GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Synechococcus elongatus PCC 7942

Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate Synpcc7942_2136 Synpcc7942_2136 dihydrodipicolinate reductase

Query= BRENDA::P9WP23
         (245 letters)



>FitnessBrowser__SynE:Synpcc7942_2136
          Length = 273

 Score =  207 bits (527), Expect = 2e-58
 Identities = 117/268 (43%), Positives = 164/268 (61%), Gaps = 29/268 (10%)

Query: 3   VGVLGAKGKVGATMVRAVAAADDLTL------SAELDAGD--------PLSLLTDGNTE- 47
           V V GA GK+G   ++A+AAADD+TL      SA++   D        PL +    + E 
Sbjct: 7   VVVNGATGKMGRETIKAIAAADDVTLVGAIARSADVQGQDIGEIVGLGPLEVPVTNDLEG 66

Query: 48  ------------VVIDFTHPDVVMGNLEFLIDNGIHAVVGTTGFTAERFQQVESWLVAKP 95
                       VV+DFTHPD +  N+   I  G+  VVGTTG   E+ Q++  +   K 
Sbjct: 67  MLCLASQEREVPVVVDFTHPDCIYDNVRKAIAYGVRPVVGTTGLNNEQLQELAEF-AEKA 125

Query: 96  NTSVLIAPNFAIGAVLSMHFAKQAARFFDSAEVIELHHPHKADAPSGTAARTAKLIAEAR 155
           +   L+ PNF+IG VL M  A QA+RF+D  E++ELHH  KADAPSGTA +TA+++AE  
Sbjct: 126 SVGCLVIPNFSIGMVLLMQAAIQASRFYDHVEILELHHDQKADAPSGTAIKTAQMLAELG 185

Query: 156 KGLPPNPDATSTSLPGARGA-DVDGIPVHAVRLAGLVAHQEVLFGTEGETLTIRHDSLDR 214
           K   P       ++PGARGA   + I +H+VRL GL+AH+EV+FG  GE LT+RHD++DR
Sbjct: 186 KTFNPPKVTEKETMPGARGAVGPENIRIHSVRLPGLIAHEEVIFGAPGEILTLRHDTMDR 245

Query: 215 TSFVPGVLLAVRRIAERPGLTVGLEPLL 242
           + ++PGVLLAVR++ +  GL  GL+ +L
Sbjct: 246 SCYMPGVLLAVRKVRQLTGLIYGLDRIL 273


Lambda     K      H
   0.319    0.135    0.389 

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: 200
Number of extensions: 12
Number of successful extensions: 4
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: 245
Length of database: 273
Length adjustment: 24
Effective length of query: 221
Effective length of database: 249
Effective search space:    55029
Effective search space used:    55029
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: 47 (22.7 bits)

Align candidate Synpcc7942_2136 Synpcc7942_2136 (dihydrodipicolinate reductase)
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.21284.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21284.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.