GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Methylocystis bryophila S285

Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_085770628.1 B1812_RS05150 ROK family protein

Query= BRENDA::Q8R8N4
         (312 letters)



>NCBI__GCF_002117405.1:WP_085770628.1
          Length = 304

 Score =  141 bits (355), Expect = 2e-38
 Identities = 103/318 (32%), Positives = 153/318 (48%), Gaps = 30/318 (9%)

Query: 1   MRIGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVK 60
           +R+GVDLGGT      ++  G ++     PT P   Y AI   I  L   +   +G    
Sbjct: 6   LRVGVDLGGTKTEAIAIDPSGAMLLRRRVPT-PASDYAAILTTIVALVHAIEAELG---- 60

Query: 61  DVKSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDANVAALAEAT 120
            V  +G+GVPG      G +  +  L   + P AK++ + +     +ENDAN  AL+EAT
Sbjct: 61  GVARVGVGVPGWISPRSGFIRNSNTLVLNQRPFAKDLEQALARETRIENDANCFALSEAT 120

Query: 121 FGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGD------NGIRCNC 174
            GA +G      + LGTGVG G  L G +  GA+  A E GH  +         G RC C
Sbjct: 121 DGAAQGRDVVFGVILGTGVGGGLTLRGALLRGANAIAGEWGHNPLPRMSPDEFPGPRCYC 180

Query: 175 GKIGCFETYASATAL-IREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEAL 233
           G++GC ET+    AL +R G+K+                 E + A+ V   A   +  AL
Sbjct: 181 GRMGCIETFLCGGALALRYGEKSG----------------ESVGAEEVARRADHGEALAL 224

Query: 234 KIFEEYVKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYAD 293
              + Y   LA  + +++N+ DP++I+LGGGV+N  D L + L+K V +      L    
Sbjct: 225 DALDSYRDRLARALASVVNIVDPDMIVLGGGVSNI-DRLYEGLEKLVGDYAFTDALATPI 283

Query: 294 IRKAELGNDAGIIGAAIL 311
           +R    G+ +G+ GAA L
Sbjct: 284 VRNRH-GDSSGVRGAAWL 300


Lambda     K      H
   0.318    0.140    0.397 

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: 251
Number of extensions: 11
Number of successful extensions: 4
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: 312
Length of database: 304
Length adjustment: 27
Effective length of query: 285
Effective length of database: 277
Effective search space:    78945
Effective search space used:    78945
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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