GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcrB in Azospirillum brasilense Sp245

Align 4-hydroxybenzoyl-CoA reductase subunit beta; 4-HBCR subunit beta; EC 1.3.7.9 (characterized)
to candidate AZOBR_RS20525 AZOBR_RS20525 FAD-binding molybdopterin dehydrogenase

Query= SwissProt::O33820
         (324 letters)



>FitnessBrowser__azobra:AZOBR_RS20525
          Length = 332

 Score =  119 bits (298), Expect = 1e-31
 Identities = 89/276 (32%), Positives = 136/276 (49%), Gaps = 16/276 (5%)

Query: 4   LTDFRTHRPATLADAVNALAAEATLPLGAGTDLLPNLRRGLGHPAALVDLTGIDGLATIS 63
           +  F   R  + ADA+    A  T  +  GT+LL  ++  +  P  LVD++ +  L  I 
Sbjct: 1   MRSFTYARADSAADAIGRAGASGTAFVAGGTNLLDLMKADVLRPEGLVDISRLP-LDRIE 59

Query: 64  TLADGSLRIGAGATLEAIAEHDAIRTTWPALAQAAESVAGPTHRAAATLGGNLCQDTRCT 123
             A+G LR+GA A     A  + ++T +P L++A  + A    R  AT GGNL Q TRC 
Sbjct: 60  ETAEGGLRLGALARNADTAYDERVQTRYPMLSKAILAGASAQLRNMATNGGNLLQRTRCY 119

Query: 124 FY-------NQSEWWRSGNGYCLKYKGDKCHVIV-KSDRCYATYHGDVAPALMVLDARAE 175
           ++       N+ E    G+G       ++ H I+  SD+C A +  D+  AL  L+A  +
Sbjct: 120 YFYDTATPCNKRE---PGSGCGAIGGVNRIHAILGASDQCIAVHPSDLCVALAALEAVVQ 176

Query: 176 IVGPAGKRTVPVAQLFRESGAE---HLTLEKGELLAAIEVPPTG-AWSAAYSKVRIRDAV 231
           + GP G+R++P  +  R  G        L  G+L+ AI++P  G A  + Y KVR R + 
Sbjct: 177 VTGPEGERSIPFGEFHRLPGDRPEIDTVLRPGDLITAIDLPAKGFAEHSTYLKVRDRASY 236

Query: 232 DFPLAGVAAALQRDGDRIAGLRVAITGSNSAPLMVP 267
            F L  VAA L+ DG  +   R+A+ G    P   P
Sbjct: 237 AFALVSVAAGLEMDGGTVREARLALGGVAHKPWRDP 272


Lambda     K      H
   0.319    0.133    0.399 

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: 234
Number of extensions: 14
Number of successful extensions: 4
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: 324
Length of database: 332
Length adjustment: 28
Effective length of query: 296
Effective length of database: 304
Effective search space:    89984
Effective search space used:    89984
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: 49 (23.5 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