GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Pseudomonas fluorescens FW300-N2E2

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate Pf6N2E2_64 3-isopropylmalate dehydratase small subunit (EC 4.2.1.33)

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_64
          Length = 214

 Score =  261 bits (668), Expect = 5e-75
 Identities = 130/202 (64%), Positives = 157/202 (77%), Gaps = 8/202 (3%)

Query: 5   FTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLD------EKGQQP- 57
           FTQHTGLV PLD ANVDTD IIPKQFL+ + RTGFG +LF++WR+LD      +  ++P 
Sbjct: 4   FTQHTGLVAPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDVGQPYQDNSKRPV 63

Query: 58  NPEFVLNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNN 117
           N +FVLN   YQGAS+LLARENFGCGSSREHAPWAL +YGF+ +IAPS+ADIF+ NSF N
Sbjct: 64  NKDFVLNAERYQGASVLLARENFGCGSSREHAPWALEEYGFRSIIAPSYADIFFNNSFKN 123

Query: 118 QLLPVTLSDAQVDELFALVKANPGIKFEVDLEAQVVKAGD-KTYSFKIDDFRRHCMLNGL 176
            LLP+ LSDA+VDELF  V+ANPG + ++DL AQ V   D K   F+ID FR+HC+LNGL
Sbjct: 124 GLLPIILSDAEVDELFQQVEANPGYQLQIDLAAQTVTRPDGKVLGFEIDAFRKHCLLNGL 183

Query: 177 DSIGLTLQHEDAIAAYENKQPA 198
           D IGLTLQ  +AIAA+E K  A
Sbjct: 184 DDIGLTLQDGEAIAAFEAKHRA 205


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: 190
Number of extensions: 5
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: 214
Length adjustment: 21
Effective length of query: 180
Effective length of database: 193
Effective search space:    34740
Effective search space used:    34740
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 Pf6N2E2_64 (3-isopropylmalate dehydratase small subunit (EC 4.2.1.33))
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.4763.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4763.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.