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 SMc02849 SMc02849 2-hydroxyacid dehydrogenase

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



>FitnessBrowser__Smeli:SMc02849
          Length = 334

 Score =  175 bits (443), Expect = 2e-48
 Identities = 118/281 (41%), Positives = 160/281 (56%), Gaps = 11/281 (3%)

Query: 36  VAALKDADGGIGSSV-KITPAMLEGA-TRLKALSTISVGFDQFDVADLTRRGIVLANTPD 93
           VAA+K AD  + +   +I  A++E A  +LK ++  S G D  DV    R+GI + NTP+
Sbjct: 44  VAAVKRADVLVPTVTDRIDAALIEQAGPQLKLIAAFSNGVDNIDVDAAARKGITVTNTPN 103

Query: 94  VLTESTADTVFSLILASARRVVELAEWV--KAGHWQHSIGPALFGVDVQGKTLGIVGLGR 151
           VLTE TAD   +LILA  RR+ E A+ +  + G W       + G  + GK +GIVG+GR
Sbjct: 104 VLTEDTADMTMALILAVPRRLAEGAQVLTDRKGEWAGWSPTWMLGRRIAGKRIGIVGMGR 163

Query: 152 IGGAVARRAALGFNMKVLYTNRS-ANPQAEEAYGARRVE-LAELLATADFVCLQVPLTPE 209
           IG AVARRA   F + + Y NR    P+ EE   A   + L ++LA  D V +  P TP 
Sbjct: 164 IGTAVARRAK-AFGLSIHYHNRHRVKPETEEMLEATYWDSLDQMLARVDIVSVNCPSTPA 222

Query: 210 TKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSP 269
           T HL+ A  L  M+  + ++N +RG  +DE ALI++L+ G I GAGLDVFE EP  +   
Sbjct: 223 TYHLLSARRLALMRPDSYIVNTARGGIIDEAALIKSLREGKIAGAGLDVFENEPCVNPK- 281

Query: 270 LLKLA---NVVALPHIGSATHETRHAMARNAAENLVAALDG 307
           L+KLA    VV LPH+ SAT E R  M      N+    DG
Sbjct: 282 LIKLAGEGKVVLLPHMSSATLEGRIDMGEKVVINIRTFFDG 322


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: 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: 334
Length adjustment: 28
Effective length of query: 293
Effective length of database: 306
Effective search space:    89658
Effective search space used:    89658
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