GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Pseudomonas putida KT2440

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate PP_2334 PP_2334 2-methylisocitrate lyase

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



>FitnessBrowser__Putida:PP_2334
          Length = 296

 Score =  525 bits (1353), Expect = e-154
 Identities = 267/291 (91%), Positives = 277/291 (95%)

Query: 4   STPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGITG 63
           STPGQRFRDAVA EHPLQVVG INANHALLAKRAGFKAIYLSGGGVAAGSLG+PDLGITG
Sbjct: 5   STPGQRFRDAVAAEHPLQVVGAINANHALLAKRAGFKAIYLSGGGVAAGSLGLPDLGITG 64

Query: 64  LDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAKRC 123
           LDDVLTDVRRITDVCDLPLLVDVDTGFG+SAFNVARTV+SM KFGAAAIHIEDQVGAKRC
Sbjct: 65  LDDVLTDVRRITDVCDLPLLVDVDTGFGASAFNVARTVRSMSKFGAAAIHIEDQVGAKRC 124

Query: 124 GHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAGAD 183
           GHRPNKEIVSQQEMVDRIKAAVDAR+DDSFVIMARTDALAVEGL +ALDRA AC+EAGAD
Sbjct: 125 GHRPNKEIVSQQEMVDRIKAAVDARSDDSFVIMARTDALAVEGLNAALDRAQACVEAGAD 184

Query: 184 MIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAFRAM 243
           MIFPEAITEL+MYK FA RVKAPILANITEFGATPLYTTE+LA  DVSLVLYPLSAFRAM
Sbjct: 185 MIFPEAITELQMYKTFADRVKAPILANITEFGATPLYTTEELASVDVSLVLYPLSAFRAM 244

Query: 244 NKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294
           NKAAENVYTA+RRDGTQ+NVIDTMQTRMELYD I YH FEQ LDALFA KK
Sbjct: 245 NKAAENVYTALRRDGTQKNVIDTMQTRMELYDAIGYHAFEQSLDALFAQKK 295


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: 354
Number of extensions: 6
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: 296
Length adjustment: 26
Effective length of query: 268
Effective length of database: 270
Effective search space:    72360
Effective search space used:    72360
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 PP_2334 PP_2334 (2-methylisocitrate lyase)
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.32113.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32113.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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