GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Acidovorax sp. GW101-3H11

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 Ac3H11_2574 Chorismate mutase I (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.51)

Query= SwissProt::P27603
         (365 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2574
          Length = 351

 Score =  290 bits (743), Expect = 3e-83
 Identities = 157/354 (44%), Positives = 220/354 (62%), Gaps = 10/354 (2%)

Query: 12  VRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHIMELNKGP 71
           V+IDS+D+++L L+++RA  A++V  VK     K E   F+RP+R A V+  I   N GP
Sbjct: 1   VQIDSIDQQLLTLLNQRALVAEQVGEVK-----KREGTPFFRPDRVAQVIDKITHANPGP 55

Query: 72  LDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPMAAIDEVF 131
           L    +A ++REIMS+CLALE P RVA LGPEGTF + AA++ FG +      A  DEVF
Sbjct: 56  LKGPHVAAIWREIMSACLALESPQRVAVLGPEGTFCEQAAIEFFGGAADLMYCANFDEVF 115

Query: 132 REVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGETTKTDRI 191
               AG+  +GVV VENSTEG V  +LD FL     + GEV L + H+LL   T   D I
Sbjct: 116 HATAAGSAQYGVVGVENSTEGVVTRSLDLFLHTPTHVVGEVSLLVRHNLL-RTTNSLDGI 174

Query: 192 TRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAAQLYGLS 251
             + +H Q+LAQC+ WL  H P+ ER  VSSNA+ A+   +    AA++ + AA  +GL 
Sbjct: 175 EAVLAHPQALAQCQAWLSKHLPHAERRPVSSNAEGARLATTNPAWAALSSERAATQFGLH 234

Query: 252 KLAEKIEDRPVNSTRFLII----GSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFHSNG 307
            ++  I+D   N TRF II      Q  PP+G D TS++VS+ N+PGA+H+LL+P  ++G
Sbjct: 235 IVSHAIQDDAYNRTRFAIICLPHTLQTPPPSGKDCTSLVVSVPNQPGAVHDLLVPLKTHG 294

Query: 308 IDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYP 361
           + +TR E+RP+R+G+W Y F+ID  GH   P +   LE++       KVLG+YP
Sbjct: 295 VSMTRFESRPARTGQWEYYFYIDLDGHPAQPHVARALEELRSLCAFYKVLGTYP 348


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: 350
Number of extensions: 12
Number of successful extensions: 4
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: 351
Length adjustment: 29
Effective length of query: 336
Effective length of database: 322
Effective search space:   108192
Effective search space used:   108192
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 Ac3H11_2574 (Chorismate mutase I (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.51))
to HMM TIGR01807 (pheA: chorismate mutase (EC 5.4.99.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.25697.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25697.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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