GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Burkholderia phytofirmans PsJN

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate BPHYT_RS33905 BPHYT_RS33905 3-isopropylmalate dehydratase small subunit

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__BFirm:BPHYT_RS33905
          Length = 217

 Score =  242 bits (617), Expect = 4e-69
 Identities = 122/205 (59%), Positives = 148/205 (72%), Gaps = 9/205 (4%)

Query: 3   EKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLD--EKGQQP--- 57
           EKF  HTG+V PLD  NVDTDAIIPKQFL+ + RTGFG + F++WR+LD  E GQ     
Sbjct: 2   EKFIVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSKR 61

Query: 58  --NPEFVLNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSF 115
             NP+FVLN P YQGAS+LLAR+NFGCGSSREHAPWAL  YGF+ +IAPSFADIFY N F
Sbjct: 62  PLNPDFVLNQPRYQGASVLLARKNFGCGSSREHAPWALEQYGFRALIAPSFADIFYNNCF 121

Query: 116 NNQLLPVTLSDAQVDELFALVKANPGIKFEVDLEAQVVKAGD--KTYSFKIDDFRRHCML 173
            N +LP+ L++ QVD LF    A  G K  VDLEAQVV+  D    Y F++  FR++C+L
Sbjct: 122 KNGVLPIVLTEQQVDHLFDETYAFNGFKLTVDLEAQVVRTSDGGTEYPFEVAAFRKYCLL 181

Query: 174 NGLDSIGLTLQHEDAIAAYENKQPA 198
           NG D IGLTL+H D I  +E ++ A
Sbjct: 182 NGFDDIGLTLRHADKIRQFEAERIA 206


Lambda     K      H
   0.321    0.138    0.416 

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: 211
Number of extensions: 8
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: 201
Length of database: 217
Length adjustment: 21
Effective length of query: 180
Effective length of database: 196
Effective search space:    35280
Effective search space used:    35280
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 (21.9 bits)
S2: 45 (21.9 bits)

Align candidate BPHYT_RS33905 BPHYT_RS33905 (3-isopropylmalate dehydratase small subunit)
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.18267.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18267.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.