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_RS27480 AZOBR_RS27480 hypothetical protein

Query= SwissProt::O33820
         (324 letters)



>FitnessBrowser__azobra:AZOBR_RS27480
          Length = 333

 Score =  135 bits (339), Expect = 2e-36
 Identities = 99/282 (35%), Positives = 140/282 (49%), Gaps = 22/282 (7%)

Query: 11  RPATLADAVNALAA--EATLPLGAGTDLLPNLRRGLGHPAALVDLTGIDGLATISTLADG 68
           R  T  +A+ A  A  E+   +  GT+L   ++ G+  PA L+D+  +DG   I T  D 
Sbjct: 8   RARTAREAIEAFVAAGESARYIAGGTNLYDLMKLGIEKPAHLIDIADLDGANRIDTDGD- 66

Query: 69  SLRIGAGATLEAIAEHDAIRTTWPALAQAAESVAGPTHRAAATLGGNLCQDTRCTFYNQS 128
            L  G  A +  +AEH  +R  +P LA++    A    R  AT+GGNL Q TRC ++   
Sbjct: 67  RLFFGGAALMADVAEHPVVRDDYPVLAESLSKAASQQLRNMATVGGNLLQRTRCPYFRNG 126

Query: 129 EWWRSGNGYCLKYK-GDKCHVIVKSDR----------CYATYHGDVAPALMVLDARAEIV 177
               +G   C K + G  C  I   DR          C A   GD   ALM +DA  E+ 
Sbjct: 127 ---ANGAYPCNKREPGSGCAAIGGLDRSQAVLGASAACNAVSPGDWPVALMAMDAAIELQ 183

Query: 178 GPAGKRTVPVAQLFR-ESGAEHL--TLEKGELLAAIEVPPTGAW-SAAYSKVRIRDAVDF 233
           G  G R +P+A+L+R  S   HL  T+ + E++  I VP T A  ++ Y KVR R++  F
Sbjct: 184 GLDGTRVIPIAELYRPPSRTPHLEFTIGREEIVTGISVPKTTAGRTSTYLKVRDRESYAF 243

Query: 234 PLAGVAAALQRDGDRIAGLRVAITGSNSAPLMV-PVDALLGG 274
            L   A AL+ DGDR+    VA+ G  + P    P +ALL G
Sbjct: 244 ALVSAAVALEMDGDRVRQAHVALGGVATVPWRARPAEALLRG 285


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: 252
Number of extensions: 16
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: 333
Length adjustment: 28
Effective length of query: 296
Effective length of database: 305
Effective search space:    90280
Effective search space used:    90280
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