GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_2652
          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.

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