GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Pseudomonas putida KT2440

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 PP_0292 PP_0292 phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide isomerase

Query= curated2:B7GVK1
         (243 letters)



>FitnessBrowser__Putida:PP_0292
          Length = 245

 Score =  327 bits (837), Expect = 2e-94
 Identities = 167/241 (69%), Positives = 193/241 (80%), Gaps = 2/241 (0%)

Query: 1   MLIIPAIDLKDGKCVRLKQGRMEDDTVFSDDPVATAQHWVNEGARRLHLVDLNGAFAGTP 60
           MLIIPAIDLKDG CVRL+QGRMED TVFSDDPV+ A  WV  G RRLHLVDLNGAF G P
Sbjct: 1   MLIIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQP 60

Query: 61  IHKPVVEAIAKAQPELPIQIGGGIRSLETIEHYLEAGVTFVIIGTKAVQEPEFVEEACKR 120
           ++  VV AIAK  P LPIQIGGGIRSLETIEHY++AGV++VIIGTKAV++PEFV EACK 
Sbjct: 61  VNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKQPEFVAEACKA 120

Query: 121 FAGHIIVGIDAMNGMVATDGWANVTDVKATDLAKRFADAGVSSIVYTDIARDGMMQGVNV 180
           F G +IVG+DA +G VATDGWA V+ V+  DLAKRF   GVS+IVYTDIA+DGMMQG NV
Sbjct: 121 FPGKVIVGLDAKDGFVATDGWAEVSSVQVIDLAKRFEADGVSAIVYTDIAKDGMMQGCNV 180

Query: 181 EQTVNLAQYSGLPVIASGGVTNLDDVRNL--KGQPGILGAITGRAIYEGTLNLREAQLLL 238
             T  LA+ + +PVIASGG+ NL D++ L     PGI+GAITGRAIYEGTL++ EAQ   
Sbjct: 181 PFTKALAEATRIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC 240

Query: 239 D 239
           D
Sbjct: 241 D 241


Lambda     K      H
   0.319    0.137    0.397 

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: 285
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: 243
Length of database: 245
Length adjustment: 24
Effective length of query: 219
Effective length of database: 221
Effective search space:    48399
Effective search space used:    48399
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 (21.7 bits)
S2: 46 (22.3 bits)

Align candidate PP_0292 PP_0292 (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.12379.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12379.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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