GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Sphingomonas koreensis DSMZ 15582

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate Ga0059261_4031 Ga0059261_4031 2-isopropylmalate synthase, yeast type

Query= SwissProt::P06208
         (619 letters)



>FitnessBrowser__Korea:Ga0059261_4031
          Length = 554

 Score =  567 bits (1461), Expect = e-166
 Identities = 295/561 (52%), Positives = 366/561 (65%), Gaps = 15/561 (2%)

Query: 31  MLKDPSSKYKPFNAPKLSNRKWPDNRITRAPRWLSTDLRDGNQSLPDPMSVEQKKEYFHK 90
           ML+DPS KY+PF    L +R+WP+  ITRAPRWLSTD+RDGNQ+L DPM  E+K  +F  
Sbjct: 1   MLRDPSVKYRPFPPIALPDRQWPNRTITRAPRWLSTDMRDGNQALIDPMDAEKKTRFFDL 60

Query: 91  LVNIGFKEIEVSFPSASQTDFDFTRYAVEN--APDDVSIQCLVQSREHLIKRTVEALTGA 148
           +  +G KEIEV FPSA  T+FDF    V +   PDDV++Q L Q+R  LI  T E+L GA
Sbjct: 61  ICRVGIKEIEVGFPSAGATEFDFISGLVRDNRIPDDVTVQVLTQARRDLIDTTFESLRGA 120

Query: 149 KKATIHTYLATSDMFREIVFNMSREEAISKAVEATKLVRKLTKDDPSQQATRWSYEFSPE 208
           K   +H Y A S  +R+IVF M R E    A++A KL+R      P    T W +++SPE
Sbjct: 121 KTGIVHVYNAVSPAWRKIVFGMDRAEVKQIAIDAAKLLRDNAAAQPD---TDWHFQYSPE 177

Query: 209 CFSDTPGEFAVEICEAVKKAWEPTEENPIIFNLPATVEVASPNVYADQIEYFATHITERE 268
            FS    +F+VE+C AV    +PT E PIIFNLPATVE A+PN+YADQIEYF  +I  R+
Sbjct: 178 TFSTAEIDFSVEVCAAVMDVLQPTVERPIIFNLPATVECATPNIYADQIEYFCRNIPNRD 237

Query: 269 KVCISTHCHNDRGCGVAATELGMLAGADRVEGCLFGNGERTGNVDLVTVAMNMYTQGVSP 328
            V +S H HNDRG GVAA ELGM+AGADRVEGCL GNGERTGN DLVTVAMNMYTQGV P
Sbjct: 238 AVVVSLHTHNDRGTGVAAAELGMMAGADRVEGCLLGNGERTGNCDLVTVAMNMYTQGVDP 297

Query: 329 NLDFSDLTSVLDVVERCNKIPVSQRAPYGGDLVVCAFSGSHQDAIKKGFNLQNKKRAQGE 388
            LDFSD+  ++  VE C  IPV  R PY GDLV  AFSGSHQDAIKKGF  Q    A+ +
Sbjct: 298 GLDFSDIDEIVKTVEYCTNIPVHPRTPYAGDLVFTAFSGSHQDAIKKGFAAQ---EARND 354

Query: 389 TQWRIPYLPLDPKDIGRDYEAVIRVNSQSGKGGAAWVILRSLGLDLPRNMQIEFSSAVQD 448
             W +PYLP+DP D+GR YEAVIRVNSQSGKGG AWV+ +  GL LP+ +Q +FS  VQ 
Sbjct: 355 QYWEVPYLPIDPADLGRSYEAVIRVNSQSGKGGVAWVLEQDKGLKLPKRLQADFSRHVQR 414

Query: 449 HADSLGRELKSDEISKLFKEAYNYNDEQYQAISLVNYNVEKFGTERRVFTGQVKVGDQIV 508
            AD   REL + +I   F E Y    +  Q  +L  Y+  +     R+F G ++V     
Sbjct: 415 VADESSRELNAQDIWATFVETYRL--KHPQRFTLGAYDETRASNGERIFAGSIEVDGVQQ 472

Query: 509 DIEGTGNGPISSLVDALSNLLNVRFAVANYTEHSLGSGSSTQAASYIHLSYRRNADNEKA 568
            + G GNG ISS+V A+     V   +A+Y EH++G GS  QAA+Y+     R AD    
Sbjct: 473 SVSGRGNGLISSVVAAMREGFGVDLDIADYAEHAIGHGSGAQAAAYVEC---RTADGRTV 529

Query: 569 YKWGVGVSEDVGDSSVRAIFA 589
             WGVG+ EDV  +SVRA+ +
Sbjct: 530 --WGVGIDEDVATASVRAVLS 548


Lambda     K      H
   0.315    0.131    0.379 

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: 819
Number of extensions: 35
Number of successful extensions: 6
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: 619
Length of database: 554
Length adjustment: 37
Effective length of query: 582
Effective length of database: 517
Effective search space:   300894
Effective search space used:   300894
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: 53 (25.0 bits)

Align candidate Ga0059261_4031 Ga0059261_4031 (2-isopropylmalate synthase, yeast type)
to HMM TIGR00970 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.23886.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23886.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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