GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Dyella japonica UNC79MFTsu3.2

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate N515DRAFT_0020 N515DRAFT_0020 methylisocitrate lyase

Query= reanno::Cup4G11:RR42_RS11260
         (302 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0020
          Length = 295

 Score =  456 bits (1174), Expect = e-133
 Identities = 225/288 (78%), Positives = 253/288 (87%)

Query: 11  SAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGISNL 70
           S GARFR ALA E PLQV+G INANHALLA+RAGYRAIYLSGGGVAAGSLGLPDLGI+ L
Sbjct: 6   SPGARFRAALAQEQPLQVIGAINANHALLARRAGYRAIYLSGGGVAAGSLGLPDLGINTL 65

Query: 71  DDVLTDVRRITDVCDVPLLVDVDTGFGASAFNVARTTRSLIKFGAGAMHIEDQVGAKRCG 130
           DDVLTDVRRITDVCD+PL+VD+DTGFG SAFN+ART +SLIKFGA A HIEDQVGAKRCG
Sbjct: 66  DDVLTDVRRITDVCDLPLMVDIDTGFGPSAFNIARTVKSLIKFGAAACHIEDQVGAKRCG 125

Query: 131 HRPGKEIVSQGEMADRIKAAVDARTDENFVIMARTDALAVEGLDKAIERAVACVEAGADA 190
           HRPGKEIVS GEMADR+KAA DA+TD +F ++ARTDA+  EG+D AIERA+ACVEAGAD 
Sbjct: 126 HRPGKEIVSSGEMADRVKAAADAKTDADFFLIARTDAIQTEGVDAAIERAIACVEAGADG 185

Query: 191 IFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVLYPLSAFRAMN 250
           IF EA+ DL  YR+F DAVK PVLANITEFG TPLF+ +EL  AGV +VLYPLSAFRAMN
Sbjct: 186 IFAEAVYDLPTYRRFADAVKAPVLANITEFGKTPLFSVDELRSAGVGIVLYPLSAFRAMN 245

Query: 251 KAAENVYAAIRRDGTQQNVVDTMQTRAELYESIGYHAYEQKLDALFAQ 298
           KAAENVY AIRRDG Q+NV+DTMQTR ELY+ IGYH +E++LD LFA+
Sbjct: 246 KAAENVYQAIRRDGHQRNVIDTMQTREELYDRIGYHDFERRLDELFAR 293


Lambda     K      H
   0.320    0.134    0.376 

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: 323
Number of extensions: 9
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: 302
Length of database: 295
Length adjustment: 27
Effective length of query: 275
Effective length of database: 268
Effective search space:    73700
Effective search space used:    73700
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: 48 (23.1 bits)

Align candidate N515DRAFT_0020 N515DRAFT_0020 (methylisocitrate lyase)
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.13854.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13854.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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