GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glk in Dyella japonica UNC79MFTsu3.2

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate N515DRAFT_2652 N515DRAFT_2652 glucokinase

Query= curated2:Q55855
         (355 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2652 N515DRAFT_2652
           glucokinase
          Length = 355

 Score =  120 bits (302), Expect = 4e-32
 Identities = 105/344 (30%), Positives = 158/344 (45%), Gaps = 37/344 (10%)

Query: 8   FLAGDIGGTKTILALVTINESSPGLARPVTLFEQTYSSPAFPDLVPMVQQFRQEAAFVLG 67
           FLA DIGGT   L LV           P  L  +++     P L  +V+ F  E      
Sbjct: 33  FLAADIGGTHARLGLVAAQPEGA----PRVLAYRSFRCADHPHLDDIVRMFCAELD-ARP 87

Query: 68  NPISVAKACFAIAGPVIDNTCRLTNLDWHLSGDRLAQELAIAQVDLINDFAAVGYGILGL 127
             + +A A +  AG V++      NL W L    LA EL + +V  +NDF A+ + I  +
Sbjct: 88  RELVLASAGYLHAGVVVNR-----NLAWPLVPATLAHELRLERVRFLNDFEALAHAIAYV 142

Query: 128 GSEDLTVLQAA--PVDPSGAIAILGAGTGLGQCYVIPQGQGRYRVFASEGAHGDFAPRSP 185
                  L+ A  P    G IA++G GTGLG     P    R  V A+E      A R  
Sbjct: 143 DEHSSVSLKTAFAPDAGKGPIAVIGPGTGLGAAVWFPGEPPR--VIATEAGQIQLAARGG 200

Query: 186 LEWQLLEYLKKKYSLGRISIERVVSGMGIAMIYEFLRHQYPERESAQFSKLYQTWNREKD 245
           LE ++L+ +    S      E V+SG G+  +Y  L   Y    S               
Sbjct: 201 LEREVLDRIAP--SDCHTPYEAVLSGPGLHRLYAALCAVYDRYPSC-------------- 244

Query: 246 QETKTVDLAAAVSQAALEGTDVLADQAMELFLGAYGAEAGNLALKLLPRGGLYVAGGIAP 305
              +  D+ AA      E  D +A +A+++F G  G+ AG+LA+     GG+Y+AGG   
Sbjct: 245 --AEPADVVAAA-----EAGDEVAYEAVQMFGGWMGSFAGDLAMLYGATGGVYLAGGFLS 297

Query: 306 KIIPLLEKGSFMQGFSDKGRMQSLMGTIPVQVVLNAKVGLIGAA 349
           +I+ LL  G  ++ F DKG M+  +  +P++VV + ++G++GAA
Sbjct: 298 RIVDLLRCGPLVERFLDKGVMRPFLHKVPIRVVDHGQLGVVGAA 341


Lambda     K      H
   0.320    0.137    0.399 

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: 285
Number of extensions: 14
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: 355
Length of database: 355
Length adjustment: 29
Effective length of query: 326
Effective length of database: 326
Effective search space:   106276
Effective search space used:   106276
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 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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