GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Caulobacter crescentus NA1000

Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate CCNA_03599 CCNA_03599 aspartate-semialdehyde dehydrogenase

Query= BRENDA::P9WNX5
         (345 letters)



>FitnessBrowser__Caulo:CCNA_03599
          Length = 348

 Score =  373 bits (958), Expect = e-108
 Identities = 208/338 (61%), Positives = 242/338 (71%), Gaps = 6/338 (1%)

Query: 5   IGIVGATGQVGQVMRTLLDERDFPASAVRFFASARSQGRKLAFRGQEIEVEDAETADPSG 64
           +G+VGATG VG +MR LL ERDFP +++R FASARS G K+ F GQ+I VEDA TAD SG
Sbjct: 13  VGVVGATGLVGGMMRELLVERDFPVASLRLFASARSAGGKIDFNGQQIVVEDAATADFSG 72

Query: 65  LDIALFSAGSAMSKVQAPRFAAAGVTVIDNSSAWRKDPDVPLVVSEVNFERDAHRRPKGI 124
           LDI  FSAG + S+  AP+ AAAG  VIDNSSAWR DP+VPLVV+EVN        PKGI
Sbjct: 73  LDIVFFSAGGSTSRELAPKAAAAGAVVIDNSSAWRSDPEVPLVVAEVN-PHALQNIPKGI 131

Query: 125 IANPNCTTMAAMPVLKVLHDEARLVRLVVSSYQAVSGSGLAGVAELAEQARA-VIGGAEQ 183
           +ANPNCTTMAAMPVLK LHD+A L RL VS+YQA SG G+ G+  L+EQ RA   G  + 
Sbjct: 132 VANPNCTTMAAMPVLKPLHDKAGLKRLTVSTYQAASGGGMEGIEVLSEQLRAGAAGDLDG 191

Query: 184 LVYDGGALEFPPPNTYVAPIAFNVVPLAGSLVDDGSGETDEDQKLRFESRKILGIPDLLV 243
           L     A   P P  +  P+A+NVVPL   L +D  G T+E+ KLR ESRKIL IP L V
Sbjct: 192 LARSPDAAPLPAPRKWAVPLAYNVVPLNYVLGED--GYTEEELKLRDESRKILEIPGLPV 249

Query: 244 SGTCVRVPVFTGHSLSINAEFAQPLSPERARELLDGATGVQLVDVPTPLAAAGVDESLVG 303
           SGTCVRVPVFTGH+LSINAEF  P+S   A +LL  A GV + DVP PLAA G D   VG
Sbjct: 250 SGTCVRVPVFTGHALSINAEFDGPVSVAEALDLLAAAPGVVIDDVPNPLAATGQDPVFVG 309

Query: 304 RIRRDPGVPDGRGLALFVSGDNLRKGAALNTIQIAELL 341
           R+R DP VP   GLALFV GDNLRKGAALN +QIAE++
Sbjct: 310 RVRPDPTVP--HGLALFVVGDNLRKGAALNAVQIAEVM 345


Lambda     K      H
   0.317    0.135    0.382 

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: 441
Number of extensions: 24
Number of successful extensions: 5
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: 345
Length of database: 348
Length adjustment: 29
Effective length of query: 316
Effective length of database: 319
Effective search space:   100804
Effective search space used:   100804
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: 49 (23.5 bits)

Align candidate CCNA_03599 CCNA_03599 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

Software error:

../bin/blast/fastacmd -i /tmp/list.21775.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21775.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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