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

GapMind for catabolism of small carbon sources

Aligments 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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources