GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Herbaspirillum seropedicae SmR1

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate HSERO_RS16505 HSERO_RS16505 3-isopropylmalate dehydratase small subunit

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__HerbieS:HSERO_RS16505
          Length = 215

 Score =  243 bits (621), Expect = 1e-69
 Identities = 119/201 (59%), Positives = 150/201 (74%), Gaps = 9/201 (4%)

Query: 4   KFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLD------EKGQQP 57
           KF  H GLV PLD ANVDTDAIIPKQFL+ + R+GFG +LF++WR+LD      +  ++P
Sbjct: 3   KFIVHEGLVAPLDRANVDTDAIIPKQFLKSIKRSGFGPNLFDEWRYLDHGEPGMDNSKRP 62

Query: 58  -NPEFVLNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFN 116
            NP+FVLN   YQG+SILL+R+NFGCGSSREHAPWAL  +GF+ VIAPSFADIF+ N + 
Sbjct: 63  LNPDFVLNQERYQGSSILLSRKNFGCGSSREHAPWALDQFGFRAVIAPSFADIFFNNCYK 122

Query: 117 NQLLPVTLSDAQVDELFALVKANPGIKFEVDLEAQVVKA--GDKTYSFKIDDFRRHCMLN 174
           N LLP+ L++ QVD LF  VKA PG +  +DLE Q+V    G +TY F+I +FR++C+LN
Sbjct: 123 NGLLPIVLTEQQVDHLFNEVKAFPGYRLVIDLEKQIVSTTNGSQTYPFEISEFRKYCLLN 182

Query: 175 GLDSIGLTLQHEDAIAAYENK 195
           G D IGLTL+  D I AYE K
Sbjct: 183 GFDDIGLTLRKADTIRAYEEK 203


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: 183
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: 215
Length adjustment: 21
Effective length of query: 180
Effective length of database: 194
Effective search space:    34920
Effective search space used:    34920
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 HSERO_RS16505 HSERO_RS16505 (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.12593.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12593.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.