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 SMa2137 SMa2137 dehydrogenase

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



>FitnessBrowser__Smeli:SMa2137
          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.

Links

Downloads

Related tools

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