Alignments for a candidate for lysA in Desulfovibrio vulgaris Hildenborough JW710

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate 208063 DVU2566 diaminopimelate decarboxylase (TIGR)

Query= curated2:O27390
         (428 letters)



>FitnessBrowser__DvH:208063
          Length = 421

 Score =  291 bits (745), Expect = 3e-83
 Identities = 173/408 (42%), Positives = 242/408 (59%), Gaps = 17/408 (4%)

Query: 16  GGADAVELADEYGTPLYVIDEMRIRENYRRLYRAFSGEYSRFQVFYACKANTNLAVMRIL 75
           G     EL + YG+PLYV  E  +R+  R + +A S  +  F+V Y+ KAN+NLA++ I+
Sbjct: 16  GLTSPTELVETYGSPLYVYSEAILRQRCREM-KALSS-HPGFRVNYSAKANSNLALLHII 73

Query: 76  EEEGSGIDAVSPGEIYTALMAGFDPDRILYTGNNVRDDELQFALDSGVRINVDSRSQLLR 135
            EEG  +DA+SPGE++  L AGF PD+ILY  NNV  +EL  A+  G+ ++VDS SQL  
Sbjct: 74  REEGLVVDAMSPGELFMNLRAGFSPDKILYVCNNVSAEELGNAVSHGLLVSVDSLSQLDL 133

Query: 136 LSEIAPEGLRISFRVNPLVGAGHHEHCITGGEMSKFGVMEREAPEVYRMAMDLGFEPVGI 195
             E+ P G R+  R NP +GAGHH+  +T G+ +KFGV      EV  +         GI
Sbjct: 134 YGEVNPGG-RVMVRFNPGIGAGHHKKVVTAGKETKFGVDPASIDEVRTILARHNLTLAGI 192

Query: 196 HAHIGSGILDPEPFMLAVETLMDIAGRVHEATGVEFEFIDFGGGLGIPYTP-EEEP-LDI 253
           + HIGS  L+PE ++ A   L+ +A R  +      E IDFGGG GIPY   + +P LD+
Sbjct: 193 NQHIGSLFLEPESYVEAARFLLTLAERFDDV-----EVIDFGGGFGIPYHKYDNQPRLDL 247

Query: 254 DEFASKITGLFKDKLSEYGLGRPMMCLEPGRYIVGDASYLLTRVNTIKES-YRKFAGVDA 312
               ++   L        G  R    +EPGRY+V +   LL  V+++K +   ++ G D 
Sbjct: 248 TAMGAQFDDLISGWAQRRGY-RGRFLVEPGRYVVAECGLLLGSVHSVKSNGANRYVGTDL 306

Query: 313 GFNTLLRPAMYGSYHHILVAERPLDEPSEKM---DVAGNVCESGDLFARDRQLPEINEGD 369
           GFN L RP MY ++H I V  R    PS+ +    V GN+CESGD+ AR+R LP + EGD
Sbjct: 307 GFNVLARPVMYDAHHDIEV-YREDGAPSDLLLPQTVVGNICESGDIIARNRPLPPVEEGD 365

Query: 370 VLAIMNAGAYSFSMSSQYNSRPRPAEVLV-REGKVDVVRERETFSDLL 416
           +L +++AGAY + MSS YN R RPAEVL+  EG+  +VR RET  DL+
Sbjct: 366 ILGVLDAGAYGYVMSSSYNQRMRPAEVLIDLEGRPRLVRRRETLDDLV 413


Lambda     K      H
   0.320    0.140    0.408 

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: 577
Number of extensions: 30
Number of successful extensions: 8
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: 428
Length of database: 421
Length adjustment: 32
Effective length of query: 396
Effective length of database: 389
Effective search space:   154044
Effective search space used:   154044
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: 51 (24.3 bits)

Align candidate 208063 DVU2566 (diaminopimelate decarboxylase (TIGR))
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

Software error:

../bin/blast/fastacmd -i /tmp/list.3373.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.3373.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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