GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Caulobacter crescentus NA1000

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate CCNA_03838 CCNA_03838 gluconate 2-dehydrogenase/glyoxylate reductase/hydroxypyruvate reductase

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



>FitnessBrowser__Caulo:CCNA_03838
          Length = 328

 Score =  192 bits (488), Expect = 9e-54
 Identities = 118/249 (47%), Positives = 151/249 (60%), Gaps = 6/249 (2%)

Query: 62  RLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWV 121
           RLK ++    G D  DVA    RGI++ NTP VLTE TAD   +LI+A++RR+VE AE V
Sbjct: 71  RLKLIANFGAGVDNIDVATANARGIIVTNTPGVLTEDTADLTMTLIMAASRRIVEGAEVV 130

Query: 122 KAGHWQHSIGPA-LFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS-ANPQA 179
           KAG + H   P  + G  + GK LGI+G+GRIG AVARRA   F M+V Y NR   +P+ 
Sbjct: 131 KAGGF-HGWSPTWMMGRRLWGKRLGIIGMGRIGQAVARRAK-AFGMQVHYHNRKPVSPRI 188

Query: 180 EEAYGARRVE-LAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238
            E  G    E L ++LA  DFV +  P TP T HL+ A  LK ++  A+++N +RG  +D
Sbjct: 189 AEELGCTYWESLDQMLARMDFVSVNCPHTPATYHLLSARRLKLLRPHAVVVNTARGEVID 248

Query: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298
           E AL   L  G I GAGLDV+E EP   +  LLKL NVV LPH+GSAT E R  M     
Sbjct: 249 EGALANMLAKGEIAGAGLDVYEHEP-AINPKLLKLPNVVLLPHMGSATVEGRIDMGEKVI 307

Query: 299 ENLVAALDG 307
            N+   +DG
Sbjct: 308 VNVKTFMDG 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: 233
Number of extensions: 15
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