GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpK in Cupriavidus basilensis 4G11

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate RR42_RS13810 RR42_RS13810 glycerol kinase

Query= SwissProt::O66131
         (496 letters)



>FitnessBrowser__Cup4G11:RR42_RS13810
          Length = 520

 Score =  600 bits (1547), Expect = e-176
 Identities = 290/496 (58%), Positives = 370/496 (74%), Gaps = 7/496 (1%)

Query: 3   QYMLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIASV 62
           Q++LA+DQGT+SSRAILF+  G +  +AQ+EF QY+P PG VEH+  EIW S LAV   V
Sbjct: 11  QFVLALDQGTSSSRAILFDHAGNVARVAQREFRQYYPHPGHVEHDPYEIWQSQLAVAHEV 70

Query: 63  LSEAQVKPEQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGYDPL 122
           L++A V   QV+ IGITNQRETTV+W++ TG PI  A+VWQ R+TA +C+ L+A G+  L
Sbjct: 71  LNDAGVAASQVSAIGITNQRETTVLWDRQTGEPIGRALVWQDRRTAPMCEALQADGHGEL 130

Query: 123 FRKKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHVTDY 182
           FR KTGL+IDAYFSGTK++W+LD+ +GARERA RGEL FGT+D+WLIW+L+ G+ HVTD 
Sbjct: 131 FRDKTGLIIDAYFSGTKLRWMLDNTEGARERAARGELAFGTVDSWLIWQLTDGKRHVTDV 190

Query: 183 SNASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIAGAA 242
           SNASRT++FNIH  +WDD+LLD+L +P+++LPEV PSS   A+TA    FG E+PIAG A
Sbjct: 191 SNASRTMLFNIHAFQWDDDLLDLLDIPRSLLPEVVPSSGEVARTA-LRLFGAEIPIAGIA 249

Query: 243 GDQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAWGIDG------K 296
           GDQQAA +GQAC + GMAKNTYGTGCF+LMNTG + V S + LLTTI W + G      +
Sbjct: 250 GDQQAATYGQACLSPGMAKNTYGTGCFLLMNTGSQPVTSHNRLLTTIGWQLGGTTPPASR 309

Query: 297 VEYALEGSIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWD 356
            +Y LEG +F+ G+ IQWLRDGL++I +A + E  A + + T+GV +VPAF GLG P+WD
Sbjct: 310 TQYCLEGGVFMGGATIQWLRDGLQIINSAPEVEPLARQCDDTEGVVLVPAFAGLGAPHWD 369

Query: 357 SEVRGAVFGLTRGTTKEHFIRATLESLAYQTKDVLAVMEADSGISLTTLRVDGGAVKNNF 416
              RG + GLTRGT + H  RA LES+A Q+ DVL  M+ D+GISL  LRVDGGA +++ 
Sbjct: 370 PFARGTLVGLTRGTGRAHIARAALESIALQSVDVLDAMQKDAGISLAELRVDGGASRSDL 429

Query: 417 LMQFQSDLLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDD 476
           LMQ Q+DLL   V RP V ETTALGAAYLAGLA GYW+  D+IA+QWQ+E RFEP +  D
Sbjct: 430 LMQMQADLLGTAVVRPRVTETTALGAAYLAGLATGYWSGEDEIASQWQMEHRFEPNLSAD 489

Query: 477 KRTMLYDGWKKAVRAA 492
            R      W +AV  A
Sbjct: 490 ARAYRLWRWHRAVERA 505


Lambda     K      H
   0.319    0.134    0.406 

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: 839
Number of extensions: 36
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: 496
Length of database: 520
Length adjustment: 34
Effective length of query: 462
Effective length of database: 486
Effective search space:   224532
Effective search space used:   224532
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: 52 (24.6 bits)

Align candidate RR42_RS13810 RR42_RS13810 (glycerol kinase)
to HMM TIGR01311 (glpK: glycerol kinase (EC 2.7.1.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.18497.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18497.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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