GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Erythrobacter gangjinensis K7-2

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_047007751.1 AAW01_RS12295 glucokinase

Query= curated2:P21908
         (324 letters)



>NCBI__GCF_001010925.1:WP_047007751.1
          Length = 324

 Score =  365 bits (937), Expect = e-106
 Identities = 175/323 (54%), Positives = 236/323 (73%), Gaps = 1/323 (0%)

Query: 1   MEIVAIDIGGTHARFSIAEVSNGRVLSLGEETTFKTAEHASLQLAWERFGEKLGRPLPRA 60
           M++V +DIGGTHARF+IA  ++   +++ E  T  T +HAS Q AWE +  + G  +P  
Sbjct: 1   MQLVTVDIGGTHARFAIATHADDGSITMDEPVTLHTDDHASFQTAWEDYRAQKGGDIPSR 60

Query: 61  AAIAWAGPVHGEVLKLTNNPWVLRPATLNEKLDIDTHVLINDFGAVAHAVAHMDSSYLDH 120
            A+A AGPV GEV++ TNNPW++RPA + EKL +D+  ++NDF AVAHAVA        H
Sbjct: 61  VAMAIAGPVGGEVIRFTNNPWIIRPALVKEKLGVDSFKIVNDFEAVAHAVARAGEDEYLH 120

Query: 121 ICGPDEALPSDGVITILGPGTGLGVAHLLR-TEGRYFVIETEGGHIDFAPLDRLEDKILA 179
           + GP+  LP  G +T++GPGTGLGVAHL R  +G Y V  TEGGHIDFAPLD +ED ILA
Sbjct: 121 LTGPEGPLPPTGRLTVMGPGTGLGVAHLYREADGTYRVSATEGGHIDFAPLDSIEDAILA 180

Query: 180 RLRERFRRVSIERIISGPGLGNIYEALAAIEGVPFSLLDDIKLWQMALEGKDNLAEAALD 239
           RLR+R  RVS+ER+++GP + +IY  LA++E      LDD+++W   + G+D+LA AA+D
Sbjct: 181 RLRKRHTRVSVERVVAGPAISDIYHTLASLERKSVPELDDVEIWTRGMNGEDSLAAAAVD 240

Query: 240 RFCLSLGAIAGDLALAQGATSVVIGGGVGLRIASHLPESGFRQRFVSKGRFERVMSKIPV 299
           RFCLSLG++AGD+ALA GA +VVI GG+G R+  HLP+SGF +RF +KGRF  +M+ +PV
Sbjct: 241 RFCLSLGSVAGDMALAHGAKAVVIAGGLGYRLRDHLPKSGFAERFRAKGRFAGLMAGLPV 300

Query: 300 KLITYPQPGLLGAAAAYANKYSE 322
           KLIT+PQPGL GAAAAY  K+ +
Sbjct: 301 KLITHPQPGLFGAAAAYCQKFGD 323


Lambda     K      H
   0.320    0.139    0.411 

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: 423
Number of extensions: 23
Number of successful extensions: 2
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: 324
Length of database: 324
Length adjustment: 28
Effective length of query: 296
Effective length of database: 296
Effective search space:    87616
Effective search space used:    87616
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 24 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