GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_03925 H281DRAFT_03925 chorismate mutase

Query= SwissProt::P27603
         (365 letters)



>FitnessBrowser__Burk376:H281DRAFT_03925
          Length = 360

 Score =  325 bits (833), Expect = 1e-93
 Identities = 170/359 (47%), Positives = 242/359 (67%), Gaps = 6/359 (1%)

Query: 5   DQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHI 64
           ++LK LR RID+LD +++ L+++RA  A EV  VK     K   A  +RPERE  V+  +
Sbjct: 7   NRLKPLRERIDALDAQLIALLNQRAAVALEVGEVK-----KHFNAPVFRPEREQQVIARL 61

Query: 65  MELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPM 124
            ++++GPL +E ++ ++REIM++  ALE+ ++ AYLGP GT+S+ A  ++FG S+   P 
Sbjct: 62  QDMSEGPLASEHISAIWREIMAASRALEKTIKAAYLGPVGTYSEQAMHEYFGQSIEGLPC 121

Query: 125 AAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGE 184
            +IDEVFR V AGA  FGVVPVENSTEGAV+ TLD  L+  + I GE+ L IHH+LL   
Sbjct: 122 PSIDEVFRSVEAGAAEFGVVPVENSTEGAVSRTLDLLLQTQLAIGGELALPIHHNLLTLN 181

Query: 185 TTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMA 244
                 +TR+ +HAQ+LAQC++WL  + P++ER AVSSNA+AA+    +   AAIAGD A
Sbjct: 182 GGLAG-VTRVCAHAQALAQCQRWLATNAPHLERQAVSSNAEAARMAAEDPTVAAIAGDRA 240

Query: 245 AQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFH 304
           A  YGL      I+D P N TRF++IG +    +G D+TS+IVS+ N+PGA+ +LL P  
Sbjct: 241 ATHYGLQVAYALIQDDPHNRTRFVMIGKERTGVSGHDQTSLIVSVANEPGAVFKLLEPLA 300

Query: 305 SNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKA 363
            + + +TR E+RP+R G W Y F+ID  GH  DP +   LE++G +A  LK+LGSYP+A
Sbjct: 301 RHSVSMTRFESRPARVGTWEYYFYIDVEGHRDDPAVAAALEELGQKAAFLKILGSYPRA 359


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: 10
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: 360
Length adjustment: 29
Effective length of query: 336
Effective length of database: 331
Effective search space:   111216
Effective search space used:   111216
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 H281DRAFT_03925 H281DRAFT_03925 (chorismate mutase)
to HMM TIGR01807 (pheA: chorismate mutase (EC 5.4.99.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.31944.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31944.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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