PSIBLAST alignment of GI: 254780142 and protein with PDB id: 1l9u

gi|21466006|pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1524
>gi|21466012|pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1524
 Score =  357 bits (917), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 122/265 (46%), Positives = 170/265 (64%), Gaps = 4/265 (1%)

Query: 1127 DITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIP 1186
            DIT GLPRV ELFEARRPK  A+++EI G +RI+     + R+ +    +G    EY +P
Sbjct: 1251 DITQGLPRVIELFEARRPKAKAVISEIDGVVRIEE---GEDRLSVFVESEGF-SKEYKLP 1306

Query: 1187 KNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHK 1246
            K+    ++DGD+VE G  +  G   P  +L  KG EA+  YL++E+Q+VYR +GV ++ K
Sbjct: 1307 KDARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDK 1366

Query: 1247 HIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITK 1306
            HIE+VVR ML+ VE+TDP D+  + G  +++ +VE LN  L  +GK  V++ P+L G+TK
Sbjct: 1367 HIEIVVRQMLKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTK 1426

Query: 1307 ASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRV 1366
            ++L TKS++SAASFQ TT VLTEAAIAGK D L G KENVI+GR IPAGTG+      +V
Sbjct: 1427 SALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQV 1486

Query: 1367 AMNRDQMILKERSNFSQNEDLKNTA 1391
               R    ++E    +     K   
Sbjct: 1487 VDQRTLKAIEEARKEAVEAKEKEAP 1511