GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Pseudomonas fluorescens GW456-L13

Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate PfGW456L13_1890 Glucokinase (EC 2.7.1.2)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1890
          Length = 319

 Score =  566 bits (1459), Expect = e-166
 Identities = 274/316 (86%), Positives = 296/316 (93%)

Query: 1   MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60
           +KLALVGDIGGTNARFALW++Q+L S++V ATAD  SPE+AI +YL   GL  G IG+VC
Sbjct: 1   LKLALVGDIGGTNARFALWKNQQLESVQVLATADFPSPEEAISLYLNGLGLAPGSIGSVC 60

Query: 61  LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120
           LSVAGPVSGDEFKFTNNHWRLS+  FC+TLQVD+LLLVNDFSAMALGMTRL+P EFRVVC
Sbjct: 61  LSVAGPVSGDEFKFTNNHWRLSRKGFCQTLQVDQLLLVNDFSAMALGMTRLQPGEFRVVC 120

Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180
           EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHI+ 
Sbjct: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIFN 180

Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240
           EIGHVSAETALSGGGLPR+YRAICAVDGHTPVL+TPEAITAAGLAGDP+A+EVL+QF  W
Sbjct: 181 EIGHVSAETALSGGGLPRVYRAICAVDGHTPVLDTPEAITAAGLAGDPIAVEVLEQFCCW 240

Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300
           LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFF+ SGFA+ FADKGCMSDYFKGIPVWLVT
Sbjct: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFLESGFARCFADKGCMSDYFKGIPVWLVT 300

Query: 301 APYSGLTGAGVALEQA 316
           APYSGL GAGVALEQ+
Sbjct: 301 APYSGLMGAGVALEQS 316


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: 458
Number of extensions: 8
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: 319
Length adjustment: 27
Effective length of query: 291
Effective length of database: 292
Effective search space:    84972
Effective search space used:    84972
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 PfGW456L13_1890 (Glucokinase (EC 2.7.1.2))
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.21057.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21057.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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