GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Desulfovibrio vulgaris Hildenborough

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 209398 DVU0462 chorismate mutase/prephenate dehydratase

Query= SwissProt::P27603
         (365 letters)



>MicrobesOnline__882:209398
          Length = 391

 Score =  251 bits (640), Expect = 3e-71
 Identities = 142/358 (39%), Positives = 205/358 (57%), Gaps = 6/358 (1%)

Query: 4   ADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKH 63
           A +L+A+RV ID LD  +L L++ RA  + EV R+K       +  + +RP RE  V  +
Sbjct: 15  AQRLQAIRVTIDGLDRDLLALLNRRAALSLEVGRIKAT-----DPGIVFRPFREREVFDN 69

Query: 64  IMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKP 123
           +   N+GPL +E +  ++REI+SS  +L++P RVAYLGPEGTFS  A ++  G ++  +P
Sbjct: 70  LEAANEGPLPDEHLRAIWREIISSSRSLQRPQRVAYLGPEGTFSYFAGMEFLGRAMDYRP 129

Query: 124 MAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVG 183
              + +VFR V       G+VP+ENS +G V  +LD FL+H++ I  E+  RI H LL G
Sbjct: 130 QPGLPDVFRAVHDRQCELGIVPLENSLQGTVGQSLDLFLQHEVFIQAELFCRISHCLL-G 188

Query: 184 ETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDM 243
                  I  +YSH Q LAQC  WL AH PN   +   S A AA+R   E  +AAI    
Sbjct: 189 TAAALADIDTVYSHPQPLAQCGGWLRAHLPNARIIPTESTAAAARRAAGEAGAAAIGHRS 248

Query: 244 AAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPF 303
            A L GL+ L   IED+P N TRF++I        G +KTS++ S+ +K GAL  +L   
Sbjct: 249 LADLLGLNVLERGIEDQPDNWTRFVVIAPAPADQQGREKTSMLFSLPDKAGALAGVLELL 308

Query: 304 HSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYP 361
              GI++ ++E+RP R  KW YVFF+D            ++E++      L++LGSYP
Sbjct: 309 AREGINMKKLESRPLRGEKWQYVFFVDVECDLGTERYARLVEELRTLCHTLRILGSYP 366


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: 334
Number of extensions: 14
Number of successful extensions: 3
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: 391
Length adjustment: 30
Effective length of query: 335
Effective length of database: 361
Effective search space:   120935
Effective search space used:   120935
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: 50 (23.9 bits)

Align candidate 209398 DVU0462 (chorismate mutase/prephenate dehydratase)
to HMM PF01817 (CM_2)

Software error:

../bin/blast/fastacmd -i /tmp/list.8873.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8873.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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