GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Marinobacter adhaerens HP15

Align Glucose kinase (characterized, see rationale)
to candidate GFF2219 HP15_2173 glucokinase

Query= uniprot:Q8P6S9
         (338 letters)



>FitnessBrowser__Marino:GFF2219
          Length = 321

 Score =  171 bits (434), Expect = 2e-47
 Identities = 103/312 (33%), Positives = 154/312 (49%), Gaps = 6/312 (1%)

Query: 19  VAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAELSCAPVRRG 78
           +  D+GGT+ R AL  +     + + +L      C +Y  L + +  + A +  + V   
Sbjct: 8   LVGDIGGTNARFALVEQGTVQPRAIKILP-----CGEYANLDDAVRDYLARVGVSEVDGA 62

Query: 79  VIASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYMTGNQVMQ 138
            +A A   +   +V   N  W+   E++R Q G     ++NDF A+A    ++  + ++ 
Sbjct: 63  CLAVAS-PVRGTQVRMTNNHWLFDTEEVRAQFGWSRFKVINDFTAMALGVPHVANDHLVH 121

Query: 139 LSGPAQGAPGPALVLGPGTGLGAALWIPNGGNSVVLPTEAGHAALAAASDLEVALLQELR 198
           + G    +  P LV+GPGTGLG +  +P     V L TE GH   A   D E+A+L+ L+
Sbjct: 122 VCGGPGDSRRPRLVMGPGTGLGVSGLVPIEHGWVPLMTEGGHVDFAPTDDAEMAVLRILK 181

Query: 199 RTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAHEALQTFC 258
                V+ E  L G GLL LY A A ++   A    P  +TAAA+   D LA   L  FC
Sbjct: 182 ARFGRVSVERILCGQGLLNLYQAHAEIQGVAAPLDAPEKITAAAVENTDRLARHTLSHFC 241

Query: 259 GFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALEQVPVRI 318
             +G V G+ +L  G   GV+L GG LP+  +F   S F     DKG +RP LE  PV +
Sbjct: 242 EILGRVAGNGVLTLGSTGGVFLCGGILPRFLEFFLESPFRNGFEDKGRMRPLLEFTPVYV 301

Query: 319 VEHGQLGVIGAA 330
           V     G++GAA
Sbjct: 302 VTEPYTGLLGAA 313


Lambda     K      H
   0.321    0.136    0.407 

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: 244
Number of extensions: 11
Number of successful extensions: 2
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: 338
Length of database: 321
Length adjustment: 28
Effective length of query: 310
Effective length of database: 293
Effective search space:    90830
Effective search space used:    90830
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 (21.9 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