GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Herbaspirillum seropedicae SmR1

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate HSERO_RS17870 HSERO_RS17870 glucokinase

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



>FitnessBrowser__HerbieS:HSERO_RS17870
          Length = 333

 Score =  245 bits (625), Expect = 1e-69
 Identities = 133/313 (42%), Positives = 175/313 (55%), Gaps = 2/313 (0%)

Query: 6   LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLE-EHKVEVKDGCIAIA 64
           L+ D+GGTNAR AL +   G I Q +   G DY      ++ YL+      V+   +AIA
Sbjct: 18  LLADIGGTNARFAL-ETGPGRIEQVQILRGADYGEFTDAVQAYLKLAGHPPVRHAVVAIA 76

Query: 65  CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124
            P+ GD + MTNH WAFSI   ++ LGF  L ++NDFTA+SMA+P L+ + L Q GG  P
Sbjct: 77  NPVQGDQIKMTNHDWAFSIEAARQLLGFELLLVVNDFTALSMAVPQLRADELQQVGGGAP 136

Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHV 184
             G PI + GAGTGLGV  L+H D  W+ L  EGGH  FAP    EA +L        HV
Sbjct: 137 KPGAPIGLVGAGTGLGVGGLLHADGHWLPLASEGGHAAFAPADPREAAVLAYAWQFHEHV 196

Query: 185 SAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRF 244
           SAER++SGPGL  ++RA++  D      L    I E A       C+  L+LFC ++G  
Sbjct: 197 SAERLVSGPGLELIHRALLAIDGHPAAELSAAQIVEGARQHGDALCQETLALFCSMLGTV 256

Query: 245 GGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNP 304
             +LAL LG  GG++I  G+VP   ++F  S FRA FE+KGR       IP Y+I  + P
Sbjct: 257 AADLALTLGALGGIYIGVGVVPHLGDYFARSPFRARFENKGRMSVLTKAIPTYVITAEYP 316

Query: 305 GLLGSGAHLRQTL 317
              G  A L   L
Sbjct: 317 AFTGVSAILADRL 329


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: 358
Number of extensions: 15
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: 321
Length of database: 333
Length adjustment: 28
Effective length of query: 293
Effective length of database: 305
Effective search space:    89365
Effective search space used:    89365
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: 48 (23.1 bits)

Align candidate HSERO_RS17870 HSERO_RS17870 (glucokinase)
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.27800.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27800.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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