GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Escherichia coli BW25113

Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate 14469 b0331 2-methylisocitrate lyase (NCBI)

Query= SwissProt::P77541
         (296 letters)



>FitnessBrowser__Keio:14469
          Length = 296

 Score =  573 bits (1478), Expect = e-168
 Identities = 296/296 (100%), Positives = 296/296 (100%)

Query: 1   MSLHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLG 60
           MSLHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLG
Sbjct: 1   MSLHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLG 60

Query: 61  ISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGA 120
           ISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGA
Sbjct: 61  ISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGA 120

Query: 121 KRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEA 180
           KRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEA
Sbjct: 121 KRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEA 180

Query: 181 GAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAF 240
           GAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAF
Sbjct: 181 GAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAF 240

Query: 241 RAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLFARSQVK 296
           RAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLFARSQVK
Sbjct: 241 RAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLFARSQVK 296


Lambda     K      H
   0.319    0.133    0.369 

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: 396
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: 296
Length of database: 296
Length adjustment: 26
Effective length of query: 270
Effective length of database: 270
Effective search space:    72900
Effective search space used:    72900
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 14469 b0331 (2-methylisocitrate lyase (NCBI))
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.2251.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2251.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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