GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Burkholderia phytofirmans PsJN

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate BPHYT_RS35090 BPHYT_RS35090 diaminopimelate decarboxylase

Query= SwissProt::E0IWI3
         (420 letters)



>FitnessBrowser__BFirm:BPHYT_RS35090
          Length = 413

 Score =  532 bits (1371), Expect = e-156
 Identities = 254/405 (62%), Positives = 323/405 (79%), Gaps = 2/405 (0%)

Query: 15  ENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIHILRLMREQGVKVDS 74
           + L+ L  E G P+WVYDA  IRR+IA L+ FDV+R+AQKACSN+HIL+LMR++G  VD+
Sbjct: 6   QQLVELAHEHGTPLWVYDADTIRRRIAELRSFDVIRYAQKACSNLHILKLMRDEGAMVDA 65

Query: 75  VSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVS 134
           VSLGEI+R+LAAG+ P   P+ +VFTAD+ID ATL  V E +I VNAGS+DML+Q+G+ +
Sbjct: 66  VSLGEIKRSLAAGFKPDGDPEGVVFTADLIDHATLATVIEHRITVNAGSLDMLEQIGRHA 125

Query: 135 P-GHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIG 193
           P GHRVWLR+NPGFGHGHS KTNTGGE+SKHGIW  D+P A+++++R+ L+LVG+HMHIG
Sbjct: 126 PEGHRVWLRINPGFGHGHSNKTNTGGEHSKHGIWLDDVPRAVELVRRYRLKLVGLHMHIG 185

Query: 194 SGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAARE 253
           SGVDY HL +VC AMV  V   G D++AISAGGGLSVPY++GE  +D  HY+ LW+AAR 
Sbjct: 186 SGVDYGHLSRVCEAMVEAVKGLGHDIEAISAGGGLSVPYREGEPDIDVAHYFRLWDAARR 245

Query: 254 QIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDAGFNDLMRPAMYGS 313
           QI  H+GH V+LEIEPGRFLVAQSGVL+ +V ++ +  ++ F L+DAGFNDL+RP+ YGS
Sbjct: 246 QIETHVGHRVRLEIEPGRFLVAQSGVLVAEVHALNRRPAQQFALLDAGFNDLVRPSFYGS 305

Query: 314 YHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRALPEVKAGDYLVLH 373
           +H ++ L  DG +L  AP     VAGPLCE+GDVFTQ E G +  R++   + GD++V H
Sbjct: 306 HHEMTVLRRDG-ALSEAPIDSFAVAGPLCEAGDVFTQAESGVITNRSIHTPEVGDFIVFH 364

Query: 374 DTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALE 418
           D GAYGASMSSNYNSRPL PEVL D+G+ RLIRRRQTI+ELLALE
Sbjct: 365 DAGAYGASMSSNYNSRPLAPEVLLDHGKPRLIRRRQTIDELLALE 409


Lambda     K      H
   0.320    0.136    0.405 

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: 621
Number of extensions: 33
Number of successful extensions: 3
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: 420
Length of database: 413
Length adjustment: 31
Effective length of query: 389
Effective length of database: 382
Effective search space:   148598
Effective search space used:   148598
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: 50 (23.9 bits)

Align candidate BPHYT_RS35090 BPHYT_RS35090 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

Software error:

../bin/blast/fastacmd -i /tmp/list.8726.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8726.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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