GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_078429099.1 BK574_RS14475 ROK family protein

Query= curated2:Q9KCZ4
         (330 letters)



>NCBI__GCF_002019605.1:WP_078429099.1
          Length = 302

 Score =  160 bits (404), Expect = 5e-44
 Identities = 96/305 (31%), Positives = 154/305 (50%), Gaps = 24/305 (7%)

Query: 10  DVGGTTIKMAFLTTAGEIVDKWEIPTNKQDGGALITTNIADALDKRLSGHHKSKSDLIGI 69
           D+GGT+IK       G+++    +PT+   GGA +   +       LS     K D+ G+
Sbjct: 7   DIGGTSIKYGVANKEGQLLFSSSVPTDAYLGGAAVIQKVV-----LLSKELMKKWDIHGV 61

Query: 70  GLGAPGFIEMDTGFIYHAV-NI-GWRDFPLKDKLEEETKLPVIVDNDANIAALGEMWKGA 127
            +   G I+ D G + +A  NI  +    +++++ ++ KLPV V+ND N  A+GE W+GA
Sbjct: 62  SISTAGQIDSDNGIVVYATDNIPNYTGLNIEERIYDQLKLPVKVENDVNCTAIGEHWQGA 121

Query: 128 GDGAKNMLLITLGTGVGGGIVANGNILHGVNGMAGEIGHITVIPEGGAPCNCGKTGCLET 187
                + L ITLGTGVGG +  NG +  G    AGEIGH+T+ P  G  C CG  GC E 
Sbjct: 122 AQNTDDFLCITLGTGVGGALFLNGRLYTGQGFSAGEIGHMTLYPH-GEKCTCGSNGCYEQ 180

Query: 188 VASATGIARIATEGVTEHKESQLALDYDKHG-VLTAKDVFSAADASDAFALSVVDHIAYY 246
            AS++ +  + ++               K+G  ++  D F    + +  ++ + +     
Sbjct: 181 YASSSALEDLVSK---------------KYGHAISLIDFFVHVKSGETKSIQIYNQWIDD 225

Query: 247 LGFAIANLANALNPEKIVIGGGVSKAGDTLLKPIKQHFEAYALPRVADGAEFRIATLGND 306
           L   +  L + +NP+ IVIGGG+S+ G+ LL  IK       +P  A   E ++A  GN 
Sbjct: 226 LTTGLKTLIHIINPKLIVIGGGISEQGEFLLNSIKNSVYQKVMPNHARNLEIQLAEYGNK 285

Query: 307 AGVIG 311
           A ++G
Sbjct: 286 ANLLG 290


Lambda     K      H
   0.316    0.137    0.405 

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: 261
Number of extensions: 13
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: 330
Length of database: 302
Length adjustment: 27
Effective length of query: 303
Effective length of database: 275
Effective search space:    83325
Effective search space used:    83325
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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