GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Pseudomonas stutzeri RCH2

Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate GFF1941 Psest_1984 chorismate mutase domain of proteobacterial P-protein, clade 2

Query= SwissProt::P27603
         (365 letters)



>FitnessBrowser__psRCH2:GFF1941
          Length = 365

 Score =  690 bits (1780), Expect = 0.0
 Identities = 347/365 (95%), Positives = 357/365 (97%)

Query: 1   MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60
           MS+ADQLKALRVRIDSLDERILDLISERARCAQEVARVKTA+  + E AVFYRPEREAWV
Sbjct: 1   MSDADQLKALRVRIDSLDERILDLISERARCAQEVARVKTAALAEGESAVFYRPEREAWV 60

Query: 61  LKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120
           LKHIMELN+GPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGH+VI
Sbjct: 61  LKHIMELNRGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHAVI 120

Query: 121 SKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180
           S PMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL
Sbjct: 121 STPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180

Query: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240
           LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA
Sbjct: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240

Query: 241 GDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300
           GDMAAQLYGL+KLAEKIEDRP NSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL
Sbjct: 241 GDMAAQLYGLTKLAEKIEDRPDNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300

Query: 301 MPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360
           +PFH+NGIDLTRIETRPSRSGKWTYVFFID +GHHQDPLIK+VLEKIG EAVALKVLGSY
Sbjct: 301 VPFHANGIDLTRIETRPSRSGKWTYVFFIDFLGHHQDPLIKDVLEKIGQEAVALKVLGSY 360

Query: 361 PKAVL 365
           PKAVL
Sbjct: 361 PKAVL 365


Lambda     K      H
   0.319    0.133    0.390 

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: 546
Number of extensions: 9
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: 365
Length of database: 365
Length adjustment: 30
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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: 49 (23.5 bits)

Align candidate GFF1941 Psest_1984 (chorismate mutase domain of proteobacterial P-protein, clade 2)
to HMM TIGR01807 (pheA: chorismate mutase (EC 5.4.99.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.18354.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18354.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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