GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Shewanella oneidensis MR-1

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 199942 SO0756 phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (NCBI ptt file)

Query= BRENDA::P0AB91
         (350 letters)



>FitnessBrowser__MR1:199942
          Length = 352

 Score =  530 bits (1365), Expect = e-155
 Identities = 258/349 (73%), Positives = 298/349 (85%)

Query: 1   MNYQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGP 60
           M YQNDD+RI E+KELLPP+A+LE+FPA+ENAA TV +AR++IH IL   DDRLLVVIGP
Sbjct: 1   MYYQNDDVRINEVKELLPPIAILERFPASENAAATVFNARQSIHNILAREDDRLLVVIGP 60

Query: 61  CSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQIN 120
           CSIHDP AA EY  RL+ LRE  +D+LEIVMRVYFEKPRTTVGWKGLINDP+MDNSF++N
Sbjct: 61  CSIHDPKAALEYGQRLVVLRERYQDQLEIVMRVYFEKPRTTVGWKGLINDPYMDNSFKLN 120

Query: 121 DGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLS 180
           DGLR ARKLL+D+NDSG+P AGEFLDMITPQY+AD+M WGAIGARTTESQVHRELASGLS
Sbjct: 121 DGLRTARKLLVDLNDSGMPTAGEFLDMITPQYVADMMCWGAIGARTTESQVHRELASGLS 180

Query: 181 CPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPN 240
           CPVGFKNGTDGTIKVAIDAI AA APH FLSVTK+GHSAIV+T GN DCHIILRGG+EPN
Sbjct: 181 CPVGFKNGTDGTIKVAIDAIGAANAPHHFLSVTKFGHSAIVSTKGNPDCHIILRGGREPN 240

Query: 241 YSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVM 300
           YSA HVA++ + L KA L   +MIDFSHANSSKQ+++QM V  +V +Q+A G +AI GVM
Sbjct: 241 YSASHVAQISDQLKKAKLVDNIMIDFSHANSSKQYQRQMVVANEVAEQVAAGNQAIFGVM 300

Query: 301 VESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           VESHLVEG Q L  G+ L YG+S+TDACIGWED++ LL  L  +V  RR
Sbjct: 301 VESHLVEGRQDLIEGQALCYGQSVTDACIGWEDSERLLAVLNQSVVERR 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: 466
Number of extensions: 4
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 199942 SO0756 (phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (NCBI ptt file))
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

Software error:

../bin/blast/fastacmd -i /tmp/list.8728.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8728.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.