GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Dinoroseobacter shibae DFL-12

Align hexokinase (EC 2.7.1.1) (characterized)
to candidate 3608608 Dshi_2001 ROK family protein (RefSeq)

Query= BRENDA::Q5SLJ4
         (302 letters)



>FitnessBrowser__Dino:3608608
          Length = 414

 Score =  132 bits (332), Expect = 1e-35
 Identities = 79/215 (36%), Positives = 119/215 (55%), Gaps = 14/215 (6%)

Query: 39  VAEALAEAAERAEREAGVRGEAIGLGTPGPLDFRRGVIRFAPNIPGVQDFPIRRILEEAT 98
           + E LA AA   +R A     A+G+G PG +    G + ++P + G QD  ++ I+E+  
Sbjct: 145 IDEVLAAAALPRDRVA-----ALGVGLPGAVHHETGRVAWSPILAG-QDHALQAIIEDRF 198

Query: 99  GRPVFLENDANAAALAEHHLGAAQGEESSLYLTVSTGIGGGVVLGGRVLRGERGQGGELG 158
           G P  LENDAN   LAE   GA +  +    +T+  G+G G+VL  R+ RG +G G ELG
Sbjct: 199 GLPAHLENDANVLTLAELWFGAGRAMQDFAVVTIEQGVGMGLVLNNRLFRGAQGLGLELG 258

Query: 159 HLTLLPGGPACGCGLEGCLEALAAGRALERDATYAFQRPVDTRE--------LFRLFQAG 210
           H  +   G  C CG  GCLEA  A  AL R+A+ A  R   + +        LF   +AG
Sbjct: 259 HTKVQLDGALCRCGQRGCLEAYLADYALVREASTALDRDPRSAQTAAAMLESLFDQAKAG 318

Query: 211 DPKAERLVLQAARYVGIGLASLVKAFDPGVVVLGG 245
           +  A+ +  +A R++ +GLA++V+ FDP +++L G
Sbjct: 319 NGAAKAIFQRAGRFLSLGLANVVQLFDPELIILSG 353


Lambda     K      H
   0.318    0.141    0.414 

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: 176
Number of extensions: 9
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: 302
Length of database: 414
Length adjustment: 29
Effective length of query: 273
Effective length of database: 385
Effective search space:   105105
Effective search space used:   105105
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 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:

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