GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kguD in Sinorhizobium meliloti 1021

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate SMa2137 SMa2137 dehydrogenase

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



>lcl|FitnessBrowser__Smeli:SMa2137 SMa2137 dehydrogenase
          Length = 324

 Score =  194 bits (493), Expect = 2e-54
 Identities = 124/272 (45%), Positives = 157/272 (57%), Gaps = 3/272 (1%)

Query: 37  AALKDADGGIGSSV-KITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVL 95
           AAL++AD  + +   KI+  MLEG  R K L    VGF+  D A  T+ G+V+ NTP VL
Sbjct: 47  AALEEADAVLPTVTDKISADMLEGGIRAKILGNFGVGFNHIDTAAATKVGLVVTNTPGVL 106

Query: 96  TESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGA 155
           T++TAD   +L+L  ARR  E    ++AG W       L G  V GKT+GI+G+GRIG A
Sbjct: 107 TDATADLAMTLLLMCARRAGEGERELRAGKWTGWRPTHLCGSHVTGKTVGIIGMGRIGQA 166

Query: 156 VARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIG 215
           VARR   GF M V++ + S +    +    +   + ++LATADFV L  P   E  HLI 
Sbjct: 167 VARRCHFGFGMDVVFFD-SHSIAGLDVPARQLPSVDDVLATADFVSLHCPGGGENYHLID 225

Query: 216 AAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLAN 275
              L  MK SA LIN +RG  VDE AL+ AL+   I GAGLDVFE EP      L +  +
Sbjct: 226 DDRLACMKWSAFLINTARGDVVDEHALVRALETRRIAGAGLDVFEGEP-RVPGRLAERQD 284

Query: 276 VVALPHIGSATHETRHAMARNAAENLVAALDG 307
           VV LPH+GSAT ETR AM     ENL A   G
Sbjct: 285 VVLLPHLGSATKETRVAMGMRVIENLKAFFSG 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: 215
Number of extensions: 12
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: 324
Length adjustment: 28
Effective length of query: 293
Effective length of database: 296
Effective search space:    86728
Effective search space used:    86728
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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