GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Echinicola vietnamensis KMM 6221, DSM 17526

Align Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized)
to candidate Echvi_3892 Echvi_3892 Transcriptional regulator/sugar kinase

Query= SwissProt::Q9X1I0
         (317 letters)



>FitnessBrowser__Cola:Echvi_3892
          Length = 412

 Score =  133 bits (335), Expect = 6e-36
 Identities = 85/282 (30%), Positives = 141/282 (50%), Gaps = 7/282 (2%)

Query: 38  ENGKEDVIRRIAETILEVSD--GEEAPYVGIGSPGSIDRENGIVRFSPNFPDWHNVPLTD 95
           E    D I    ET ++ S    E+   +G+  PG +D  NG+   +  +  +    L +
Sbjct: 128 EKSTFDKIGDFMETYMQESGIPNEKIIAIGMSMPGLVDSVNGV---NHTYLKFGKKSLVE 184

Query: 96  ELAKRTGKKVFLENDANAFVLGEKWFGAGRGHDHIVALTLGTGIGGGVVTHGYLLTGRDG 155
               R  +KVF+ENDA A  L E  F   + +++++ + +G GIG G++  G L  G  G
Sbjct: 185 NFEARFDRKVFIENDARAMTLAEFKFSQDQKYNNVLGIFVGWGIGLGIIIDGKLYRGGAG 244

Query: 156 IGAELGHV-VVEPNGPMCNCGTRGCLEAVASATAIRRFLREGYKKYHSSLVYKLAGSP-E 213
              E  H  + E     C CG +GCLEAVAS TA+ R   E  +K   S++ ++A    E
Sbjct: 245 FAGEFSHSPIFESREISCTCGKKGCLEAVASGTAMVRMAEEAIEKDSDSILSRMARERGE 304

Query: 214 KADAKHLFDAARQGDRFALMIRDRVVDALARAVAGYIHIFNPEIVIIGGGISRAGEILFG 273
             D   + DAA  GD+ A+ I   V   L R ++  I + NP+++I+GG ++ A + L  
Sbjct: 305 GIDPSLIVDAALAGDQRAITILSDVGLDLGRGISILIQLLNPDLIIVGGSVAEAQQYLIT 364

Query: 274 PLREKVVDYIMPSFVGTYEVVASPLVEDAGILGAASIIKERI 315
           P+++ +  + M       E+    L ++ G+LG  +++ E I
Sbjct: 365 PIQQALNIFSMAKSREKSELTLYKLGKEVGLLGGVAVVIENI 406


Lambda     K      H
   0.320    0.142    0.418 

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: 278
Number of extensions: 17
Number of successful extensions: 4
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: 317
Length of database: 412
Length adjustment: 29
Effective length of query: 288
Effective length of database: 383
Effective search space:   110304
Effective search space used:   110304
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 (21.7 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