GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|NCBI__GCF_000009985.1:WP_011384540.1 AMB_RS10820 benzoyl-CoA
           reductase subunit C
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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