GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Sphingomonas koreensis DSMZ 15582

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate Ga0059261_4223 Ga0059261_4223 3-isopropylmalate dehydratase, large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Korea:Ga0059261_4223
          Length = 478

 Score =  597 bits (1538), Expect = e-175
 Identities = 297/470 (63%), Positives = 367/470 (78%), Gaps = 9/470 (1%)

Query: 4   TLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMDH 63
           TLYEK++ AHVV   ++ T L+YIDRHLVHEVTSPQAF+GLRA+GR VR+P  T A  DH
Sbjct: 7   TLYEKIWAAHVVERRDDGTCLIYIDRHLVHEVTSPQAFEGLRANGRRVRRPDLTLAVPDH 66

Query: 64  NVSTQTKDINACGEMARI-------QMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQG 116
           N+ T T  ++A G    I       Q+  L +N  EFG++ +      QGIVHV+GPEQG
Sbjct: 67  NLPT-TPRVDAAGNRLPIADRESAQQLAALERNVAEFGIDYFGATAAEQGIVHVVGPEQG 125

Query: 117 VTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAP 176
            TLPG T+VCGDSHT+ HGA GALAFGIGTSEVEHVLATQTL   ++KTM+I V G    
Sbjct: 126 FTLPGTTLVCGDSHTSAHGALGALAFGIGTSEVEHVLATQTLLLSQSKTMEIRVDGTLGF 185

Query: 177 GITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPD 236
           G++AKD+VLAIIGKTG+AGGTG+VVE+ GE IR LS+EGR+T+ NM+IE GA++GL+APD
Sbjct: 186 GVSAKDVVLAIIGKTGAAGGTGYVVEYTGEVIRALSIEGRLTVSNMSIEGGARSGLIAPD 245

Query: 237 ETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQ 296
           E TF Y+KGR  APKG+ ++ AVA+WKTL TD GA +D VVTL   +I+P +TWGT+P  
Sbjct: 246 EKTFAYLKGRPMAPKGEQWEQAVAWWKTLPTDAGAQYDRVVTLNGSDIAPSLTWGTSPED 305

Query: 297 VISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLR 356
           V+ +   +PDP SFADP +R +A+K+L YMGL PG  + ++A++ +FIGSCTNSRIEDLR
Sbjct: 306 VVPITGVVPDPESFADPAKRVAAQKSLDYMGLAPGTRMQDIAVENIFIGSCTNSRIEDLR 365

Query: 357 AAAEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNN 415
           AAA++ KGR VA G+ QAL+VPGSG VK QAEAEGLD+IF++AGFEWR PGCSMCLAMN 
Sbjct: 366 AAADVVKGRHVADGIRQALIVPGSGLVKRQAEAEGLDRIFLDAGFEWREPGCSMCLAMNP 425

Query: 416 DRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           D++  GERCASTSNRNF GRQG G RTHLVSPAMAAAAAVTG   D+R++
Sbjct: 426 DKVPAGERCASTSNRNFVGRQGPGARTHLVSPAMAAAAAVTGRLTDVRDL 475


Lambda     K      H
   0.317    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: 768
Number of extensions: 26
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: 466
Length of database: 478
Length adjustment: 33
Effective length of query: 433
Effective length of database: 445
Effective search space:   192685
Effective search space used:   192685
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 Ga0059261_4223 Ga0059261_4223 (3-isopropylmalate dehydratase, large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.11586.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11586.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.