Alignments for a candidate for trpB in Desulfovibrio vulgaris Miyazaki F

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate 8501513 DvMF_2237 tryptophan synthase subunit beta (RefSeq)

Query= uniprot:P50383
         (425 letters)



>FitnessBrowser__Miya:8501513
          Length = 440

 Score =  128 bits (322), Expect = 3e-34
 Identities = 126/396 (31%), Positives = 177/396 (44%), Gaps = 66/396 (16%)

Query: 54  TIERYIKIPEEVRDR--YLS--IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKI 109
           T ERY   P+ + +   YL+   GR TPLF    L   L   A+IY K E     G+HK+
Sbjct: 70  TFERYHADPDFLAELEYYLTRYSGRQTPLFLCANLTARLGG-AKIYLKREDLNHLGAHKV 128

Query: 110 NTAIPQAYFAKEEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSI 169
           N  I Q   AK  G + V+ ETGAGQ G A A  A++  M+ TI M     E++ +    
Sbjct: 129 NNTIGQILLAKRMGKKKVIAETGAGQHGVATAATAALMGMQCTIHMGAEDMERQKLNVFR 188

Query: 170 MQLYGANVYASPTNLTEYGRKILETNPQHPGSLGIAMSEAIEYAL---KNEFRYLVGSVL 226
           M++ GA V  + +     G++ L+           A+ EA+   L   +N F YL+GS +
Sbjct: 189 MRMMGAEVVPAMS-----GQRTLKE----------AVDEALAAWLGDAENTF-YLLGSAV 232

Query: 227 D------VVLLHQSVIGQETITQ-LDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKR 279
                  +V   QSVIG+E   Q L+  G   D  + CVGGGSN  G    FI + +G R
Sbjct: 233 GPHPYPRIVRHFQSVIGREARAQMLEAEGRLPDCAVACVGGGSNAIGLFAEFIAD-EGVR 291

Query: 280 YIAVSSA---------------EIPKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPI 324
            I V  A                 P    G + Y   D AG               P  +
Sbjct: 292 LIGVEPAGRGLTYGDHAATLCMGTPGVMHGFHSYMLKDEAG--------------EPAAV 337

Query: 325 Y--AGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFEAAKIFIENQGIVPAPESAHAIRA 382
           Y  + GL Y GV P  S L   G  E+    + E  +A  I    +GI+PA ES+HA+  
Sbjct: 338 YSISAGLDYPGVGPEHSHLKDIGRAEYASVTDAEALDAFFILSRTEGIIPALESSHALAH 397

Query: 383 VVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESMM 418
            +  A    ++    +I+ NLSG G  D++  E M+
Sbjct: 398 AMKLAPALGRD---AIILVNLSGRGDKDVAQVEEMV 430


Lambda     K      H
   0.318    0.138    0.403 

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: 413
Number of extensions: 26
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: 425
Length of database: 440
Length adjustment: 32
Effective length of query: 393
Effective length of database: 408
Effective search space:   160344
Effective search space used:   160344
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 8501513 DvMF_2237 (tryptophan synthase subunit beta (RefSeq))
to HMM TIGR00263 (trpB: tryptophan synthase, beta subunit (EC 4.2.1.20))

Software error:

../bin/blast/fastacmd -i /tmp/list.20799.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.20799.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.