BLAST/PSIBLAST alignment of GI: 254780511 and GI: 209547954 at iteration 1
>gi|209547954|ref|YP_002279871.1| flagellar biosynthesis protein FliR [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 250
>gi|209533710|gb|ACI53645.1| type III secretion system inner membrane R protein [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 250
 Score =  209 bits (532), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 110/247 (44%), Positives = 161/247 (65%), Gaps = 8/247 (3%)

Query: 1   MTISPEIIMMSLFLIVCRVGSCIMLLPGLSMSYIPMQVRLCFAMAFSIVLLPFLWDTIDL 60
           M   P+  +++LFL+ CR+G C++ LPG S + +P Q+R+  A+A SI ++P LWDT+  
Sbjct: 1   MITDPQGTVLALFLVFCRIGGCVLALPGFSSARVPEQLRVFIALALSIAVMPLLWDTVYP 60

Query: 61  QNFVNRAYYSKLVMVELFLGCVHGLLIRVYTLGLQFTGSVISTAIGLNLQTSMGISDSLA 120
                   Y  L++ E  +G ++G+L R+YTLG+QF  ++I+T +G    T  G +D + 
Sbjct: 61  AVHTGSGTYIGLIVSESLIGVMYGMLARIYTLGMQFAATIIATMVGY---TQPGSADIIE 117

Query: 121 ETPLNSLIGII---GLLALWVIDFHHQVFYALVKSYGTIPIGQELNFGNIFSSFVNMLQT 177
           +TP +SL G I   G++ L+++DFHH VF AL+ SY T+P G  +       SF + L+ 
Sbjct: 118 DTPESSLSGFITFAGIMILFIMDFHHIVFRALIDSYTTMPFGGLMQMRATLISFSDTLEQ 177

Query: 178 TFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLC-LSIEIIV 236
           T  IMLRLSSPFL + ++FN+SIG +NKL PQIP+YFISTPYL+ +G LFL   SI  +V
Sbjct: 178 TTYIMLRLSSPFLIYGLIFNVSIGFINKLAPQIPVYFISTPYLL-MGGLFLVYFSIAALV 236

Query: 237 YQFSHSF 243
            QF  SF
Sbjct: 237 SQFGQSF 243