GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Pedobacter sp. GW460-11-11-14-LB5

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate CA265_RS15850 CA265_RS15850 3-isopropylmalate dehydrogenase

Query= BRENDA::Q9SA14
         (404 letters)



>FitnessBrowser__Pedo557:CA265_RS15850
          Length = 363

 Score =  353 bits (906), Expect = e-102
 Identities = 184/362 (50%), Positives = 253/362 (69%), Gaps = 9/362 (2%)

Query: 45  NITLLPGDGIGPEVISVAKNVLQKAGFLQGLEFDFQEMPFGGAALDLVGVPLPEETSTAA 104
           NI ++PGDGIGPEV +  K  L+K   + G EF F+E   G AA+++ G PLP+ET   A
Sbjct: 4   NILVIPGDGIGPEVTTWGKAALEKIAEIFGHEFAFEEALMGHAAIEVTGEPLPDETLEKA 63

Query: 105 KQSDAILLGAIGGYKWDKNEK-HLRPEMGLLNIRRDLNVFANLRPATVLPQLVDASTLKK 163
           +QSDAIL GAIG  K+D +    +RPE GLL IR++L +FANLRP  +  +L+ AS++K 
Sbjct: 64  RQSDAILFGAIGHAKYDNDPSLKVRPEQGLLKIRKELGLFANLRPILLFDELLQASSIKP 123

Query: 164 EVAQGVDMMIVRELTGGIYFGEPRGITINENGEEVGFNTEIYAAHEIDRIARVAFETARK 223
           E+ +G D++  RELTG +YFGE               +  IY  +E++RIA  A++ A++
Sbjct: 124 EILRGTDILFFRELTGDVYFGEKT----RSEDRNTASDLMIYHRYEVERIAHKAYQAAQQ 179

Query: 224 RRGKLCSVDKANVLDASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVT 283
           R  +LCSVDKANVL++S LWR+ V  +A +YPDVE  HM++DNAAMQL+++PK+FD ++T
Sbjct: 180 RNKRLCSVDKANVLESSRLWRETVQEIAKQYPDVETEHMFIDNAAMQLIKNPKKFDVVLT 239

Query: 284 NNIFGDILSDEASMITGSIGMLPSASLGESGPGLFEPIHGSAPDIAGQDKANPLATILSA 343
            N+FGDIL+DEAS I GS+GML SAS+GES  G FEPIHGSA DIAG+D ANPLA+ILSA
Sbjct: 240 ANLFGDILTDEASQIAGSMGMLASASVGES-TGFFEPIHGSAHDIAGKDLANPLASILSA 298

Query: 344 AMLLKYGLGEEKAAKMIEDAVVDALNKGFRTGDIYSPGN---KLVGCKEMGEEVLKSVDS 400
           A++L+ G G ++ AK++ D +   L +GFRT DI        K++G  EMG+ VLK +  
Sbjct: 299 ALMLEIGFGLKEEAKLLVDTIDQVLKEGFRTHDIADQSTNRFKVLGTAEMGKLVLKFLSQ 358

Query: 401 KV 402
           K+
Sbjct: 359 KL 360


Lambda     K      H
   0.317    0.136    0.389 

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: 394
Number of extensions: 14
Number of successful extensions: 5
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: 404
Length of database: 363
Length adjustment: 30
Effective length of query: 374
Effective length of database: 333
Effective search space:   124542
Effective search space used:   124542
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: 50 (23.9 bits)

Align candidate CA265_RS15850 CA265_RS15850 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

Software error:

../bin/blast/fastacmd -i /tmp/list.32513.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32513.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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