GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Sphingomonas koreensis DSMZ 15582

Align Glucose kinase (characterized, see rationale)
to candidate Ga0059261_0355 Ga0059261_0355 glucokinase, proteobacterial type

Query= uniprot:Q8P6M4
         (344 letters)



>FitnessBrowser__Korea:Ga0059261_0355
          Length = 323

 Score =  168 bits (425), Expect = 2e-46
 Identities = 109/325 (33%), Positives = 163/325 (50%), Gaps = 10/325 (3%)

Query: 23  LAADVGGTHVRVGRVSHGADAPIELSQYRTYRCADHASLD----AILADFLRDSRAVDAV 78
           +A D+GGTH R           + + +  T + A+H S      A      R+     A+
Sbjct: 4   VAVDIGGTHARFAIAEVEGGRVVSIGEPVTQKTAEHGSFQLAWQASARALGREMPRAAAI 63

Query: 79  VIASAGVALDDGRFISNNLPWTIAPRQLRDTLGVRAVHLVNDFEAVAYAAPQMEQRAVVQ 138
            IAS    ++D      N PW I P  +++ L V +  L+NDF AV +A  Q+     + 
Sbjct: 64  AIASP---INDELIKLTNNPWIIRPPLIKERLEVDSYSLINDFGAVGHAVAQLPSEHFLH 120

Query: 139 LSGPTPRHAQPGGPILVVGPGTGLGAA-VWINGPRQPTVLATEAGQVALASNDPDTAQVL 197
           + GP    A+ G  I V GPGTGLG A V+  GP    V++TE G +  A  D     ++
Sbjct: 121 ICGPDAPFAEKGA-ITVCGPGTGLGVAQVFRTGPLSYHVISTEGGHMDFAPLDGIEDSIV 179

Query: 198 RILARDASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALHSDDALARRCL 257
           + L    + +  E +++GPG+  +Y  L E+           +I   A    D+LA   L
Sbjct: 180 KRLRSTYTRVSAERIVAGPGIVPIYETLAEIEGKRTHRLNDKEIWTLAFEGKDSLAMAAL 239

Query: 258 QLFCALLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAKGRMRPVLERI 317
             FC  LG+  GD+ALA+G + GV +AGG+   +   L  S F +RF+AKGR + ++  I
Sbjct: 240 DRFCLSLGAVAGDLALAHGPT-GVVIAGGLGLKLKDHLVNSGFGQRFIAKGRFQALMSSI 298

Query: 318 PVKLVEHGQLGVLGAASWYLQHHTE 342
           PVKL+ H Q G+ GAA+ Y Q HT+
Sbjct: 299 PVKLITHPQPGLYGAAAAYAQEHTQ 323


Lambda     K      H
   0.321    0.136    0.410 

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: 372
Number of extensions: 19
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: 344
Length of database: 323
Length adjustment: 28
Effective length of query: 316
Effective length of database: 295
Effective search space:    93220
Effective search space used:    93220
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 (21.9 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