GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI in Desulfovibrio vulgaris Miyazaki F

Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate 8499267 DvMF_0046 ornithine carbamoyltransferase (RefSeq)

Query= SwissProt::P11724
         (305 letters)



>FitnessBrowser__Miya:8499267
          Length = 300

 Score =  295 bits (754), Expect = 1e-84
 Identities = 147/296 (49%), Positives = 204/296 (68%), Gaps = 6/296 (2%)

Query: 4   RHFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPLKSRVLGMVFEKASTRTRLSFEAG 63
           RHF    D   E    L++R  E+KD  +RG + E  K+ +L  +FEKASTRTR+SFE  
Sbjct: 3   RHFTRIRDLGYEGAWKLLQRAKEMKDTAHRGKIMEG-KTAIL--IFEKASTRTRVSFEMA 59

Query: 64  MIQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSKVPVI 123
           +  LGG  IF++P ++QLGR EP+ D+ARV+SR  D +++RTF  + +TE A +  +PVI
Sbjct: 60  VRHLGGSTIFMTPAESQLGRSEPLRDTARVLSRYADCMVVRTFGQSKITELAEYGSIPVI 119

Query: 124 NGLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLRVACP 183
           N L+D+ HPCQ++ D+ T +E    +    VAW+GDGNNM NS+IEAA+ F F+L +A P
Sbjct: 120 NALTDEGHPCQVMGDVLTMYERTPDLSTVRVAWVGDGNNMANSWIEAAVYFPFELFMAFP 179

Query: 184 EGYEPKAEFVAL---AGDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRPY 240
           EGYEP  + +     AG ++ +  DPR AV GAH V+TDVWASMGQE+E   R A F+ Y
Sbjct: 180 EGYEPDRDLLGYALNAGAKIFLTHDPRMAVEGAHYVNTDVWASMGQEEEQKKREAAFKGY 239

Query: 241 QVNAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLE 296
            ++  ++  AA D  FMHCLPAHRGEE+++E+++ P S+ +DQAENRLH QKA+LE
Sbjct: 240 CIDTEMMALAAPDAKFMHCLPAHRGEEVTDEVMESPASIIFDQAENRLHIQKAILE 295


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: 258
Number of extensions: 13
Number of successful extensions: 3
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: 300
Length adjustment: 27
Effective length of query: 278
Effective length of database: 273
Effective search space:    75894
Effective search space used:    75894
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 8499267 DvMF_0046 (ornithine carbamoyltransferase (RefSeq))
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.17078.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17078.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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