GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Pseudomonas fluorescens GW456-L13

Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate PfGW456L13_1873 Ornithine carbamoyltransferase (EC 2.1.3.3)

Query= SwissProt::P08308
         (336 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1873
          Length = 336

 Score =  617 bits (1591), Expect = 0.0
 Identities = 300/336 (89%), Positives = 320/336 (95%)

Query: 1   MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60
           MAFN+HNRNLLSL HH+ RELRYLLDLSRDLKRAKYTGTEQQHLK  NIALIFEKTSTRT
Sbjct: 1   MAFNIHNRNLLSLEHHTPRELRYLLDLSRDLKRAKYTGTEQQHLKGNNIALIFEKTSTRT 60

Query: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120
           RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK
Sbjct: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120

Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180
           FAGVPVFNGLTDEYHPTQM+ADVLTMREH+DKP+H+ISYAYLGDARNNMGNSLLLIGAKL
Sbjct: 121 FAGVPVFNGLTDEYHPTQMIADVLTMREHADKPIHEISYAYLGDARNNMGNSLLLIGAKL 180

Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240
           GMDVRI APKALWP D+ VA+CK++ EESGA++TLTEDPK AVKGVDF+HTDVWVSMGEP
Sbjct: 181 GMDVRICAPKALWPADDLVARCKQYGEESGARITLTEDPKAAVKGVDFIHTDVWVSMGEP 240

Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300
           VEAW ERI++LLPYQVN E+MKATGNPR KFMHCLPAFHN +TKVGKQIAEQYP L+NGI
Sbjct: 241 VEAWAERIQQLLPYQVNAELMKATGNPRTKFMHCLPAFHNCDTKVGKQIAEQYPYLSNGI 300

Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLADI 336
           EVT+DVFESP  IAFEQAENRMHTIKAILVSTLAD+
Sbjct: 301 EVTDDVFESPACIAFEQAENRMHTIKAILVSTLADL 336


Lambda     K      H
   0.318    0.133    0.387 

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: 481
Number of extensions: 6
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: 336
Length of database: 336
Length adjustment: 28
Effective length of query: 308
Effective length of database: 308
Effective search space:    94864
Effective search space used:    94864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate PfGW456L13_1873 (Ornithine carbamoyltransferase (EC 2.1.3.3))
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.14359.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14359.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.