GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Pseudomonas fluorescens FW300-N2C3

Align Monofunctional chorismate mutase; EC 5.4.99.5 (characterized)
to candidate AO356_09710 AO356_09710 chorismate mutase

Query= SwissProt::Q9HU05
         (185 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_09710
          Length = 187

 Score = 90.9 bits (224), Expect = 1e-23
 Identities = 70/177 (39%), Positives = 91/177 (51%), Gaps = 11/177 (6%)

Query: 10  LLALLLLQGPLLQAQPLSPALQQLLSLSSQRLQLADQVAQSKAQSGKAVQDSPREEQQLQ 69
           L A LL       + P   AL  LL+   +RL +ADQVA SK  SGK V+D  RE + + 
Sbjct: 11  LSAALLASTAAAASTPAPEALTPLLNAIGERLAIADQVALSKWDSGKPVEDRQREREVIA 70

Query: 70  MLAGQAGSHGVGAEQVRLLFAAQIEANKLVQYRLLSRPLPDAGQAVDLER------IRSR 123
               QA ++ +  E V   FAAQIEANK+VQY  LS    D G+A DL R      IR +
Sbjct: 71  AAVAQAPAYKLSNETVEAFFAAQIEANKMVQYINLSDWALD-GKAPDLPRPDLVGQIRPQ 129

Query: 124 LNQLNLELLRGYAPALAELRVDDCRPRLNQALQRQVRVDRLDELHAIALSRAAGDLC 180
           L++L   LL+  A   A  R D   P+  Q L      D+   +H +AL RA  +LC
Sbjct: 130 LDRLQKRLLQQLAD-FAPYRTD---PQCPQWLAHATHHDKQHPVHRLALIRATAELC 182


Lambda     K      H
   0.320    0.133    0.374 

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: 88
Number of extensions: 4
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: 185
Length of database: 187
Length adjustment: 20
Effective length of query: 165
Effective length of database: 167
Effective search space:    27555
Effective search space used:    27555
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: 44 (21.6 bits)

Align candidate AO356_09710 AO356_09710 (chorismate mutase)
to HMM TIGR01806 (putative chorismate mutase (EC 5.4.99.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.15110.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15110.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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