERRRR   +   G+L+
Sbjct: 226 DLKKGDEVRVAGPFGQAFLMPDAPNANIIMICTGTGSAPFRAFTERRRRNA-QDASGKLM 284

Query: 306 LFFGARAPEELPYFGPLQKLPKEFIDINFAFSRVPGEPKRYVQDAIRERADKVFQMLQDD 365
           LFFGAR PEELPYFGPL KLPK  ID+N AFSRVP  PK+YVQD IRER+D +  +L   
Sbjct: 285 LFFGARTPEELPYFGPLMKLPKSLIDVNLAFSRVPDRPKQYVQDKIRERSDDLAALLASA 344

Query: 366 NCYIYICGLKGMEAGVLEAFRDICRAKGADWDALRPQLLSKARFHVETY 414
           + +++ICGLKGME G  EAF DICR  G DW  LRP++  + R+HVETY
Sbjct: 345 DTHVFICGLKGMEQGCDEAFADICRLHGLDWADLRPRMREEGRYHVETY 393


Lambda     K      H
   0.319    0.136    0.425 

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: 596
Number of extensions: 18
Number of successful extensions: 6
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: 414
Length of database: 393
Length adjustment: 31
Effective length of query: 383
Effective length of database: 362
Effective search space:   138646
Effective search space used:   138646
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: 50 (23.9 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 (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