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 GFF836 Psest_0850 glucokinase, proteobacterial type

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



>FitnessBrowser__psRCH2:GFF836
          Length = 319

 Score =  412 bits (1058), Expect = e-120
 Identities = 201/318 (63%), Positives = 238/318 (74%)

Query: 1   MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60
           M+LALVGDIGGTNARFALWRD  L S+RV A AD ++PE A++ YL   GL  G + A C
Sbjct: 1   MRLALVGDIGGTNARFALWRDSRLESVRVLAAADFATPEMAVEYYLASLGLAPGSVEAAC 60

Query: 61  LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120
           L+ AGPV G++F FTNNHWRL+++ FC  LQ+ ELLL+NDF+AMALGMTR+     R++C
Sbjct: 61  LACAGPVKGEQFTFTNNHWRLTRSDFCGALQMGELLLINDFAAMALGMTRVGEAGRRMIC 120

Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180
            G  EP  PA+VIGPGTGLGV  LL LG G + ALPGEGGHVDLP++   E  LWQ ++ 
Sbjct: 121 AGEAEPDAPALVIGPGTGLGVAGLLPLGGGSWRALPGEGGHVDLPVADAHEAALWQMLFA 180

Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240
           ++GHV AE  LSGGGL  LYR +C V G  P L +P  +TAA LAGD VA+  L+QF +W
Sbjct: 181 QLGHVRAEDVLSGGGLLLLYRTVCTVAGLAPRLASPAEVTAAALAGDHVAVATLEQFCVW 240

Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300
           LGRVAGNNVLT G RGGVYIVGGV+PRFADFF  SGFA+ F  KGCMS Y   +PVWLVT
Sbjct: 241 LGRVAGNNVLTLGARGGVYIVGGVVPRFADFFAASGFARGFTSKGCMSRYLGDVPVWLVT 300

Query: 301 APYSGLTGAGVALEQAFA 318
           A + GL GAGVALEQA A
Sbjct: 301 AEFPGLEGAGVALEQALA 318


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: 371
Number of extensions: 11
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 GFF836 Psest_0850 (glucokinase, proteobacterial type)
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.28772.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28772.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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