GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Sinorhizobium meliloti 1021

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate SMc00641 SMc00641 D-3-phosphoglycerate dehydrogenase

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



>FitnessBrowser__Smeli:SMc00641
          Length = 531

 Score =  184 bits (466), Expect = 5e-51
 Identities = 105/270 (38%), Positives = 155/270 (57%), Gaps = 5/270 (1%)

Query: 46  IGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFS 105
           I S+ K+T  ++  AT LK +    +G D  D+   +RRGI++ NTP   + +TA+   +
Sbjct: 51  IRSATKVTEKLIAAATNLKVVGRAGIGVDNVDIPAASRRGIIVMNTPFGNSITTAEHAIA 110

Query: 106 LILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFN 165
           L+ A AR++       +AG W+ S      GV++ GK LG++G G IG  V  RA +G  
Sbjct: 111 LMFAVARQLPAADGSTQAGKWEKS---KFMGVEITGKVLGVIGAGNIGSIVCARA-IGLK 166

Query: 166 MKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKS 225
           M V+  +   + +  E  G  +VEL ELLA ADF+ L VPLT +T++++ A  +   K  
Sbjct: 167 MHVIAYDPFLSKERAEEMGVVKVELDELLAQADFISLHVPLTDKTRNILNAEAIAKAKPG 226

Query: 226 AILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSA 285
             +IN +RG  VDEKAL EAL+ G + GAG DVFE EP  ++SPL  L NVV  PH+G++
Sbjct: 227 VRIINCARGGLVDEKALAEALKAGHVAGAGFDVFEVEP-ATESPLFGLPNVVCTPHLGAS 285

Query: 286 THETRHAMARNAAENLVAALDGTLTSNIVN 315
           T E +  +A   AE +   L     +N +N
Sbjct: 286 TTEAQENVALQVAEQMSEYLVKGAVTNAIN 315


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: 329
Number of extensions: 20
Number of successful extensions: 4
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: 531
Length adjustment: 31
Effective length of query: 290
Effective length of database: 500
Effective search space:   145000
Effective search space used:   145000
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