GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Dinoroseobacter shibae DFL-12

Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate 3607683 Dshi_1092 carboxyvinyl-carboxyphosphonatephosphorylmutase (RefSeq)

Query= SwissProt::Q56062
         (295 letters)



>FitnessBrowser__Dino:3607683
          Length = 293

 Score =  168 bits (426), Expect = 1e-46
 Identities = 102/274 (37%), Positives = 150/274 (54%), Gaps = 7/274 (2%)

Query: 5   SPGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTL 64
           S  +  R+ LA++    +    +A  A L  + GY   ++SG   +A  +G PDLG+ + 
Sbjct: 2   SAARTLRSLLAQDRCHVMPCCFDALSAKLIAQEGYDLTFMSGFAASASRIGAPDLGLMSY 61

Query: 65  DDVLTDIRRITDVCPLPLLVDADIGFGSSAFNVARTVKSIAKAGAAALHIEDQVGAKRCG 124
            +V+   R IT+   +PL+ D D G+G+ A NV RTV   AKAG A++ IEDQ+  KRCG
Sbjct: 62  GEVVDQARNITEAVDIPLIGDGDTGYGN-AMNVRRTVTGFAKAGCASVMIEDQLAPKRCG 120

Query: 125 HRPNKAIVSKEEMVDRIRAAVDARTD-----PNFVIMARTDALAVEGLEAALDRAQAYVD 179
           H P KA+V ++E  DRIRAAVDAR +      + +I+ARTDA    GL  A+DRA  + +
Sbjct: 121 HTPGKAVVGRDEAFDRIRAAVDAREEIRAAGGDILILARTDARHEHGLAEAIDRAARFAE 180

Query: 180 AGADMLFPEAITELSMYRRFADVAQVPILANITEFGATPLFTTDELRSAHVAMALYPLSA 239
            GAD+LF EA    +  R        P +ANI E GATP      +     A+A YPLS 
Sbjct: 181 LGADILFVEAPRTEAEMRTVCAELPGPKMANIVEGGATPDLPNAAMHDIGYAIAAYPLSL 240

Query: 240 FRAMNRAAEKVYTVLRQEGTQKNVIDIMQTRNEL 273
             A  +A  +    +R +  + +++D  + R  +
Sbjct: 241 MAAAMQAMVRTLRGMRDD-RRPDLMDFAELRTRI 273


Lambda     K      H
   0.320    0.133    0.371 

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: 210
Number of extensions: 12
Number of successful extensions: 5
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: 295
Length of database: 293
Length adjustment: 26
Effective length of query: 269
Effective length of database: 267
Effective search space:    71823
Effective search space used:    71823
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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