GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Escherichia coli BW25113

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 17613 b3553 putative dehydrogenase (VIMSS)

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



>FitnessBrowser__Keio:17613
          Length = 324

 Score =  327 bits (837), Expect = 3e-94
 Identities = 177/320 (55%), Positives = 223/320 (69%), Gaps = 7/320 (2%)

Query: 4   IVAWKSLPEDVLAYLQQHAQVVQV-----DATQHDAFVAALKDADGGIGSSVKITPAMLE 58
           ++ +K+LP+D+L  LQ+H  V QV        + +A + A  +A+G +GS+  +  A+LE
Sbjct: 5   VILYKALPDDLLQRLQEHFTVHQVANLSPQTVEQNAAIFA--EAEGLLGSNENVNAALLE 62

Query: 59  GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118
              +L+A STISVG+D FDV  LT R I+L +TP VLTE+ ADT+ +L+L++ARRVVE+A
Sbjct: 63  KMPKLRATSTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARRVVEVA 122

Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178
           E VKAG W  SIGP  +G DV  KTLGIVG+GRIG A+A+RA  GFNM +LY  R  + +
Sbjct: 123 ERVKAGEWTASIGPDWYGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNARRHHKE 182

Query: 179 AEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238
           AEE + AR  +L  LL  +DFVCL +PLT ET HL GA +   MK SAI INA RG  VD
Sbjct: 183 AEERFNARYCDLDTLLQESDFVCLILPLTDETHHLFGAEQFAKMKSSAIFINAGRGPVVD 242

Query: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298
           E ALI ALQ G IH AGLDVFE EPL  DSPLL +ANVVA+PHIGSATHETR+ MA  A 
Sbjct: 243 ENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSMANVVAVPHIGSATHETRYGMAACAV 302

Query: 299 ENLVAALDGTLTSNIVNREV 318
           +NL+ AL G +  N VN  V
Sbjct: 303 DNLIDALQGKVEKNCVNPHV 322


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: 238
Number of extensions: 4
Number of successful extensions: 2
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: 324
Length adjustment: 28
Effective length of query: 293
Effective length of database: 296
Effective search space:    86728
Effective search space used:    86728
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