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 3609586 Dshi_2970 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)

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



>FitnessBrowser__Dino:3609586
          Length = 328

 Score =  180 bits (456), Expect = 5e-50
 Identities = 126/318 (39%), Positives = 171/318 (53%), Gaps = 9/318 (2%)

Query: 4   IVAWKSLPEDVLAYLQQHAQVVQVDAT---QHDAFVAALKDADGGIGS-SVKITPAMLEG 59
           +V  + LPE V   L++   V   ++      DA  AA++ AD  + + S  I  AML G
Sbjct: 8   VVVTRRLPEAVETRLKELFDVELNESDTPMSRDALQAAMRRADVLVPTVSDHIDGAMLAG 67

Query: 60  A-TRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118
              RLK ++    G D  DVA   +RGI ++NTP VLT+ TAD   +LILA  RR+ E  
Sbjct: 68  VGDRLKLIANYGAGVDHIDVATARQRGIHVSNTPGVLTDDTADMTLALILAVTRRIPEGL 127

Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178
             ++ G W      AL G  + G+ LGI+G+GRIG AVARRA   F M++ Y NR    +
Sbjct: 128 ALMQTGAWTGWSPTALMGGRIAGRRLGILGMGRIGQAVARRAK-AFGMQIHYHNRRRLHK 186

Query: 179 A--EEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGAT 236
              EE        L ++++  D + +  P TP T HL+ A  LK MK SA+++N SRG  
Sbjct: 187 GIEEELEATWWESLDQMVSRMDVISVNCPHTPSTFHLMNARRLKLMKPSAVIVNTSRGEV 246

Query: 237 VDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARN 296
           +DE AL   L+ G I GAGLDVFE      +  L +L NVV LPH+GSAT E R  M   
Sbjct: 247 IDENALTRMLRAGDIAGAGLDVFE-HGHEVNPRLRELPNVVLLPHMGSATEEGRAEMGEK 305

Query: 297 AAENLVAALDGTLTSNIV 314
              N+    DG    ++V
Sbjct: 306 VIINIKTFDDGHRPPDLV 323


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: 234
Number of extensions: 11
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: 328
Length adjustment: 28
Effective length of query: 293
Effective length of database: 300
Effective search space:    87900
Effective search space used:    87900
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