GapMind for catabolism of small carbon sources

 

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

Align Benzoyl-CoA reductase subunit C; 3-hydroxybenzoyl-CoA reductase subunit gamma; EC 1.3.7.8; EC 1.3.99.n1 (characterized)
to candidate WP_011384540.1 AMB_RS10820 benzoyl-CoA reductase subunit C

Query= SwissProt::O87874
         (386 letters)



>NCBI__GCF_000009985.1:WP_011384540.1
          Length = 391

 Score =  530 bits (1365), Expect = e-155
 Identities = 244/385 (63%), Positives = 316/385 (82%)

Query: 2   STADIIARCEALYEDLDFTAARQWKEADPSRKVIAYMPVYVPREIIHAAGMLPLGIMGGG 61
           S ADI+A C+ ++EDL+FT AR+WK+A P RKVI ++PVY P E+IHAAG LPLGI GGG
Sbjct: 7   SVADIMAVCQEMFEDLNFTYARKWKDAKPGRKVIGFLPVYSPIEMIHAAGCLPLGIFGGG 66

Query: 62  DGLEVIHGDAFYQSYICRIPRSTIELGLSKRMDFVDGMLFPSICDVIRNLSGMWKLMFPG 121
           D +EVIHGDA+YQSYICRIPRSTIELG++ R+DFVDGM+FP +CDVIRNLSG+WKLMFP 
Sbjct: 67  DQMEVIHGDAYYQSYICRIPRSTIELGVTNRLDFVDGMIFPFVCDVIRNLSGIWKLMFPN 126

Query: 122 KYVRYFDVPQNYRDDVGGNYYTAELNELREGLEHLSGRKITDDALRASIKVYNENRKLVQ 181
            + ++FD PQNY   +GG YY  EL+EL+EGLE L+GRKI+D  ++ SI +YNENR+L++
Sbjct: 127 VWSKFFDTPQNYDKSIGGTYYIQELHELKEGLETLTGRKISDADIQRSIGLYNENRRLIR 186

Query: 182 DVYGLRSREPWKVPSADVYLLMRAGLVLPVEEHNQMLKDYLAAAVKVEAQKRDNCRVIIN 241
           +VY  R+++PW  P+++VY+LMRAGL++ VEEHNQMLKDY+AAA   +  KRDN R+ I 
Sbjct: 187 EVYAFRAKQPWLAPTSEVYVLMRAGLMMDVEEHNQMLKDYMAAAANEDRPKRDNVRISIY 246

Query: 242 GSFCEQPPLNLIKSIELSGCYIVDDDYMIVHRFLRNEVSTAGDPMQNLSLAFLHESISTA 301
           GSFCEQPPLNLIKSIE++GCY+VDDDY + +RFL  +V T G+P++ L++ +L  S+ T+
Sbjct: 247 GSFCEQPPLNLIKSIEMAGCYVVDDDYSLNNRFLMVDVPTTGNPLEALAMTYLENSVETS 306

Query: 302 AKYDDKEEDKGKYLLEQVRTNAAEGVIFAAPSFCDPALLERPMLADRCSENKVPYISFKY 361
            KY    + KG++ ++ V+   AEGVI+A PSFCDPALL+RPM+ ++ SE  +PYI+FKY
Sbjct: 307 CKYVPDGKVKGQFHVDAVKACGAEGVIYATPSFCDPALLDRPMVCNKLSEAGIPYIAFKY 366

Query: 362 AENSGQMQPIREQAGTFADSIKLWS 386
           AENSGQMQPIREQAGTFADSIKLWS
Sbjct: 367 AENSGQMQPIREQAGTFADSIKLWS 391


Lambda     K      H
   0.321    0.138    0.412 

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: 506
Number of extensions: 9
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: 386
Length of database: 391
Length adjustment: 30
Effective length of query: 356
Effective length of database: 361
Effective search space:   128516
Effective search space used:   128516
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