GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Chryseobacterium viscerum 687B-08

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_103233526.1 C1634_RS17380 glucokinase

Query= curated2:Q9A6N3
         (331 letters)



>NCBI__GCF_002899945.2:WP_103233526.1
          Length = 349

 Score =  117 bits (292), Expect = 6e-31
 Identities = 86/295 (29%), Positives = 136/295 (46%), Gaps = 20/295 (6%)

Query: 40  YRGEDYGTAEDAIEEYLRKVGVKHPDQAVVAVAGPIDHGQVHMTNLDWRISEDGLRRAGG 99
           Y  ++Y    D ++++++   +++  +  +AV GP+ +G+     L W +  +   R  G
Sbjct: 54  YATKEYAAFSDILKKFIQDNQLQNVKRLGMAVPGPVLYGKSSPVRLGWNLDVEEYARDFG 113

Query: 100 FRNAKLINDFTAQALAAPRVGPKDLRQIGELPTSGEGDLAILGPGTGFGVAGLVRRHGQE 159
           F    ++ND  A A     +   DL  I        G++A+L PG G G AG        
Sbjct: 114 FEKVDMLNDLEASAYGMALLEDNDLEAIYTSGHLERGNVAVLAPGNGLGEAGYFFDGKYL 173

Query: 160 IPLATEGGHVAFAPVDDVEIEVLRALTRRLDGGRVSVERILSGPGMEDLH---------- 209
            P ATEGGH  F+P  +VE+E  + L      G VS E +LS  G+ +++          
Sbjct: 174 RPFATEGGHSEFSPRTNVEVEFYQFLNNIY--GIVSWENVLSKSGLFNIYRFLRDVKRHP 231

Query: 210 ----VDLAAAEGRGVEALTAKQITERAVEGCADSLATVNRFCAILGSTAGDIALTLGARG 265
               +    A+G  VE L  K   E  V  C  +L T   F   L   A ++ L L A G
Sbjct: 232 EPEWLSERLAQGNFVEEL-YKAAVEENVLICKIALDT---FLEFLAREANNLTLKLKATG 287

Query: 266 GVFIAGGIAPRIIDILEKSPFRERFDSKGRLSGFTRSIPTHVILHPHTALIGAAV 320
           G+ IAG I   I + ++K+ F E+F    ++    RS P +++   HTAL G A+
Sbjct: 288 GLLIAGDIPQTIREYIDKAKFYEKFKISDKMEEMLRSTPIYLVKQNHTALNGIAL 342


Lambda     K      H
   0.319    0.140    0.408 

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: 277
Number of extensions: 18
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: 331
Length of database: 349
Length adjustment: 28
Effective length of query: 303
Effective length of database: 321
Effective search space:    97263
Effective search space used:    97263
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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 (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