GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoC in Bacteroides thetaiotaomicron VPI-5482

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate 352790 BT3263 putative deoxyribose-phosphate aldolase (NCBI ptt file)

Query= BRENDA::P0A6L0
         (259 letters)



>FitnessBrowser__Btheta:352790
          Length = 300

 Score =  166 bits (420), Expect = 5e-46
 Identities = 100/240 (41%), Positives = 138/240 (57%), Gaps = 14/240 (5%)

Query: 15  MDLTTLNDDDTDEKVIALCHQAKT------PVGNTAAICIYPRFIPIARKTLKEQGTPEI 68
           +DLTTLN  D+DE V+    +          + N AAIC+YP F  I + TL+  G   I
Sbjct: 55  IDLTTLNSTDSDESVMHFTEKVNEFDNEFPDMKNVAAICVYPNFADIVKNTLQVDG---I 111

Query: 69  RIATVTN-FPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALMAGNEQVGFDLVKACKE 127
            IA V+  FP     I++ +AET  AIA GADE+D+V      ++G+ +   + ++  KE
Sbjct: 112 NIACVSGGFPSSQTFIEVKVAETALAIADGADEIDIVISIGKFLSGDYETMCEEIQELKE 171

Query: 128 ACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIKTSTGKVAVNATPESARIMME 187
            C   +  LKVI+ETG LK  + I+KAS +S+ +GADFIKTSTGK    ATPE+A +M E
Sbjct: 172 VCKERH--LKVILETGALKTASNIKKASILSMYSGADFIKTSTGKQQPAATPEAAYVMCE 229

Query: 188 VIRD--MGVEKTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFGASSLLASLL 245
            I++        +GFKPAGG+ T  DA  Y  I  E+ G +W + R +R G S L   LL
Sbjct: 230 AIKEYYQKTNNKIGFKPAGGINTVHDAIIYYTIVKEILGEEWLNNRLFRLGTSRLANLLL 289


Lambda     K      H
   0.317    0.133    0.373 

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: 183
Number of extensions: 11
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: 259
Length of database: 300
Length adjustment: 26
Effective length of query: 233
Effective length of database: 274
Effective search space:    63842
Effective search space used:    63842
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: 47 (22.7 bits)

Align candidate 352790 BT3263 (putative deoxyribose-phosphate aldolase (NCBI ptt file))
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.12015.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12015.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.