GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoD in Phaeobacter inhibens BS107

Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate GFF371 PGA1_c03820 purine nucleoside phosphorylase deoD-type

Query= BRENDA::O34925
         (233 letters)



>FitnessBrowser__Phaeo:GFF371
          Length = 234

 Score =  260 bits (664), Expect = 2e-74
 Identities = 124/231 (53%), Positives = 179/231 (77%), Gaps = 1/231 (0%)

Query: 1   MSVHIGAEKGQIADTVLLPGDPLRAKFIAETYLENVECYNEVRGMYGFTGTYKGKKISVQ 60
           M+VHIGA KG+IA+TVLLPGDP RAK+ AET+L++V   NEVRGM GFTGT+ G  +++Q
Sbjct: 1   MTVHIGAAKGEIAETVLLPGDPYRAKWAAETFLKDVRLVNEVRGMLGFTGTWNGHPVTIQ 60

Query: 61  GTGMGVPSISIYVNELIQSYDVQNLIRVGSCGAIRKDVKVRDVILAMTSSTDSQMNRVAF 120
           G+GMG+PS+SIYVNELI+ YD + LIR+GSCG ++  VK+RDVILAMT++T    +R  F
Sbjct: 61  GSGMGMPSLSIYVNELIRDYDAKTLIRIGSCGGMQDKVKIRDVILAMTATTTGSPSRGIF 120

Query: 121 GSVDFAPCADFELLKNAYDAAKDKGVPVTVGSVFTADQFYNDDSQI-EKLAKYGVLGVEM 179
             V+FAPCAD+ LL+ A  AA+   +   +G ++++D FY++   + E++ ++G+LGVEM
Sbjct: 121 KEVNFAPCADWSLLQAAVKAAETHELTPHIGGIYSSDVFYDERPDLNEQMVRHGILGVEM 180

Query: 180 ETTALYTLAAKHGRKALSILTVSDHVLTGEETTAEERQTTFHDMIEVALHS 230
           E   LYTLAA++G +AL++LTVSDH+ TGE   +++R+ +F DM+E+AL +
Sbjct: 181 EAAELYTLAARYGCRALAVLTVSDHLGTGEALPSDQRERSFGDMVEIALEA 231


Lambda     K      H
   0.317    0.133    0.370 

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: 189
Number of extensions: 7
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: 233
Length of database: 234
Length adjustment: 23
Effective length of query: 210
Effective length of database: 211
Effective search space:    44310
Effective search space used:    44310
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 (21.6 bits)
S2: 46 (22.3 bits)

Align candidate GFF371 PGA1_c03820 (purine nucleoside phosphorylase deoD-type)
to HMM TIGR00107 (deoD: purine nucleoside phosphorylase (EC 2.4.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.18249.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18249.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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