RPSBLAST alignment of GI: 254780237 and protein with PDBid: 3iyd
>3iyd_A DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12} Length = 329
Score = 346 bits (890), Expect = 3e-96
Identities = 146/334 (43%), Positives = 218/334 (65%), Gaps = 10/334 (2%)
Query: 2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
+Q + E +KP ++ Q + EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1 MQGSVTEFLKPRLVDIE---QVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57
Query: 62 AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +T+ K G G VTA DI
Sbjct: 58 EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117
Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALY 177
D+E++ P HVIC+L +A + M + V +G GYVPA H + PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177
Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
SP+++++Y VE+AR Q D DKL + ++T+G+I E+++ A+ IL +QL F++ +
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237
Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
++ ++ F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+ N
Sbjct: 238 RQPEVKEE---KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294
Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328