GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Caulobacter crescentus NA1000

Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate CCNA_03852 CCNA_03852 phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide isomerase

Query= curated2:Q9A230
         (241 letters)



>FitnessBrowser__Caulo:CCNA_03852
          Length = 244

 Score =  463 bits (1191), Expect = e-135
 Identities = 241/241 (100%), Positives = 241/241 (100%)

Query: 1   MILYPAIDLKDGQCVRLLHGDMDKATVFNTSPADQAQRFVQDGFSWLHVVDLNGAIEGKS 60
           MILYPAIDLKDGQCVRLLHGDMDKATVFNTSPADQAQRFVQDGFSWLHVVDLNGAIEGKS
Sbjct: 4   MILYPAIDLKDGQCVRLLHGDMDKATVFNTSPADQAQRFVQDGFSWLHVVDLNGAIEGKS 63

Query: 61  VNTAAVEQILESISIPVQLGGGIRTLEGVEAWIEAGVSRVILGTVAVHDPELVKKAARLW 120
           VNTAAVEQILESISIPVQLGGGIRTLEGVEAWIEAGVSRVILGTVAVHDPELVKKAARLW
Sbjct: 64  VNTAAVEQILESISIPVQLGGGIRTLEGVEAWIEAGVSRVILGTVAVHDPELVKKAARLW 123

Query: 121 PEQIAVAVDVRDGKVAVDGWTGLSDLSAIDLSRRFEDAGVAALIITDISRDGALTGVNVE 180
           PEQIAVAVDVRDGKVAVDGWTGLSDLSAIDLSRRFEDAGVAALIITDISRDGALTGVNVE
Sbjct: 124 PEQIAVAVDVRDGKVAVDGWTGLSDLSAIDLSRRFEDAGVAALIITDISRDGALTGVNVE 183

Query: 181 GVGELADAVSIPVIASGGVAAVADIERLKARQGVEIAGAILGRSLYAGTIKPSEALIAAA 240
           GVGELADAVSIPVIASGGVAAVADIERLKARQGVEIAGAILGRSLYAGTIKPSEALIAAA
Sbjct: 184 GVGELADAVSIPVIASGGVAAVADIERLKARQGVEIAGAILGRSLYAGTIKPSEALIAAA 243

Query: 241 A 241
           A
Sbjct: 244 A 244


Lambda     K      H
   0.318    0.135    0.384 

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: 418
Number of extensions: 21
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: 241
Length of database: 244
Length adjustment: 23
Effective length of query: 218
Effective length of database: 221
Effective search space:    48178
Effective search space used:    48178
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

Align candidate CCNA_03852 CCNA_03852 (phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide isomerase)
to HMM TIGR00007 (hisA: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.29606.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29606.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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