GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Microvirga lotononidis WSM3557

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_009493232.1 MICLODRAFT_RS27800 glucokinase

Query= curated2:B9JYQ5
         (340 letters)



>NCBI__GCF_000262405.1:WP_009493232.1
          Length = 332

 Score =  230 bits (586), Expect = 4e-65
 Identities = 134/330 (40%), Positives = 189/330 (57%), Gaps = 5/330 (1%)

Query: 12  FPVLVGDIGGTNARFWILMDAHAAPKEFANIHTADFPTIDQAIQDCILDKSGFQPRSAIL 71
           FPVL+GDIGGTNARF +L    AA K      TA  P    AI+  +    G  PRSAI+
Sbjct: 4   FPVLLGDIGGTNARFAVLPAPGAAVKLLPRTLTAQTPDPVGAIRIALEAYDGPAPRSAII 63

Query: 72  AVAGPIKDDEIPLTNCPWVIRPKAMIADLGFDDVLVVNDFEAQALAAASL--GRNDREPI 129
           AVA  +    I LTN  WVI  +A+   L  + V +VND+   A + A L   + D  PI
Sbjct: 64  AVATRVDAPAIRLTNAHWVIDAEAIGKALDLERVTLVNDYTPVAASVAVLDEAKGDLAPI 123

Query: 130 GPLTETSLNSRVILGPGTGLGVGGLLYTHHTWFPVPGEGGHVDIGPRSDRDWQIFPHIER 189
           G        +RV+LGPGTGLG G L+        +  E GH++ GP +D +  I+PH+ER
Sbjct: 124 GTFAPPKHGARVVLGPGTGLGAGALVPVEDRLAILATEAGHIEFGPTNDEETAIWPHLER 183

Query: 190 IEGRISGEQILCGRGILHLYNAICAADGIEPVWTDPADVTQHALKGNDPVCVETMTLFVT 249
           + GRISGE +L G G+  +  A+ A   ++  +T P DV   A +GN  + V+ +  F  
Sbjct: 184 VGGRISGEVVLSGPGLFRIAKALAAHRCVDCPFTIPNDVLAAAREGN-ALAVDALRHFSR 242

Query: 250 YLGRIAGDMALVFMARGGVFLSGGISQKIIPLLKSPVFRAAFEDKAPHTEMMKTIPTFVA 309
           +LGR AGD+AL F + GGVF++GGI+ ++I +L+S  FR AF+ KAPH    + +P +  
Sbjct: 243 FLGRFAGDLALTFESSGGVFIAGGIAPRMIDILQSGDFRDAFDRKAPHDAWARKVPVYAI 302

Query: 310 IHPQAALSGLAAYARTPSSYGVKHEGRRWQ 339
           ++P+ AL GLAA    P  +  + +G  WQ
Sbjct: 303 VNPEPALEGLAAIVSNPQRFIFQSQG--WQ 330


Lambda     K      H
   0.322    0.140    0.445 

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: 351
Number of extensions: 17
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: 340
Length of database: 332
Length adjustment: 28
Effective length of query: 312
Effective length of database: 304
Effective search space:    94848
Effective search space used:    94848
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 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