GapMind for catabolism of small carbon sources

 

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

Align Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 (characterized)
to candidate 353951 BT4425 deoxyribose-phosphate aldolase (NCBI ptt file)

Query= SwissProt::P39121
         (223 letters)



>FitnessBrowser__Btheta:353951
          Length = 238

 Score =  224 bits (570), Expect = 1e-63
 Identities = 115/212 (54%), Positives = 148/212 (69%), Gaps = 1/212 (0%)

Query: 3   LANIIDHTALKPHTQKADILKLIEEAKTYKFASVCVNPTWVELAAKELKGTGVDVCTVIG 62
           LA +IDHT LKP     +I KL  EA+ Y+FA V +NP  VE   K L+G+GV V   IG
Sbjct: 18  LAGMIDHTFLKPFGTAENIEKLCAEARQYQFAMVAINPAEVETCVKLLEGSGVRVGAAIG 77

Query: 63  FPLGANTTETKAFETKDAISKGATEVDMVINIAALKDKEDDVVEADIRGVVEAVAGKALV 122
           FPLG NT E KAFET+DAI+KGATE+D VIN+ AL+  + D+V+ +I  +V       ++
Sbjct: 78  FPLGQNTVECKAFETRDAIAKGATEIDTVINVRALQKGQTDIVKKEIEDMVSICKPAGVI 137

Query: 123 -KVIIETCLLTDEEKERACRLAVSAGADFVKTSTGFSTGGATKEDIALMRKTVGPDIGVK 181
            KVI+ETC LTDEEKE  CR+A  AG DFVKTSTGF T GA   D+ALMR+ VGP IGVK
Sbjct: 138 CKVILETCYLTDEEKETVCRIAKEAGVDFVKTSTGFGTAGANVHDVALMRRVVGPVIGVK 197

Query: 182 ASGGVRTKEDVDTMVEAGASRIGASAGVSIVK 213
           A+GG+R  +    +++ GA+RIG S+G+ IV+
Sbjct: 198 AAGGIRDLDTALALIQVGATRIGTSSGIQIVE 229


Lambda     K      H
   0.312    0.130    0.356 

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: 215
Number of extensions: 8
Number of successful extensions: 2
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: 223
Length of database: 238
Length adjustment: 23
Effective length of query: 200
Effective length of database: 215
Effective search space:    43000
Effective search space used:    43000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 46 (22.3 bits)

Align candidate 353951 BT4425 (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.5849.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5849.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.