Alignments for a candidate for leuD in Pseudomonas fluorescens FW300-N1B4

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate Pf1N1B4_14 3-isopropylmalate dehydratase small subunit (EC 4.2.1.33)

Query= uniprot:Q845W4
         (216 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_14
          Length = 214

 Score =  318 bits (814), Expect = 6e-92
 Identities = 151/210 (71%), Positives = 173/210 (82%)

Query: 1   MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60
           M+ FT HTG+VAPLDR NVDTD IIPKQFLKSIKRTGFGPN FDEWRYLD G+P QDNSK
Sbjct: 1   MKAFTQHTGLVAPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDVGQPYQDNSK 60

Query: 61  RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120
           RPLN DFVLN  RYQGAS+L+ R+NFGCGSSREHAPWAL++YGFR+IIAPS+ADIFFNN 
Sbjct: 61  RPLNKDFVLNAERYQGASVLLARENFGCGSSREHAPWALEEYGFRSIIAPSYADIFFNNS 120

Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDGRDYPFEITAFRKYCLL 180
           FKNGLLPI+L++ +VD L  +  A  GYQL +DL+AQ V  PDG+   FEI AFRK+CLL
Sbjct: 121 FKNGLLPIILSDAEVDELFQQVEATPGYQLQVDLQAQTVTRPDGKVLSFEIDAFRKHCLL 180

Query: 181 NGFDDIGLTLRHADKIRQFEAERLAKQPWL 210
           NG DDIGLTL+  + I  FEA+  A QPWL
Sbjct: 181 NGLDDIGLTLQDHEAIATFEAKHRASQPWL 210


Lambda     K      H
   0.322    0.141    0.437 

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: 233
Number of extensions: 5
Number of successful extensions: 1
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: 216
Length of database: 214
Length adjustment: 22
Effective length of query: 194
Effective length of database: 192
Effective search space:    37248
Effective search space used:    37248
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 Pf1N1B4_14 (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.17577.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.17577.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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