GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Mariniradius saccharolyticus AK6

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_040480287.1 C943_RS09665 ROK family protein

Query= curated2:Q9KCZ4
         (330 letters)



>NCBI__GCF_000330725.2:WP_040480287.1
          Length = 294

 Score =  111 bits (277), Expect = 3e-29
 Identities = 94/318 (29%), Positives = 143/318 (44%), Gaps = 40/318 (12%)

Query: 2   SDRWYVGVDVGGTTIKMAFLTTAGEIVDKWEIPTNKQDGGALITTNIADALDKRLSGHHK 61
           ++R  +G+D+GGT IK   L    E+VD   I T  Q+    I   IAD +   L  HH 
Sbjct: 4   TERPILGLDIGGTNIKAGVLV-GSELVDIRMIETPSQESQEYILETIADLIGTYL--HH- 59

Query: 62  SKSDLIGIGLGAPGFIEMDTGFIYHAVNI-GWRDFPLKDKLEEETKLPVIVDNDANIAAL 120
              D   IG+G PG I+ D G + +  NI  ++   L++ LE     PV ++NDAN  AL
Sbjct: 60  ---DFFAIGVGIPGLIDTDLGIVLNLENIPSFKRVHLREFLELRFGKPVYINNDANCFAL 116

Query: 121 GEMWKGAGDGAKNMLLITLGTGVGGGIVANGNILHGVNGMAGEIGHITVIPEGGAPCNCG 180
           GE   GA    K+++ ITLGTG+G GI+ANG++  G N  AGE      + +        
Sbjct: 117 GEYKFGAAKIYKHVVGITLGTGLGAGIIANGHLYCGFNCAAGEWCSAPYLDQDFEFYCSS 176

Query: 181 KTGCLETVASATGIARIATEGVTEHKESQLALDYDKHGVLTAKDVFSAADASDAFALSVV 240
           K    +  A A  +++ A +G                               D  AL   
Sbjct: 177 KFFYAKYHAKAKSLSKRAKDG-------------------------------DKEALRAY 205

Query: 241 DHIAYYLGFAIANLANALNPEKIVIGGGVSKAGDTLLKPIKQHFEAYALPRVADGAEFRI 300
               ++LG  I N+   L P+ IV+GG + KA     + +  +   +  P V+   +  I
Sbjct: 206 AEYGHHLGELIKNILYTLAPQAIVLGGSIRKAYPFFRESMLANIATFKYPSVSANLKILI 265

Query: 301 ATLGNDAGVIGGGWLVKQ 318
           + L ++ G+ G   LV +
Sbjct: 266 SEL-DETGIHGAVALVDE 282


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: 243
Number of extensions: 12
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 330
Length of database: 294
Length adjustment: 27
Effective length of query: 303
Effective length of database: 267
Effective search space:    80901
Effective search space used:    80901
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 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