GapMind for catabolism of small carbon sources

 

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

Align Benzoyl-CoA reductase subunit B; 3-hydroxybenzoyl-CoA reductase subunit beta; EC 1.3.7.8; EC 1.3.99.n1 (characterized)
to candidate WP_011384539.1 AMB_RS10815 benzoyl-CoA reductase subunit B

Query= SwissProt::O87875
         (432 letters)



>NCBI__GCF_000009985.1:WP_011384539.1
          Length = 432

 Score =  690 bits (1780), Expect = 0.0
 Identities = 325/428 (75%), Positives = 372/428 (86%), Gaps = 1/428 (0%)

Query: 5   TNPEVIKESSMVKQKEMIAGNYDRLTGTKESGEKVVSTFVPGNLNELIMCFDMVNNLPET 64
           + PE +KE SM  QK MIA NYD +T   E+G KV STFVPGNLNEL+MCFD+VNNLPE 
Sbjct: 2   SKPEAVKEPSMEMQKAMIARNYDAITSKHETGRKVSSTFVPGNLNELLMCFDIVNNLPEI 61

Query: 65  NAIQNGMRKQSGGMIMDAEKAGHSEDVCTYVKADIGMMGRGNIAPNGKPMPAPDMLLLSY 124
           NAIQ GMRK SGG IM+AEK+GHSEDVCTYVKADIG M +GNIAPNGKP P PD+L+LSY
Sbjct: 62  NAIQAGMRKASGGYIMEAEKSGHSEDVCTYVKADIGQMSKGNIAPNGKPYPNPDVLMLSY 121

Query: 125 TGCFTFMKWFELLRHEYKCPTVMLQIPYQGDGKITKNMRDFVVKQLKEEVIPMFEQVSGV 184
           TGC+TFMKWFELLR EYKCPT+ML +PY+GDG  TKNMRD++VKQLKE VIP  EQVSGV
Sbjct: 122 TGCYTFMKWFELLREEYKCPTLMLHVPYEGDGHSTKNMRDYIVKQLKEVVIPGLEQVSGV 181

Query: 185 KFDIDRLREYLKNSAKAEDDLVWVLESAKNRPSPIDAYFGGVYYIGPMFTAFRGTADAVE 244
           KFDIDRLR+YL+NSAKAED+LVW LE  K +PSPIDAYFGGVYYIGP+FTAFRGT DAV 
Sbjct: 182 KFDIDRLRQYLRNSAKAEDNLVWCLEQGKVKPSPIDAYFGGVYYIGPIFTAFRGTEDAVS 241

Query: 245 YYGLLRGEIEQRIREGKGPITPEGD-MKEEKYRLVVEGPPNWTSFREFWKLFYDEGAVVV 303
           YY +LR E++ RI   +GP+TPEG    ++KYRL+VEGPPNWT+FREFWK+FYDEGA+VV
Sbjct: 242 YYEMLRKEVQGRIENHQGPLTPEGTYFNDQKYRLIVEGPPNWTNFREFWKMFYDEGAIVV 301

Query: 304 ASSYTKVGGLYDQGFRHDPNDPLGTLADYCLGCYTNNNLPQRVELLEKYMNEYQADGLLI 363
           ASSYTKVGGLYDQGFRHDP++PL +LADYCLGCYTN NLP RV+LL KY+ EY+ADGLLI
Sbjct: 302 ASSYTKVGGLYDQGFRHDPDNPLESLADYCLGCYTNLNLPTRVDLLAKYVEEYEADGLLI 361

Query: 364 NSIKSCNSFSAGQLLMMREIEKRTGKPAAFIETDLVDPRYFSHANVKNRLESYFQMVDQK 423
           NSIKSCNSFSAGQL++M+E+E+RTG+P AFIETDLVDPRYFS ANVKNRLESYFQM++QK
Sbjct: 362 NSIKSCNSFSAGQLMIMKEVERRTGRPGAFIETDLVDPRYFSAANVKNRLESYFQMIEQK 421

Query: 424 RSGASLAT 431
           R G    T
Sbjct: 422 RRGGGSKT 429


Lambda     K      H
   0.318    0.136    0.405 

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: 725
Number of extensions: 24
Number of successful extensions: 2
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: 432
Length of database: 432
Length adjustment: 32
Effective length of query: 400
Effective length of database: 400
Effective search space:   160000
Effective search space used:   160000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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