GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Burkholderia phytofirmans PsJN

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate BPHYT_RS05010 BPHYT_RS05010 RpiR family transcriptional regulator

Query= ecocyc::GLUCOKIN-MONOMER
         (321 letters)



>FitnessBrowser__BFirm:BPHYT_RS05010
          Length = 638

 Score =  261 bits (668), Expect = 2e-74
 Identities = 138/316 (43%), Positives = 192/316 (60%), Gaps = 4/316 (1%)

Query: 6   LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKV-EVKDGCIAIA 64
           L+ D+GGTNAR AL + + GEI   K Y   DYP +  VI+ YL++ K+  V    IAIA
Sbjct: 22  LLADIGGTNARFAL-ETSPGEIGSVKVYPCADYPGVAEVIKKYLKDTKIGRVNHAAIAIA 80

Query: 65  CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124
            P+ GD V+MTNH W+FSI   ++ LGF  L ++NDFTA++MA+P L     +Q G    
Sbjct: 81  NPVDGDQVSMTNHDWSFSIEATRRALGFDTLLVVNDFTALAMALPGLTDAQRVQVGVGAR 140

Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHV 184
                I + G GTG+GV+ L+  D RW++L  EGGH  FAP  E E I+L+  R +  HV
Sbjct: 141 RPNSVIGLLGPGTGMGVSGLIPADDRWIALGSEGGHATFAPADEREDIVLQYARKKWSHV 200

Query: 185 SAERVLSGPGLVNLYRAIVKAD-NRLPENLKPKDITERALADSCTDCRRALSLFCVIMGR 243
           S ERV +GPG+  +YRA+   D  R+  N+   +I +RAL         ++ +FC I+G 
Sbjct: 201 SFERVAAGPGIEVIYRALAGRDKKRVAANVDTIEIVKRALEGEPL-AAESVDVFCGILGT 259

Query: 244 FGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDN 303
           F GN+A+ LG  GG++I GG+VPR  EFF  S FR  FE KGRF+ Y+ ++P Y+I  + 
Sbjct: 260 FAGNIAVTLGALGGIYIGGGVVPRLGEFFSRSSFRKRFEAKGRFEAYLQNVPTYVITAEY 319

Query: 304 PGLLGSGAHLRQTLGH 319
           P  LG  A L + L +
Sbjct: 320 PAFLGVSAILAEQLSN 335


Lambda     K      H
   0.322    0.141    0.426 

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: 562
Number of extensions: 25
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: 321
Length of database: 638
Length adjustment: 33
Effective length of query: 288
Effective length of database: 605
Effective search space:   174240
Effective search space used:   174240
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: 51 (24.3 bits)

Align candidate BPHYT_RS05010 BPHYT_RS05010 (RpiR family transcriptional regulator)
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.5976.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5976.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.