GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoC in Synechococcus elongatus PCC 7942

Align Deoxyribose-phosphate aldolase; DERA; EC 4.1.2.4; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase (uncharacterized)
to candidate Synpcc7942_0983 Synpcc7942_0983 deoxyribose-phosphate aldolase

Query= curated2:Q5N4L8
         (228 letters)



>FitnessBrowser__SynE:Synpcc7942_0983
          Length = 228

 Score =  454 bits (1167), Expect = e-133
 Identities = 228/228 (100%), Positives = 228/228 (100%)

Query: 1   MAELSSDFDLAPYIEHSLLDPAATLEQIDQLCQEADRYHFAAVCLFPWVVRQAREWLNGR 60
           MAELSSDFDLAPYIEHSLLDPAATLEQIDQLCQEADRYHFAAVCLFPWVVRQAREWLNGR
Sbjct: 1   MAELSSDFDLAPYIEHSLLDPAATLEQIDQLCQEADRYHFAAVCLFPWVVRQAREWLNGR 60

Query: 61  SPRLCTVIDFPNGASTAASKVYAAQEAVENGAQELNVVVNLGWLRSDRADLVHQELAEIV 120
           SPRLCTVIDFPNGASTAASKVYAAQEAVENGAQELNVVVNLGWLRSDRADLVHQELAEIV
Sbjct: 61  SPRLCTVIDFPNGASTAASKVYAAQEAVENGAQELNVVVNLGWLRSDRADLVHQELAEIV 120

Query: 121 EATGVPIKAILEATRLNPSELEQLTDLCLDAGVTMLQTSTGWFGGATPALVQQLRQLTRN 180
           EATGVPIKAILEATRLNPSELEQLTDLCLDAGVTMLQTSTGWFGGATPALVQQLRQLTRN
Sbjct: 121 EATGVPIKAILEATRLNPSELEQLTDLCLDAGVTMLQTSTGWFGGATPALVQQLRQLTRN 180

Query: 181 RVGIHAAGGIRTWDQAAALVEAGAIRLGTSYGPMILQQRLAASTPAPA 228
           RVGIHAAGGIRTWDQAAALVEAGAIRLGTSYGPMILQQRLAASTPAPA
Sbjct: 181 RVGIHAAGGIRTWDQAAALVEAGAIRLGTSYGPMILQQRLAASTPAPA 228


Lambda     K      H
   0.319    0.132    0.394 

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: 340
Number of extensions: 5
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: 228
Length of database: 228
Length adjustment: 23
Effective length of query: 205
Effective length of database: 205
Effective search space:    42025
Effective search space used:    42025
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 (21.8 bits)
S2: 46 (22.3 bits)

Align candidate Synpcc7942_0983 Synpcc7942_0983 (deoxyribose-phosphate aldolase)
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.20092.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20092.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.