GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Caulobacter crescentus NA1000

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate CCNA_00193 CCNA_00193 3-isopropylmalate dehydrogenase

Query= BRENDA::P24404
         (370 letters)



>FitnessBrowser__Caulo:CCNA_00193
          Length = 350

 Score =  421 bits (1083), Expect = e-122
 Identities = 220/359 (61%), Positives = 262/359 (72%), Gaps = 13/359 (3%)

Query: 5   SLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDADMEKA 64
           +L LLPGDGIGPE   +VR++     +A      V E L GG++YD HG  ++D   E+A
Sbjct: 3   TLLLLPGDGIGPEVCAQVRRVA----AALTPDLKVDEALYGGASYDTHGTPLTDEVREQA 58

Query: 65  LAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASSLKPE 124
           LA+DA+L GAVGGPKW   P   RPEAGLL LRK +++FANLRPA C+ ALA ASSLKPE
Sbjct: 59  LASDAVLMGAVGGPKWADAPRHLRPEAGLLNLRKAMDVFANLRPAYCFEALAGASSLKPE 118

Query: 125 LVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFELARSR 184
           LV GLDI+ VREL GGVYFG+P+ I DL +GQK+G DTQ+Y T EIER+  VAFELAR R
Sbjct: 119 LVSGLDIMFVRELVGGVYFGQPRGIEDLADGQKKGFDTQVYTTSEIERVGRVAFELARGR 178

Query: 185 DNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFDVIVT 244
            N+V S EK NVM+SG+LW QV+TE HA +Y DVQLEH+LAD   MQLVR PKQFDVIVT
Sbjct: 179 TNKVHSAEKSNVMESGLLWKQVITELHAREYPDVQLEHILADNCAMQLVRAPKQFDVIVT 238

Query: 245 DNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSIANPI 304
           DNLFGD+LSD AAMLTGSLGMLPSA+LGAP      +  +YEP+HGSAPDIAGK +ANP+
Sbjct: 239 DNLFGDILSDAAAMLTGSLGMLPSAALGAPG-----KPGLYEPIHGSAPDIAGKGLANPL 293

Query: 305 AMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDAVLA 363
           A I SF M LR+S    + A  L AA+   LD G RT D+       + T+ MGDAVLA
Sbjct: 294 AAILSFEMALRWSLKQTEAADALLAAVKAALDNGARTRDLGG----SLTTTQMGDAVLA 348


Lambda     K      H
   0.319    0.135    0.387 

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: 480
Number of extensions: 19
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: 370
Length of database: 350
Length adjustment: 29
Effective length of query: 341
Effective length of database: 321
Effective search space:   109461
Effective search space used:   109461
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate CCNA_00193 CCNA_00193 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

Software error:

../bin/blast/fastacmd -i /tmp/list.31807.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31807.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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