GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Cupriavidus basilensis 4G11

Align isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) (characterized)
to candidate RR42_RS22955 RR42_RS22955 isocitrate dehydrogenase

Query= BRENDA::Q945K7
         (374 letters)



>FitnessBrowser__Cup4G11:RR42_RS22955
          Length = 343

 Score =  272 bits (695), Expect = 1e-77
 Identities = 146/338 (43%), Positives = 212/338 (62%), Gaps = 11/338 (3%)

Query: 44  ITATLFPGDGIGPEIAESVKKVFTTAGVPIEWEEHYVGTEIDPRTQSFLTWESLESVRRN 103
           I ATL PGDGIGPE+ ++  KV    G P  W+    G     +    L   +L+S+RR 
Sbjct: 9   IPATLIPGDGIGPEVVQATVKVLDALGAPFSWDVQQAGMAGIEQGGDPLPQATLDSIRRT 68

Query: 104 KVGLKGPMATPIGKGHRSLNLTLRKELNLYANVRPCYSL-PGYKTRYDDVDLITIRENTE 162
            + LKGP+ TP+G G RS+N+ LR+  NL+ANVRP  +L PG   R++D+DL+ +REN  
Sbjct: 69  GLALKGPLTTPVGGGFRSVNVRLREAFNLFANVRPARTLVPG---RFEDIDLVLVRENVG 125

Query: 163 GEYSGLEHQVVRG-----VVESLKIITRQASLRVAEYAFLYAKTHGRERVSAIHKANIMQ 217
           G Y   ++ +  G     V  S    TR A  R+A +AF YA  + R++++ +HKANI++
Sbjct: 126 GFYVAHDYYIAVGDDPHAVAVSTGTNTRDACRRIARFAFEYAVKNQRKKITVVHKANILK 185

Query: 218 KTDGLFLKCCREVAEKYP-EITYEEVVIDNCCMMLVKNPALFDVLVMPNLYGDIISDLCA 276
              G+FL+  REVA+ Y   +  ++ ++D C M LV NP  FD+L+  NL+GDI+SD  A
Sbjct: 186 ALTGIFLEAAREVAQDYVGRVEMDDRIVDACAMQLVLNPWQFDMLLCTNLFGDILSDQIA 245

Query: 277 GLVGGLGLTPSCNIGEDGVALAEAVHGSAPDIAGKNLANPTALLLSGVMMLRHLKFNEQA 336
           GLVGGLG+ P  NIGE   A+ EAVHGSAPDIAGK +ANP +L+L+  +ML H+   + A
Sbjct: 246 GLVGGLGMAPGANIGETA-AIFEAVHGSAPDIAGKGIANPISLMLAAGLMLEHVGRQDLA 304

Query: 337 EQIHSAIINTIAEGKYRTADLGGSSTTTEFTKAICDHL 374
            ++  AI  T+ + + +T DL GS++T +F +A+   L
Sbjct: 305 VRLRQAIDLTLNQDQVKTGDLKGSASTLQFAEAVIKRL 342


Lambda     K      H
   0.318    0.134    0.389 

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: 287
Number of extensions: 14
Number of successful extensions: 6
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: 374
Length of database: 343
Length adjustment: 29
Effective length of query: 345
Effective length of database: 314
Effective search space:   108330
Effective search space used:   108330
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: 49 (23.5 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