GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_0355 Ga0059261_0355
           glucokinase, proteobacterial type
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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