GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Klebsiella michiganensis M5al

Align Glucose kinase (characterized, see rationale)
to candidate BWI76_RS20510 BWI76_RS20510 glucokinase

Query= uniprot:Q8P6M4
         (344 letters)



>FitnessBrowser__Koxy:BWI76_RS20510
          Length = 321

 Score =  173 bits (438), Expect = 6e-48
 Identities = 109/313 (34%), Positives = 164/313 (52%), Gaps = 8/313 (2%)

Query: 23  LAADVGGTHVRVGRVSHGADAPIELSQYRTYRCADHASLDAILADFLRDSRA-VDAVVIA 81
           L  DVGGT+ R+      +    E+S+ +TY   D+ SL+A++  +L +    V+   IA
Sbjct: 6   LVGDVGGTNARLALCDLTSG---EISRAKTYSGLDYPSLEAVVQVYLEEHNVQVEDGCIA 62

Query: 82  SAGVALDDGRFISNNLPWTIAPRQLRDTLGVRAVHLVNDFEAVAYAAPQMEQRAVVQLSG 141
            A     D   ++N+  W  +  +++  LG   + ++NDF AV+ A P ++   ++Q  G
Sbjct: 63  IACPITGDWVAMTNHT-WAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKAEHLIQFGG 121

Query: 142 PTPRHAQPGGPILVVGPGTGLGAAVWINGPRQPTVLATEAGQVALASNDPDTAQVLRILA 201
             P     G PI V G GTGLG A  ++  ++   L  E G V  A N  +   +L  L 
Sbjct: 122 AKPVE---GKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEGIILEELR 178

Query: 202 RDASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALHSDDALARRCLQLFC 261
            +  ++  E VLSGPGL NLY A+ +     P +  P D+T  AL       RR L LFC
Sbjct: 179 TELGHVSAERVLSGPGLVNLYHAIVKSDGRLPENLQPKDVTERALADTCIDCRRALSLFC 238

Query: 262 ALLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAKGRMRPVLERIPVKL 321
            ++G   G++AL  G  GGVY+AGGI+P   +F  AS FR  F  KGR +  ++ IPV L
Sbjct: 239 VIMGRFGGNLALTLGTFGGVYIAGGIVPRFLEFFKASGFRGGFEDKGRFKAFVQDIPVYL 298

Query: 322 VEHGQLGVLGAAS 334
           + H   G+LG+ +
Sbjct: 299 IVHDNPGLLGSGA 311


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: 296
Number of extensions: 21
Number of successful extensions: 3
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: 321
Length adjustment: 28
Effective length of query: 316
Effective length of database: 293
Effective search space:    92588
Effective search space used:    92588
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