GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Shewanella amazonensis SB2B

Align 2-methylisocitrate lyase; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate 6939200 Sama_3294 2-methylisocitrate lyase (RefSeq)

Query= SwissProt::Q8EJW1
         (292 letters)



>FitnessBrowser__SB2B:6939200
          Length = 294

 Score =  508 bits (1309), Expect = e-149
 Identities = 259/292 (88%), Positives = 274/292 (93%)

Query: 1   MTQSAGLRFRQALANSKPLQIVGTTNAYFALMAEQTGFQALYLSGAGVANASYGLPDLGM 60
           MT SAG RFR ALA SKPLQIVGTTNAYFALMAE+TGFQALYLSGAGVANASYGLPDLGM
Sbjct: 1   MTHSAGKRFRDALARSKPLQIVGTTNAYFALMAEKTGFQALYLSGAGVANASYGLPDLGM 60

Query: 61  TSMNDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEKIGVAAVHMEDQVSQKR 120
           TSMNDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEK+GVAAVHMEDQVSQKR
Sbjct: 61  TSMNDVLIDAGRITSATQLPLLVDIDTGWGGAFNIARTIKEFEKVGVAAVHMEDQVSQKR 120

Query: 121 CGHRPNKAVVSTEEMVDRIKAAVDARTDPNFVIMARTDAVAVEGLEAGIERAKAYIAAGA 180
           CGHRPNKAVVSTEEMVDRIKAAVDARTD NFVIMARTDAVAVEGL+AGIERA+AYI AGA
Sbjct: 121 CGHRPNKAVVSTEEMVDRIKAAVDARTDENFVIMARTDAVAVEGLDAGIERAQAYIEAGA 180

Query: 181 DMIFAEALTELDQYRHFKAQVKAPILANMTEFGQTQLFNKEELAQAGADMVLYPLGTFRA 240
           DMIFAEALTEL QYR FK  VKAPILANMTEFGQT+LF+K  L +AGADMVLYPLGTFRA
Sbjct: 181 DMIFAEALTELPQYRKFKDAVKAPILANMTEFGQTELFDKSALYEAGADMVLYPLGTFRA 240

Query: 241 ANQAALKVMQALMNDGHQRNVLDTMQTRADLYKYLGYHAFEDKLDQLFSQDK 292
           ANQAALKVMQALMNDGHQRNVL TMQ+R +LY++L YH+FED LD+LF++ K
Sbjct: 241 ANQAALKVMQALMNDGHQRNVLSTMQSRKELYEFLNYHSFEDTLDRLFAEGK 292


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: 408
Number of extensions: 10
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: 294
Length adjustment: 26
Effective length of query: 266
Effective length of database: 268
Effective search space:    71288
Effective search space used:    71288
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 6939200 Sama_3294 (2-methylisocitrate lyase (RefSeq))
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.26863.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26863.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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