GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Pseudomonas simiae WCS417

Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate GFF4362 PS417_22335 ornithine carbamoyltransferase

Query= SwissProt::P08308
         (336 letters)



>FitnessBrowser__WCS417:GFF4362
          Length = 336

 Score =  604 bits (1557), Expect = e-177
 Identities = 292/336 (86%), Positives = 318/336 (94%)

Query: 1   MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60
           MAFNM NR+LLSLMHH+TREL YLLDLSRDLKRAKYTGTE+ HLK KNIALIFEKTSTRT
Sbjct: 1   MAFNMRNRSLLSLMHHTTRELNYLLDLSRDLKRAKYTGTERPHLKGKNIALIFEKTSTRT 60

Query: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120
           RCAFEVAA+DQGA+VTYIDP SSQIGHKESMKDTARVLGRM+DAIEYRGF+QEIVEELAK
Sbjct: 61  RCAFEVAAHDQGAHVTYIDPVSSQIGHKESMKDTARVLGRMFDAIEYRGFEQEIVEELAK 120

Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180
           FAGVPVFNGLT E+HPTQM+AD LTMREHSDKPLHDISYAYLGDAR NMGNSLL+IGAKL
Sbjct: 121 FAGVPVFNGLTAEFHPTQMIADTLTMREHSDKPLHDISYAYLGDARYNMGNSLLMIGAKL 180

Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240
           GMDVRI APKALWPH++F+ QC+ FAEESGA++T+TEDPKEAVKGVDF+HTD+WVSMGEP
Sbjct: 181 GMDVRIGAPKALWPHEDFIKQCQAFAEESGARITITEDPKEAVKGVDFIHTDIWVSMGEP 240

Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300
           VEAW ERI++LLPYQVN ++MKA+GNPR KFMHCLPAFHNSETKVGK IA +YPNLANG+
Sbjct: 241 VEAWDERIEQLLPYQVNAKMMKASGNPRVKFMHCLPAFHNSETKVGKDIAARYPNLANGV 300

Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLADI 336
           EVTEDVFESP NIAFEQAENRMHTIKAILVS LADI
Sbjct: 301 EVTEDVFESPANIAFEQAENRMHTIKAILVSALADI 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: 497
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 GFF4362 PS417_22335 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.23056.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23056.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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