GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Synechococcus elongatus PCC 7942

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Synpcc7942_1501 Synpcc7942_1501 D-3-phosphoglycerate dehydrogenase

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



>FitnessBrowser__SynE:Synpcc7942_1501
          Length = 546

 Score =  172 bits (436), Expect = 2e-47
 Identities = 109/317 (34%), Positives = 169/317 (53%), Gaps = 6/317 (1%)

Query: 1   MKKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADG-GIGSSVKITPAMLEG 59
           M K++    + +  L  L Q AQV              + + D   + S  ++T  ++E 
Sbjct: 18  MPKVLVSDPIDQVGLDILSQVAQVDVKTGLSPSELAQIIGEYDALMLRSGTRVTAEVIEA 77

Query: 60  ATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAE 119
             +L+ +    VG D  DV   TRRGIV+ N+P+  T + A+   +++L+ +R + +   
Sbjct: 78  GQKLRIIGRAGVGVDNVDVPAATRRGIVVVNSPEGNTIAAAEHTLAMMLSLSRHIPDANA 137

Query: 120 WVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQA 179
             K+G W      +  G +V  KTLG+VGLG+IG  VA   A    MK+L  +   + + 
Sbjct: 138 STKSGGWDRK---SFVGTEVYKKTLGVVGLGKIGSHVAT-VAKAMGMKLLAYDPFISAER 193

Query: 180 EEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDE 239
            E  GAR VEL  L   AD++ L +P TPET +LI A  L  MK +  +IN +RG  ++E
Sbjct: 194 AEQIGARLVELDILFQEADYITLHIPKTPETANLINAETLAKMKPTTRIINCARGGVINE 253

Query: 240 KALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLA-NVVALPHIGSATHETRHAMARNAA 298
           +AL +A+  G I GA LDV++ EPL +DSPL  L  N++  PH+G++T E +  +A + A
Sbjct: 254 QALADAIAAGKIGGAALDVYDQEPLQADSPLRALGKNLILTPHLGASTTEAQVNVAVDVA 313

Query: 299 ENLVAALDGTLTSNIVN 315
           E +   L G    + VN
Sbjct: 314 EQIRDVLLGLPARSAVN 330


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: 338
Number of extensions: 18
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: 546
Length adjustment: 32
Effective length of query: 289
Effective length of database: 514
Effective search space:   148546
Effective search space used:   148546
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: 50 (23.9 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