GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS03615 CA265_RS03615 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino]imidazole-4- carboxamide isomerase

Query= curated2:A6GY76
         (241 letters)



>FitnessBrowser__Pedo557:CA265_RS03615
          Length = 249

 Score =  175 bits (443), Expect = 9e-49
 Identities = 88/244 (36%), Positives = 152/244 (62%), Gaps = 6/244 (2%)

Query: 1   MRIIPAIDIIDGKCVRLSKGDYNTKIIYNENPLEVAKKFEAHGVQYLHLVDLDGAKSSQI 60
           M IIPAIDI+DGK VRL +GDYN K  Y  +  E+ +K+ ++G  ++H++DL+GAK    
Sbjct: 1   MYIIPAIDILDGKVVRLREGDYNQKTEYAVSIPEMIEKYRSNGTDFIHIIDLNGAKGD-F 59

Query: 61  INYKILEKIASQTALKIDFGGGLKSDNDLRIAFESGANQITGGSIAVKNPEVFNEWIIKY 120
            N K L +I  +T +K+ +GGG+++   +    ++G +++  G+ A+ NP+   +    +
Sbjct: 60  SNQKTLFEIIKKTEMKVQYGGGIRTIEQVTNLLDAGIHRVIVGTQAITNPDFLPQLSEAF 119

Query: 121 G-----ADKIILGADANNEKVAISGWLEESKEELIPFIQNYQNQGIEYVICTDIAKDGML 175
                 A++I++  D  +E +  SGW+E S  +L+ ++    + G    +CTDI+KDG L
Sbjct: 120 AKKDDYANRIVIAIDVLDEVIKYSGWMESSPIKLMDYVDKCLSLGFFRFLCTDISKDGKL 179

Query: 176 AGPSFNLYAKILSETKGIKLIASGGISTFDELPKLAQLGCEGTIIGKAIYENRITLKQLE 235
            G + +LY K+L  +  IKLIASGG+S+  ++  LA+      ++GKAIYE+RIT+++++
Sbjct: 180 GGAAIDLYEKLLEHSPMIKLIASGGVSSMQDIYDLAKYPIRSVVVGKAIYEDRITIEEIK 239

Query: 236 NFIL 239
            + L
Sbjct: 240 EWNL 243



 Score = 26.9 bits (58), Expect = 4e-04
 Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 2/89 (2%)

Query: 153 IQNYQNQGIEYVICTDIAKDGMLAGPSFNLYAKILSETKGIKLIASGGISTFDELPKLAQ 212
           I+ Y++ G +++   D+            L+ +I+ +T+ +K+   GGI T +++  L  
Sbjct: 36  IEKYRSNGTDFIHIIDLNGAKGDFSNQKTLF-EIIKKTE-MKVQYGGGIRTIEQVTNLLD 93

Query: 213 LGCEGTIIGKAIYENRITLKQLENFILNK 241
            G    I+G     N   L QL      K
Sbjct: 94  AGIHRVIVGTQAITNPDFLPQLSEAFAKK 122


Lambda     K      H
   0.317    0.138    0.391 

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: 196
Number of extensions: 9
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 241
Length of database: 249
Length adjustment: 24
Effective length of query: 217
Effective length of database: 225
Effective search space:    48825
Effective search space used:    48825
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 (21.6 bits)
S2: 46 (22.3 bits)

Align candidate CA265_RS03615 CA265_RS03615 (1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino]imidazole-4- carboxamide 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.19462.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19462.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.