Alignments for a candidate for trpA in Desulfovibrio vulgaris Miyazaki F

Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate 8501003 DvMF_1740 tryptophan synthase subunit alpha (RefSeq)

Query= uniprot:H0BV16
         (269 letters)



>FitnessBrowser__Miya:8501003
          Length = 270

 Score =  181 bits (458), Expect = 2e-50
 Identities = 106/245 (43%), Positives = 147/245 (60%), Gaps = 5/245 (2%)

Query: 1   MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60
           +SR+ +  +A  A GR AL+P++TAGFP  D     M G+   GADVIE+GVPFSDP+AD
Sbjct: 18  VSRLEARVTAANAAGRPALVPFLTAGFPTLDRFWEEMDGLDRGGADVIEIGVPFSDPVAD 77

Query: 61  GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120
           GPV++ A  +AL  G+ +  +LD ++  R       +VLMGY NP  +Y    G      
Sbjct: 78  GPVVEAASLRALENGVTLRWILDGLKA-RAGRYEAELVLMGYYNPFLQY----GLENLAA 132

Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180
           D+AAAGV G ++ D P EE     A L A G+DLI L+ P +++ERMAE A VASGYVY 
Sbjct: 133 DAAAAGVAGFIVPDLPLEEDAEMRALLAARGIDLIALVGPNTSEERMAEYAAVASGYVYV 192

Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240
           VS+ G+TG        V Q L R R+   +P+ +GFGI++    +      DAVV GS +
Sbjct: 193 VSVLGITGVREGLPPEVPQTLARARKAFRLPLALGFGIKEPKQLEGFPDRPDAVVFGSAL 252

Query: 241 IQLIE 245
           ++ I+
Sbjct: 253 LRHID 257


Lambda     K      H
   0.321    0.137    0.389 

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: 217
Number of extensions: 10
Number of successful extensions: 4
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: 269
Length of database: 270
Length adjustment: 25
Effective length of query: 244
Effective length of database: 245
Effective search space:    59780
Effective search space used:    59780
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: 47 (22.7 bits)

Align candidate 8501003 DvMF_1740 (tryptophan synthase subunit alpha (RefSeq))
to HMM TIGR00262 (trpA: tryptophan synthase, alpha subunit (EC 4.2.1.20))

Software error:

../bin/blast/fastacmd -i /tmp/list.5944.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.5944.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.