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_2264 Ga0059261_2264 D-3-phosphoglycerate dehydrogenase

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



>FitnessBrowser__Korea:Ga0059261_2264
          Length = 525

 Score =  179 bits (454), Expect = 1e-49
 Identities = 109/320 (34%), Positives = 173/320 (54%), Gaps = 6/320 (1%)

Query: 2   KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADG-GIGSSVKITPAMLEGA 60
           K +++ K  P+    + ++  +V ++     +   A +   DG  I S+ K+T  +L+ A
Sbjct: 3   KVLISDKMDPKAAQIFRERGVEVDEITGKTPEELKAIIGQYDGLAIRSATKVTKEILDAA 62

Query: 61  TRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEW 120
           T LK +    +G D  D+ + + +G+V+ NTP   + +TA+   +L+ A AR++ E    
Sbjct: 63  TNLKVVGRAGIGVDNVDIPNASAKGVVVMNTPFGNSITTAEHAIALMFALARQLPEANTQ 122

Query: 121 VKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAE 180
            +AG W  +      GV+V GKTLG++G G IG  VA RA  G  MKV+  +   +P+  
Sbjct: 123 TQAGLWPKN---GFMGVEVTGKTLGLIGAGNIGSIVADRAH-GLRMKVVAYDPFLSPERA 178

Query: 181 EAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEK 240
              G  +VEL +LLA ADF+ L  PLT +T++++ A  L   KK   +IN +RG  +DE 
Sbjct: 179 VEMGVEKVELEQLLARADFITLHTPLTEQTRNILSAENLAKTKKGVRIINCARGGLIDEA 238

Query: 241 ALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAEN 300
           AL + L +G + GA LDVF TEP   +  L    N VA PH+G++T E +  +A   AE 
Sbjct: 239 ALKDLLDSGHVAGAALDVFVTEP-AKEHALFNTPNFVATPHLGASTSEAQVNVAIQVAEQ 297

Query: 301 LVAALDGTLTSNIVNREVLS 320
           +   L     +N +N   L+
Sbjct: 298 MADYLVNGGVTNALNMPSLT 317


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: 354
Number of extensions: 14
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: 525
Length adjustment: 31
Effective length of query: 290
Effective length of database: 494
Effective search space:   143260
Effective search space used:   143260
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