GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Dechlorosoma suillum PS

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Dsui_0124 Dsui_0124 lactate dehydrogenase-like oxidoreductase

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



>FitnessBrowser__PS:Dsui_0124
          Length = 322

 Score =  161 bits (407), Expect = 2e-44
 Identities = 107/286 (37%), Positives = 146/286 (51%), Gaps = 13/286 (4%)

Query: 39  LKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTES 98
           L  A   I + + I+ A++    +LK ++  + G +  D+    R+GIV++N       +
Sbjct: 40  LAGASIAIVNKLPISGALMARLPQLKMVAVAATGTNNVDLEAARRQGIVVSNIQGYAVHT 99

Query: 99  TADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGV---DVQGKTLGIVGLGRIGGA 155
             + VFSL+LA +R ++   + V  G WQ +     F     D+ G TLG+VG G +G  
Sbjct: 100 VPEHVFSLLLALSRNLLAYRQSVAEGRWQRAEQFCFFDHPIRDLHGATLGVVGGGSLGQG 159

Query: 156 VARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIG 215
           V R A   F MKVL   R         Y A     A +LA AD + L  PLT ET+HLIG
Sbjct: 160 VVRLAQ-AFGMKVLQAERKGAAVVRPGYTA----FATVLAEADALSLHCPLTAETRHLIG 214

Query: 216 AAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLK--- 272
           AAEL++MK SA+LIN +RG  VDE AL  AL+ G I GAG DV   EP   D PLL    
Sbjct: 215 AAELQAMKPSALLINTARGGLVDEAALARALREGWIAGAGFDVLTAEPPTDDHPLLSPDL 274

Query: 273 --LANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVNR 316
               N +  PH+  A+     A+A    +NL A   G +T    NR
Sbjct: 275 LAAPNFLLTPHVAWASAPAMQALADQLIDNLEAFARGAMTPGAANR 320


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: 206
Number of extensions: 10
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: 321
Length of database: 322
Length adjustment: 28
Effective length of query: 293
Effective length of database: 294
Effective search space:    86142
Effective search space used:    86142
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