GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Desulfovibrio vulgaris Miyazaki F

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate 8499506 DvMF_0276 aspartate kinase (RefSeq)

Query= SwissProt::A4VJB4
         (412 letters)



>FitnessBrowser__Miya:8499506
          Length = 409

 Score =  440 bits (1131), Expect = e-128
 Identities = 226/409 (55%), Positives = 305/409 (74%), Gaps = 1/409 (0%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60
           M ++VQKFGGTSV  +E ++QV EKV++    G   VVV+SA SGETNRL+ LA++ S  
Sbjct: 1   MRILVQKFGGTSVANLECMKQVREKVRRALRDGYKPVVVLSARSGETNRLLALAEEWSTD 60

Query: 61  PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120
           P P E+D +++TGEQV++AL +M L   G+ A S TG QV I T  A  +ARI+ IDA R
Sbjct: 61  PDPAEVDALIATGEQVSVALFSMLLKDSGIKARSMTGFQVPITTSDAFGRARIMDIDASR 120

Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           ++++++   V+VVAGFQGV  +G +TTLGRGGSDT+ VALAAAL + EC+IYTDVDGVYT
Sbjct: 121 LRKELETHDVIVVAGFQGVTSEGRVTTLGRGGSDTSAVALAAALGSVECEIYTDVDGVYT 180

Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI 240
           TDP + + A++LD+++++EMLEMAS+G+KVLQIR+VEFA KY VP+ V  +F + PGT++
Sbjct: 181 TDPNLCSTARKLDRVSYDEMLEMASMGAKVLQIRSVEFAKKYKVPVHVRSTFTDTPGTMV 240

Query: 241 TLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAH 300
           T  E+  ME  ++SGIA+++D+A++T+R VPD PGV+  I GP+S   + VDMIVQN + 
Sbjct: 241 T-QEDCEMEAVLVSGIAYDKDQARVTLRSVPDKPGVSAAIFGPLSQQGILVDMIVQNPSR 299

Query: 301 DNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASRM 360
           D  TD TFTV R D    L +++ I A  GA+E + DT +AKVS +GVGMR+H+GVA++ 
Sbjct: 300 DGVTDMTFTVPRKDLKKTLALMEEIRARTGAQEVLHDTQVAKVSAIGVGMRNHSGVAAKA 359

Query: 361 FEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPAGN 409
           F AL  ENINI MISTSEIK++ +IEEKY ELAVR LH AF L+   GN
Sbjct: 360 FAALHAENINILMISTSEIKITCLIEEKYTELAVRTLHDAFGLNHDLGN 408


Lambda     K      H
   0.317    0.133    0.357 

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: 451
Number of extensions: 9
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: 412
Length of database: 409
Length adjustment: 31
Effective length of query: 381
Effective length of database: 378
Effective search space:   144018
Effective search space used:   144018
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate 8499506 DvMF_0276 (aspartate kinase (RefSeq))
to HMM TIGR00656 (aspartate kinase, monofunctional class (EC 2.7.2.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.8852.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8852.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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