GapMind for Amino acid biosynthesis

 

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

Align 3-isopropylmalate dehydratase large subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate H281DRAFT_02541 H281DRAFT_02541 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33)

Query= SwissProt::P15717
         (466 letters)



>FitnessBrowser__Burk376:H281DRAFT_02541
          Length = 465

 Score =  476 bits (1224), Expect = e-139
 Identities = 238/466 (51%), Positives = 310/466 (66%), Gaps = 6/466 (1%)

Query: 1   MAKTLYEKLFDAHVVFEAPNETPLLYIDRHLVHEVTSPQAFDGLRAHHRPVRQPGKTFAT 60
           MA+TL+++++DAHVV +      LL IDRHL+H+++ P  F+ L A   PV +P  +FAT
Sbjct: 1   MAQTLFDRIWDAHVVTDLGGGWALLAIDRHLLHDLSGPGGFETLAARELPVSRPDLSFAT 60

Query: 61  MDHNVST---QTKDINASGEMARIQMQELIKNCNEFGVELYDLNHPYQGIVHVMGPEQGV 117
            DH VS+   +T + N +G      ++     C+   V  YDL    QGIVHVM PE G+
Sbjct: 61  ADHAVSSAPHRTGETNPAGAKLYASLRRF---CDSASVPFYDLGKAGQGIVHVMAPEMGL 117

Query: 118 TLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVTGNAAPG 177
           TLPG TIVCGDSHT THG  GALAFGIG+SE+ HVLATQT++Q + + M+I  TG  A G
Sbjct: 118 TLPGTTIVCGDSHTCTHGGLGALAFGIGSSELAHVLATQTVRQKKPRQMRITYTGVLAKG 177

Query: 178 ITAKDIVLAIIGKTGSAGGTGHVVEFCGDAIRALSMEGRMTLCNMAIEMGAKAGLVAPDE 237
           + AKD+ L +I K G + G G+ +E CG A++ LS+E R+TLCNM++E+G+K     PD+
Sbjct: 178 VFAKDLALHVIAKLGCSAGVGYAIEHCGPALKRLSVEERLTLCNMSVELGSKIAFCPPDD 237

Query: 238 TTFNYVKGRLHAPKGRDFDEAVEYWKTLKTDDGATFDTVVALRAEEIAPQVTWGTNPGQV 297
            TF++++G  +AP G +F+ AV  W+ L++DD A FD  V++   ++ P VTWGT P   
Sbjct: 238 VTFDFLRGLPYAPAGDEFEHAVSEWRKLRSDDNAHFDVEVSIDLSDVEPMVTWGTTPEHA 297

Query: 298 ISVTDIIPDPASFSDPVERASAEKALAYMGLQPGVPLTDVAIDKVFIGSCTNSRIEDLRA 357
           ++VT  +PDP   +D   R   E AL YMGL  G  L   ++D VFIGSC NSRI DLR 
Sbjct: 298 LAVTSAVPDPTDSTDAERRKGVEAALEYMGLCGGQSLAGTSVDWVFIGSCANSRISDLRE 357

Query: 358 AAEVAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417
           AA + +G+ VAP VQA VVPGS  VK  AEAEGL  +F  AGFEWR PGCSMC+A N D 
Sbjct: 358 AASIVRGKHVAPNVQAWVVPGSQLVKEIAEAEGLADVFRSAGFEWREPGCSMCVAANGDV 417

Query: 418 LNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           + PG+R  STSNRNF GRQG G RTHL SPA AAAAA+ G   D R
Sbjct: 418 VPPGQRIVSTSNRNFIGRQGPGARTHLASPATAAAAAIAGAIVDPR 463


Lambda     K      H
   0.318    0.134    0.396 

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: 672
Number of extensions: 30
Number of successful extensions: 2
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: 466
Length of database: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
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: 51 (24.3 bits)

Align candidate H281DRAFT_02541 H281DRAFT_02541 (3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.20884.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20884.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.