GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Pseudomonas simiae WCS417

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate GFF4115 PS417_21080 2-methylisocitrate lyase

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



>FitnessBrowser__WCS417:GFF4115
          Length = 297

 Score =  552 bits (1423), Expect = e-162
 Identities = 282/293 (96%), Positives = 288/293 (98%)

Query: 2   SNSTPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGI 61
           + +TPGQRFRDAVA+EHPLQVVG INANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGI
Sbjct: 5   NKTTPGQRFRDAVASEHPLQVVGAINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGI 64

Query: 62  TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAK 121
           TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAK
Sbjct: 65  TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAK 124

Query: 122 RCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAG 181
           RCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESAL+RAAACIEAG
Sbjct: 125 RCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALERAAACIEAG 184

Query: 182 ADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAFR 241
           ADM+FPEAITELEMYKLFASRVKAPILANITEFGATPLY TEQL  ADVS+VLYPLSAFR
Sbjct: 185 ADMVFPEAITELEMYKLFASRVKAPILANITEFGATPLYATEQLKSADVSIVLYPLSAFR 244

Query: 242 AMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294
           AMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK
Sbjct: 245 AMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 297


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: 369
Number of extensions: 4
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 GFF4115 PS417_21080 (2-methylisocitrate lyase)
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.17606.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17606.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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