GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Phaeobacter inhibens BS107

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF2436 PGA1_c24680 glyoxylate reductase GyaR

Query= reanno::BFirm:BPHYT_RS11290
         (321 letters)



>FitnessBrowser__Phaeo:GFF2436
          Length = 318

 Score =  181 bits (458), Expect = 3e-50
 Identities = 108/248 (43%), Positives = 141/248 (56%), Gaps = 3/248 (1%)

Query: 60  ATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAE 119
           A R + L+   VG++  DV      GI ++NTP  +T++TADT  +L+L +ARR  E   
Sbjct: 67  APRCRLLANFGVGYNHIDVDAAKTAGIAVSNTPGAVTDATADTALTLMLMTARRAGEGER 126

Query: 120 WVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQA 179
            V++G WQ      + G+ + GK +GIVG GRIG A+ARR   GF M V Y  RS     
Sbjct: 127 LVRSGQWQGWHPTQMLGLHLTGKHVGIVGFGRIGEAIARRCHFGFGMSVSYLARSEKSPG 186

Query: 180 EEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDE 239
             A   R   L  L A+ D + L VP   ET+HLI A  L +M+  A+LIN +RG  VDE
Sbjct: 187 FPA--VRADSLTALAASVDVLVLAVPGGAETRHLINAEVLAAMRPEALLINIARGEVVDE 244

Query: 240 KALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAE 299
            ALI ALQ G I GAGLDV+E EP      L ++  V  LPH+G+AT E R  M   A +
Sbjct: 245 AALISALQTGQIAGAGLDVYEFEP-EVPLALQQMEQVTLLPHLGTATEEVRSDMGHLALD 303

Query: 300 NLVAALDG 307
           N+ A L G
Sbjct: 304 NVAAFLAG 311


Lambda     K      H
   0.317    0.131    0.366 

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: 179
Number of extensions: 8
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: 321
Length of database: 318
Length adjustment: 28
Effective length of query: 293
Effective length of database: 290
Effective search space:    84970
Effective search space used:    84970
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: 48 (23.1 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