GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Marinobacter adhaerens HP15

Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate GFF771 HP15_750 ornithine carbamoyltransferase

Query= SwissProt::P11724
         (305 letters)



>FitnessBrowser__Marino:GFF771
          Length = 304

 Score =  389 bits (999), Expect = e-113
 Identities = 193/299 (64%), Positives = 229/299 (76%)

Query: 1   MSVRHFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPLKSRVLGMVFEKASTRTRLSF 60
           M+ RHFL+  D +  EL  L+   + L++   +G + + LK+RVL M+FEK+STRTR+SF
Sbjct: 1   MAARHFLTLNDMTTNELESLVDHATALRNEWRQGKVRDSLKNRVLAMIFEKSSTRTRVSF 60

Query: 61  EAGMIQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSKV 120
           EAGM QLGG A+FLSPRDTQLGRGEPI DSA V+S M+D VMIRTFAH T+  FAA S+V
Sbjct: 61  EAGMTQLGGSAMFLSPRDTQLGRGEPIEDSAIVISSMVDAVMIRTFAHETVERFAAASRV 120

Query: 121 PVINGLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLRV 180
           PVIN L+DD HPCQLLADMQTF EHRGSI+G TVAWIGDGNNMC+SYI AA +FDF L +
Sbjct: 121 PVINALTDDFHPCQLLADMQTFREHRGSIRGATVAWIGDGNNMCHSYINAAAQFDFNLNI 180

Query: 181 ACPEGYEPKAEFVALAGDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRPY 240
           ACPEGYEP    +    DR++V R+P EA   A L+ TDVWASMGQEDE  AR   F  Y
Sbjct: 181 ACPEGYEPAESMLKGHEDRVKVFREPAEAARNAQLLVTDVWASMGQEDEQKARERAFSGY 240

Query: 241 QVNAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLELLI 299
           Q+N  LL  A  DVLFMHCLPAHRGEEIS ++++ P SV W++AENRLHAQKALLE LI
Sbjct: 241 QINPGLLSVADKDVLFMHCLPAHRGEEISADMMEHPASVVWNEAENRLHAQKALLEFLI 299


Lambda     K      H
   0.322    0.136    0.404 

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: 306
Number of extensions: 7
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: 305
Length of database: 304
Length adjustment: 27
Effective length of query: 278
Effective length of database: 277
Effective search space:    77006
Effective search space used:    77006
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate GFF771 HP15_750 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.2217.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2217.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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