GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Shewanella amazonensis SB2B

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 6936469 Sama_0657 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

Query= BRENDA::P0AB91
         (350 letters)



>FitnessBrowser__SB2B:6936469
          Length = 352

 Score =  525 bits (1352), Expect = e-154
 Identities = 259/349 (74%), Positives = 291/349 (83%)

Query: 1   MNYQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGP 60
           M YQNDD+RI E+KELLPP+A+LE+FPATENA+ TV +AR  IH +L   DDRLLVVIGP
Sbjct: 1   MYYQNDDVRINEVKELLPPIAILERFPATENASATVFNARSNIHNLLAKKDDRLLVVIGP 60

Query: 61  CSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQIN 120
           CSIHDP AA EY  RLLALRE+  D+LE+VMRVYFEKPRTTVGWKGLINDP+MDNSF++N
Sbjct: 61  CSIHDPEAALEYGQRLLALREQYSDQLEVVMRVYFEKPRTTVGWKGLINDPYMDNSFKLN 120

Query: 121 DGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLS 180
           DGLR ARKLLL++N  G+P AGEFLDMITPQY+ADLM WGAIGARTTESQVHRELASGLS
Sbjct: 121 DGLRTARKLLLELNHMGMPTAGEFLDMITPQYVADLMCWGAIGARTTESQVHRELASGLS 180

Query: 181 CPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPN 240
           CPVGFKNGTDGTIK+AIDAI AA APH FLSVTK+GHSAIV+T GN DCHIILRGG+EPN
Sbjct: 181 CPVGFKNGTDGTIKIAIDAIGAAAAPHHFLSVTKFGHSAIVSTKGNPDCHIILRGGREPN 240

Query: 241 YSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVM 300
           YS +HVA+++  L  AGLP  VMIDFSHANSSKQF +QM V  DV  Q+A G K I GVM
Sbjct: 241 YSREHVAKIQTELQSAGLPDNVMIDFSHANSSKQFTRQMVVADDVAGQLADGNKGIFGVM 300

Query: 301 VESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           VESHL EG Q    G PL YGKS+TDAC+GW+D+  LL  L  AV ARR
Sbjct: 301 VESHLNEGRQEHIPGVPLEYGKSVTDACLGWDDSAKLLATLNQAVLARR 349


Lambda     K      H
   0.317    0.134    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: 455
Number of extensions: 7
Number of successful extensions: 1
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: 350
Length of database: 352
Length adjustment: 29
Effective length of query: 321
Effective length of database: 323
Effective search space:   103683
Effective search space used:   103683
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: 49 (23.5 bits)

Align candidate 6936469 Sama_0657 (phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq))
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

Software error:

../bin/blast/fastacmd -i /tmp/list.7830.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7830.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.