GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Pseudomonas stutzeri RCH2

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate GFF2276 Psest_2321 methylisocitrate lyase

Query= reanno::pseudo6_N2E2:Pf6N2E2_6061
         (294 letters)



>FitnessBrowser__psRCH2:GFF2276
          Length = 297

 Score =  531 bits (1368), Expect = e-156
 Identities = 272/294 (92%), Positives = 281/294 (95%)

Query: 1   MSNSTPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLG 60
           M+  + GQRFRDAVA+EHPLQVVG INANHALLAKRAGFKAIYLSGGGVAAGSLG+PDLG
Sbjct: 1   MTLPSAGQRFRDAVASEHPLQVVGAINANHALLAKRAGFKAIYLSGGGVAAGSLGLPDLG 60

Query: 61  ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA 120
           ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA
Sbjct: 61  ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA 120

Query: 121 KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEA 180
           KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGL SALDRAAACIEA
Sbjct: 121 KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLNSALDRAAACIEA 180

Query: 181 GADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAF 240
           GADMIFPEAITEL MYK FA RVKAPILANITEFGATPLYTTE+LA  DVSLVLYPLSAF
Sbjct: 181 GADMIFPEAITELAMYKTFADRVKAPILANITEFGATPLYTTEELASVDVSLVLYPLSAF 240

Query: 241 RAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294
           RAMNKAAENVYTA+RRDGTQ+NVIDTMQTRMELYDRI+YH FEQ LD+LFA KK
Sbjct: 241 RAMNKAAENVYTALRRDGTQKNVIDTMQTRMELYDRINYHAFEQHLDSLFAQKK 294


Lambda     K      H
   0.320    0.134    0.375 

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: 353
Number of extensions: 5
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: 294
Length of database: 297
Length adjustment: 26
Effective length of query: 268
Effective length of database: 271
Effective search space:    72628
Effective search space used:    72628
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 GFF2276 Psest_2321 (methylisocitrate lyase)
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.9775.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9775.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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