GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Azospirillum brasilense Sp245

Align SDR family oxidoreductase (characterized, see rationale)
to candidate AZOBR_RS04635 AZOBR_RS04635 oxidoreductase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>FitnessBrowser__azobra:AZOBR_RS04635
          Length = 247

 Score =  264 bits (674), Expect = 1e-75
 Identities = 138/248 (55%), Positives = 176/248 (70%), Gaps = 6/248 (2%)

Query: 5   TGRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHL-LDV 63
           TGRL GK  L+T A QG+GRA    FAREGA V+A   + + +E+L  I    T + LDV
Sbjct: 2   TGRLDGKRALVTGAGQGMGRAIALAFAREGASVVAASRTLSKMEDLPRIDSKITPVALDV 61

Query: 64  TDDDAIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVLPG 123
           TD  A++ +VA+ G +D+L N AG+V  G IL+C D+ W  S + N  +MFHTIRA LPG
Sbjct: 62  TDPAAVRRVVAEAGPLDILVNNAGWVHNGTILDCSDEDWARSLDQNVTSMFHTIRAALPG 121

Query: 124 MLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICPGT 183
           M+ ++ GSIVN+AS ASS+ GVANR AYG SKAAV+GLTK+VA DF+  G+RCNA+CPGT
Sbjct: 122 MIERRQGSIVNVASVASSLTGVANRTAYGTSKAAVIGLTKAVARDFIGAGVRCNALCPGT 181

Query: 184 IESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFTTG 243
             SPSL +RI + A   G     +RA F+ARQPMGR+G  EE+AA A+YLASDES F TG
Sbjct: 182 THSPSLEERIQSSADPEG-----MRAQFIARQPMGRLGTVEEMAAAAVYLASDESGFMTG 236

Query: 244 SIHMIDGG 251
           S+ + DGG
Sbjct: 237 SLLVADGG 244


Lambda     K      H
   0.316    0.129    0.359 

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: 185
Number of extensions: 9
Number of successful extensions: 3
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: 254
Length of database: 247
Length adjustment: 24
Effective length of query: 230
Effective length of database: 223
Effective search space:    51290
Effective search space used:    51290
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: 46 (22.3 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