Alignments for a candidate for trpA in Phaeobacter inhibens BS107

Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate GFF482 PGA1_c04930 tryptophan synthase alpha chain

Query= uniprot:M4NLA4
         (266 letters)



>FitnessBrowser__Phaeo:GFF482
          Length = 263

 Score =  215 bits (548), Expect = 7e-61
 Identities = 111/249 (44%), Positives = 156/249 (62%), Gaps = 1/249 (0%)

Query: 1   MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60
           M+RID +FA LKAA++   + +V AGDP  +  + L+  L  AG D+IELG+PF+DPMAD
Sbjct: 1   MTRIDAKFAELKAADKKAFVAYVMAGDPDFDTSLELVKGLPAAGVDVIELGLPFTDPMAD 60

Query: 61  GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120
           GP IQ A +RA+  G+ L   L     FR+ D  TPIV+MGY NPI + G   F  +A +
Sbjct: 61  GPTIQLAGQRALEAGMTLQRTLDLARTFREEDNTTPIVMMGYYNPIYSRGVETFLKDAKE 120

Query: 121 AGVDGVLLVDCPLEE-SAVLQPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFA 179
           AG+DG+++VD P EE S +  P + AGL  I LA PTT+  R+ ++  +  GF+YYVS  
Sbjct: 121 AGIDGLIVVDLPPEEDSELCLPAQQAGLNFIRLATPTTDDKRLPRVLQNTSGFVYYVSIT 180

Query: 180 GITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRL 239
           GITGAA     ++   VA ++++   PV VGFGI     ++AIA  AD  V+GSA+V ++
Sbjct: 181 GITGAAEAEATNVGPEVARIKSQTDLPVIVGFGINTPEKSQAIASVADGAVVGSAIVSQI 240

Query: 240 AGATDAGEI 248
                 GE+
Sbjct: 241 GAGKPVGEV 249


Lambda     K      H
   0.322    0.136    0.394 

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: 219
Number of extensions: 7
Number of successful extensions: 2
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: 266
Length of database: 263
Length adjustment: 25
Effective length of query: 241
Effective length of database: 238
Effective search space:    57358
Effective search space used:    57358
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: 47 (22.7 bits)

Align candidate GFF482 PGA1_c04930 (tryptophan synthase alpha chain)
to HMM TIGR00262 (trpA: tryptophan synthase, alpha subunit (EC 4.2.1.20))

Software error:

../bin/blast/fastacmd -i /tmp/list.31167.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.31167.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.