GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Pseudomonas stutzeri RCH2

Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate GFF1854 Psest_1893 glucokinase, proteobacterial type

Query= reanno::WCS417:GFF4431
         (318 letters)



>FitnessBrowser__psRCH2:GFF1854
          Length = 320

 Score =  395 bits (1016), Expect = e-115
 Identities = 195/314 (62%), Positives = 233/314 (74%)

Query: 1   MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60
           M  ALVGDIGGTNARFALWRDQ +  IRV  TAD++SPE AI+ YL+E    +  + AVC
Sbjct: 1   MSTALVGDIGGTNARFALWRDQRIEQIRVLPTADYASPELAIRAYLREVDQPLDALEAVC 60

Query: 61  LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120
           L+ AGPV GD F+FTNNHW+LS+ AFC+ L V ELLL+NDF+AMALGMTRL   E   VC
Sbjct: 61  LACAGPVGGDLFRFTNNHWQLSREAFCRELGVKELLLINDFTAMALGMTRLHDGERITVC 120

Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180
           +G PEP RP +VIGPGTGLGV  LL L  G + ALPGEGGH+ LP+ S RE  +W H++ 
Sbjct: 121 QGEPEPGRPRLVIGPGTGLGVAGLLPLSGGGWRALPGEGGHICLPIGSEREAAIWAHLHR 180

Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240
             GHV+AE  LSG GL  LYRA CA+DG     ++P AIT A LAGD  A  VL+QF  W
Sbjct: 181 SQGHVNAEAVLSGPGLLTLYRACCALDGQQVEFDSPAAITKAALAGDAYATAVLEQFCRW 240

Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300
           LGR+ G+NVLT G RGGVYIVGGV+PRFA+ F+ SGF+++  +KG MS YF  +PVWLVT
Sbjct: 241 LGRIVGDNVLTLGARGGVYIVGGVVPRFAEMFLRSGFSEALREKGQMSRYFDRLPVWLVT 300

Query: 301 APYSGLTGAGVALE 314
           APY GL GAGVAL+
Sbjct: 301 APYPGLEGAGVALQ 314


Lambda     K      H
   0.320    0.139    0.429 

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: 379
Number of extensions: 15
Number of successful extensions: 1
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: 318
Length of database: 320
Length adjustment: 28
Effective length of query: 290
Effective length of database: 292
Effective search space:    84680
Effective search space used:    84680
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate GFF1854 Psest_1893 (glucokinase, proteobacterial type)
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.2732.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2732.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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