GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Paraburkholderia bryophila 376MFSha3.1

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate H281DRAFT_00509 H281DRAFT_00509 dihydrodipicolinate synthase

Query= BRENDA::Q9I4W3
         (292 letters)



>FitnessBrowser__Burk376:H281DRAFT_00509
          Length = 308

 Score =  344 bits (882), Expect = 2e-99
 Identities = 173/290 (59%), Positives = 215/290 (74%)

Query: 2   IAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIR 61
           I GS+ A++TP    G LD  +  KL+D+H+ EGTNA+V VGT+GESATL VEEH+ +++
Sbjct: 18  IRGSIPAIITPMLEDGSLDLPAFRKLIDWHVAEGTNALVVVGTSGESATLSVEEHVLMVK 77

Query: 62  RVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRH 121
             V+   GRIPVIAG+G NST EA+ LT  AK  GADA L V PYYNKPTQEG+Y+HF  
Sbjct: 78  TAVEHTAGRIPVIAGSGGNSTAEAIELTRQAKEVGADATLQVVPYYNKPTQEGIYRHFAK 137

Query: 122 IAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKDF 181
           IAE V +P ILYNVPGRT  DM  ET+ R ++VP IIG+KEATG++ RA  +I+     F
Sbjct: 138 IAETVDLPVILYNVPGRTVADMSNETILRCAQVPGIIGVKEATGNIDRAAHLIKSAPAHF 197

Query: 182 LVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLHK 241
            +YSGDD TA+ LMLLGG GNISVTANVAPRAMS+LC AA+  DA  AR I+ +L+ LHK
Sbjct: 198 GIYSGDDPTAIALMLLGGHGNISVTANVAPRAMSELCKAALAADAKTAREIHLKLLSLHK 257

Query: 242 ALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVL 291
            LFIESNPIP KWAL ++G +  GIRLPLT L  + HE +R A+R+ G+L
Sbjct: 258 NLFIESNPIPAKWALQQLGRVQGGIRLPLTPLDAQYHEVVRGALREAGLL 307


Lambda     K      H
   0.319    0.134    0.393 

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: 302
Number of extensions: 7
Number of successful extensions: 1
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: 292
Length of database: 308
Length adjustment: 27
Effective length of query: 265
Effective length of database: 281
Effective search space:    74465
Effective search space used:    74465
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: 48 (23.1 bits)

Align candidate H281DRAFT_00509 H281DRAFT_00509 (dihydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.25371.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25371.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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