GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Sphingomonas koreensis DSMZ 15582

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Ga0059261_1479 Ga0059261_1479 Lactate dehydrogenase and related dehydrogenases

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



>FitnessBrowser__Korea:Ga0059261_1479
          Length = 332

 Score =  176 bits (447), Expect = 5e-49
 Identities = 113/284 (39%), Positives = 155/284 (54%), Gaps = 6/284 (2%)

Query: 28  DATQHDAFVAALKDADGGIGSSVKITPAMLEGAT--RLKALSTISVGFDQFDVADLTRRG 85
           +A    A +AA+ D D  + +      A L  A   RLK ++    G +  D+     RG
Sbjct: 39  EAMDRAALLAAVADCDVLVPTVTDTIDADLIAAAGERLKLIANFGSGVNHIDLKAARARG 98

Query: 86  IVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLG 145
           IV+ NTP VLTE TAD   +LI++  RR+ E  + V++G W+      + G  + GK LG
Sbjct: 99  IVVTNTPGVLTEDTADMTMALIVSVPRRLAEGEKLVRSGQWKGWSPGGMLGHRIGGKKLG 158

Query: 146 IVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAY--GARRVELAELLATADFVCLQ 203
           IVG+GRIG AVARRA   F + + Y NR   P+  EA    A   +L  +L   D + + 
Sbjct: 159 IVGMGRIGQAVARRAR-AFGLSIHYHNRHRLPEVVEAELGAAWHGDLDAMLREIDILTIH 217

Query: 204 VPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEP 263
            PL  E++ LI A  +  +     LINASRG  VDE+A+++AL+ G + GAGLDV+  EP
Sbjct: 218 TPLNEESRDLIDARRIGLLGPQVYLINASRGGIVDEEAMVDALEAGRLAGAGLDVWRFEP 277

Query: 264 LPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDG 307
              D  LL L NVV  PH+GSAT+E RHA       N+    DG
Sbjct: 278 -QIDPRLLALPNVVMTPHMGSATYEGRHATGEKVIANIRFWADG 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: 241
Number of extensions: 10
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: 332
Length adjustment: 28
Effective length of query: 293
Effective length of database: 304
Effective search space:    89072
Effective search space used:    89072
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