GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Marinobacter adhaerens HP15

Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate GFF1975 HP15_1932 methylisocitrate lyase 2

Query= SwissProt::Q8EJW1
         (292 letters)



>FitnessBrowser__Marino:GFF1975
          Length = 295

 Score =  401 bits (1030), Expect = e-116
 Identities = 202/289 (69%), Positives = 236/289 (81%)

Query: 4   SAGLRFRQALANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANASYGLPDLGMTSM 63
           S G RFR+AL +++PLQIVGT NAY A+MAE+ G QA+YLSG GVANASYGLPDLGMTSM
Sbjct: 6   SPGARFRKALKDNQPLQIVGTINAYAAMMAEKVGHQAIYLSGGGVANASYGLPDLGMTSM 65

Query: 64  NDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEKIGVAAVHMEDQVSQKRCGH 123
           N+V+ D  RIT+AT +PLLVDIDTGWGGAFNIARTI+E E+ G AAVH+EDQV+QKRCGH
Sbjct: 66  NEVVEDVRRITAATDVPLLVDIDTGWGGAFNIARTIREMERAGAAAVHIEDQVAQKRCGH 125

Query: 124 RPNKAVVSTEEMVDRIKAAVDARTDPNFVIMARTDAVAVEGLEAGIERAKAYIAAGADMI 183
           RPNK +VS EEMVDRIKAAVDAR D +F IMARTDA   EGLEA IERAKA I AGAD I
Sbjct: 126 RPNKEIVSQEEMVDRIKAAVDAREDKDFFIMARTDAFQKEGLEAAIERAKACIEAGADGI 185

Query: 184 FAEALTELDQYRHFKAQVKAPILANMTEFGQTQLFNKEELAQAGADMVLYPLGTFRAANQ 243
           FAEA+TEL+ Y+ F   +  PILAN+TEFG T L+N++ELA+AGADMVLYPL  FRA N+
Sbjct: 186 FAEAVTELEHYKAFSEALDVPILANITEFGATPLYNRKELAEAGADMVLYPLSAFRAMNK 245

Query: 244 AALKVMQALMNDGHQRNVLDTMQTRADLYKYLGYHAFEDKLDQLFSQDK 292
           AAL V Q ++  G Q++V+D MQTR +LY +L YH FE KLDQLF Q K
Sbjct: 246 AALTVYQNILEKGDQKDVVDMMQTRMELYDFLNYHDFEQKLDQLFQQSK 294


Lambda     K      H
   0.319    0.132    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: 302
Number of extensions: 9
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: 292
Length of database: 295
Length adjustment: 26
Effective length of query: 266
Effective length of database: 269
Effective search space:    71554
Effective search space used:    71554
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 GFF1975 HP15_1932 (methylisocitrate lyase 2)
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.10644.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10644.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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