GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Microvirga lotononidis WSM3557

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_009762999.1 MICLODRAFT_RS16860 ROK family transcriptional regulator

Query= BRENDA::B1VZT1
         (313 letters)



>NCBI__GCF_000262405.1:WP_009762999.1
          Length = 405

 Score =  125 bits (315), Expect = 1e-33
 Identities = 95/302 (31%), Positives = 150/302 (49%), Gaps = 21/302 (6%)

Query: 1   MGLTIGVDIGGTKIAAGVVDEEGRILSTFKVATPPT---AEGIVDAICAAVAGASEG--- 54
           +G  IGV  G  +I   +VD  GR  ++  +  P     A  ++D +   +   ++G   
Sbjct: 85  LGSVIGVWTGFNRIELRLVDSAGRNRASRHIERPLRNLGANELMDVLAETITAFAQGTGA 144

Query: 55  HDVEAVGIGAAGYVDDKRATVLFAPNIDWRHEPLKDKVEQRVGLPVVVENDANAAAWGEY 114
           HDV+A+G+   GYVD +   V ++P +  R  PL   + +R+GLPV++ENDA+A A+   
Sbjct: 145 HDVKAIGLACQGYVDTRDGIVAWSPVLGTRDLPLASGLGERLGLPVLMENDASAMAFAIT 204

Query: 115 RFGAGQGHDDVICITLGTGLGGGIIIGNKLRRG-RFGVAAEFGHIRVVPDGLLCGCGSQG 173
           +  +        C+ +G G+G G +I  +L RG RFG  +EFGH+R+   G  C CG +G
Sbjct: 205 QRNSDLRSGRTACLMVGDGVGLGFLIQGELYRGARFG-GSEFGHVRLRRGGPQCRCGGRG 263

Query: 174 CWEQYASGRALVRYAKQRANATPENAAVLLGLGDGSVDGIEGKHISEAARQGDPVAVDSF 233
           C E Y +  AL R A Q  +  P  A  LL  G+ +++      I E AR GDP  ++ F
Sbjct: 264 CIEAYLADYALHRDA-QLIDHRP--APTLLLPGEDAMES-----IVEQARAGDPALLNLF 315

Query: 234 RELARWAGAGLADLASLFDPSAFIVGGGVSDEGELVLDPIRKSFRRWLIGGEWRPHAQVL 293
           +      G  +  L    +P   ++ G     G   +D +R SF    +  +  P  + L
Sbjct: 316 QAAGEVLGDAVGILIQTLEPDHIVLCG----PGTRAMDLLRPSFEA-ALESQTIPELRAL 370

Query: 294 AA 295
           AA
Sbjct: 371 AA 372


Lambda     K      H
   0.319    0.140    0.427 

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: 315
Number of extensions: 20
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: 313
Length of database: 405
Length adjustment: 29
Effective length of query: 284
Effective length of database: 376
Effective search space:   106784
Effective search space used:   106784
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.

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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