GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Pseudomonas fluorescens FW300-N1B4

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate Pf1N1B4_3819 Methylisocitrate lyase (EC 4.1.3.30)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3819
          Length = 296

 Score =  560 bits (1444), Expect = e-164
 Identities = 287/293 (97%), Positives = 291/293 (99%)

Query: 2   SNSTPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGI 61
           + STPGQRFRDAVA+EHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGI
Sbjct: 4   NKSTPGQRFRDAVASEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGI 63

Query: 62  TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAK 121
           TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAK
Sbjct: 64  TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAK 123

Query: 122 RCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAG 181
           RCGHRPNKEIV+QQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAG
Sbjct: 124 RCGHRPNKEIVTQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAG 183

Query: 182 ADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAFR 241
           ADM+FPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLA ADVSLVLYPLSAFR
Sbjct: 184 ADMVFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAAADVSLVLYPLSAFR 243

Query: 242 AMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294
           AMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK
Sbjct: 244 AMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 296


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: 378
Number of extensions: 3
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 Pf1N1B4_3819 (Methylisocitrate lyase (EC 4.1.3.30))
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.14002.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14002.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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