GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Dinoroseobacter shibae DFL-12

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 3609257 Dshi_2643 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)

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



>FitnessBrowser__Dino:3609257
          Length = 316

 Score =  194 bits (493), Expect = 2e-54
 Identities = 123/320 (38%), Positives = 176/320 (55%), Gaps = 13/320 (4%)

Query: 3   KIVAWKSLPEDVLAYLQQHAQVVQVDATQH---DAFVAALKDADG-----GIGSSVKITP 54
           K++  + LPE VLA  +        + TQ    +    AL+D D      G   S ++  
Sbjct: 2   KLLISRPLPEAVLARARARFDCTLRETTQPMRAEELRGALRDYDLVLPTLGDAFSAEVFA 61

Query: 55  AMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRV 114
            + E   RL  L+   VG++  D       G+ + NTP  +T++TADT  +LIL +ARR 
Sbjct: 62  DVPEPRARL--LANFGVGYNHIDAVAARAAGVAVTNTPGAVTDATADTALTLILMAARRA 119

Query: 115 VELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS 174
            E    V+AG W       + G+ V GKTLG++G+GRIG A+A R   GF M+V++ NRS
Sbjct: 120 GEGERLVRAGTWTGWHPTQMLGLHVTGKTLGVIGMGRIGQAIAARCHHGFGMEVVFYNRS 179

Query: 175 ANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRG 234
             P+  +    +   +AE++A AD V + VP   ET HLIGA    +M+  A+ +N +RG
Sbjct: 180 --PKTPDLPARQLASVAEVMAAADIVVVAVPGGAETHHLIGAEAFAAMQPHAVFVNIARG 237

Query: 235 ATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMA 294
             VDE ALI ALQ G +  AGLDV+E EP   ++ L+ + NVV LPH+G+A  E R AM 
Sbjct: 238 DVVDEAALIAALQAGQLGAAGLDVYEFEPAVPEA-LIGMENVVLLPHLGTAALEVREAMG 296

Query: 295 RNAAENLVAALDGTLTSNIV 314
             A +NL+A  +G    N V
Sbjct: 297 HMALDNLIACAEGAPLPNPV 316


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: 205
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: 316
Length adjustment: 27
Effective length of query: 294
Effective length of database: 289
Effective search space:    84966
Effective search space used:    84966
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