GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoD in Shewanella amazonensis SB2B

Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate 6936794 Sama_0976 purine nucleoside phosphorylase (RefSeq)

Query= BRENDA::P0ABP8
         (239 letters)



>FitnessBrowser__SB2B:6936794
          Length = 236

 Score =  341 bits (875), Expect = 7e-99
 Identities = 166/234 (70%), Positives = 197/234 (84%)

Query: 1   MATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISV 60
           MATPHINA  G FA+ VL PGDPLRAKYIAETFLE+  +V +VR MLGFTGTYKG++ISV
Sbjct: 1   MATPHINAVEGAFAETVLFPGDPLRAKYIAETFLENVEQVTDVRNMLGFTGTYKGKRISV 60

Query: 61  MGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIR 120
           MG GMGIPSCSIY  ELI D+GVK +IRVG+CGA+   VK+RDV+IGMGACTDS+VNR+R
Sbjct: 61  MGSGMGIPSCSIYATELIKDYGVKNLIRVGTCGAISTDVKVRDVIIGMGACTDSQVNRLR 120

Query: 121 FKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVE 180
           FK  DFAAIAD+ ++   V++AK  GI  RVGN+FSADLFY+PD EMFDVMEK G+LGVE
Sbjct: 121 FKGQDFAAIADYSLLSAVVESAKTHGIQTRVGNVFSADLFYTPDPEMFDVMEKMGVLGVE 180

Query: 181 MEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVL 234
           MEAAG+YGVA EFGA+AL + TVSDHIRT E+TT+ ERQTTFNDMI + L++ +
Sbjct: 181 MEAAGLYGVAHEFGARALCVVTVSDHIRTGEKTTSDERQTTFNDMIIMTLDAAI 234


Lambda     K      H
   0.322    0.138    0.401 

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: 271
Number of extensions: 11
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: 239
Length of database: 236
Length adjustment: 23
Effective length of query: 216
Effective length of database: 213
Effective search space:    46008
Effective search space used:    46008
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 (21.9 bits)
S2: 46 (22.3 bits)

Align candidate 6936794 Sama_0976 (purine nucleoside phosphorylase (RefSeq))
to HMM TIGR00107 (deoD: purine nucleoside phosphorylase (EC 2.4.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.30952.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30952.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.