GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Azospirillum brasilense Sp245

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate AZOBR_RS15560 AZOBR_RS15560 isopropylmalate isomerase

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__azobra:AZOBR_RS15560
          Length = 198

 Score =  159 bits (402), Expect = 3e-44
 Identities = 86/197 (43%), Positives = 117/197 (59%), Gaps = 10/197 (5%)

Query: 3   EKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPEFV 62
           + F   T   VPLD AN+DTD ++P +FL+K    G+G  LF+D R          P F 
Sbjct: 2   DPFVTLTAPAVPLDIANIDTDQLLPARFLKKPRSAGYGNFLFHDER---------KPGFP 52

Query: 63  LNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPV 122
           L+ P Y GA +L++  NFGCGSSRE A +AL D GF+ V+APSF DIF  N+  N LL +
Sbjct: 53  LDDPAYAGARVLVSDRNFGCGSSREGAVYALVDGGFRCVVAPSFGDIFAANAAKNGLLTI 112

Query: 123 TLSDAQVDELFALVKANPGIKFEVDLEAQVVKAGD-KTYSFKIDDFRRHCMLNGLDSIGL 181
           TL +  V EL   ++  PG    VDL AQ +   D +   F ID F++ C++ GLD + L
Sbjct: 113 TLPEETVAELRRQLQEAPGAAVTVDLPAQTLSGPDGQPLPFAIDPFKKECLIEGLDDVAL 172

Query: 182 TLQHEDAIAAYENKQPA 198
           TL+H+DAI A++    A
Sbjct: 173 TLRHQDAIDAFDRADAA 189


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: 129
Number of extensions: 7
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: 198
Length adjustment: 21
Effective length of query: 180
Effective length of database: 177
Effective search space:    31860
Effective search space used:    31860
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 AZOBR_RS15560 AZOBR_RS15560 (isopropylmalate isomerase)
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.29099.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29099.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.