TBLASTN 2.2.15 [Oct-15-2006] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= P0AG30|RHO_ECOLI Transcription termination factor rho (EC 3.6.1.-) (ATP-dependent helicase rho).... (419 letters) Database: st 220 sequences; 4,870,572 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value AE008883 AE006468 |AE008883| Salmonella typhimurium LT2, section... 791 0.0 AE008761 AE006468 |AE008761| Salmonella typhimurium LT2, section... 79 1e-15 AE008832 AE006468 |AE008832| Salmonella typhimurium LT2, section... 74 4e-14 AE008787 AE006468 |AE008787| Salmonella typhimurium LT2, section... 65 1e-11 AE008880 AE006468 |AE008880| Salmonella typhimurium LT2, section... 47 6e-06 AE008878 AE006468 |AE008878| Salmonella typhimurium LT2, section... 28 2.7 AE008719 AE006468 |AE008719| Salmonella typhimurium LT2, section... 27 3.5 AE008850 AE006468 |AE008850| Salmonella typhimurium LT2, section... 27 4.5 AE008898 AE006468 |AE008898| Salmonella typhimurium LT2, section... 27 5.9 AE008872 AE006468 |AE008872| Salmonella typhimurium LT2, section... 26 7.7 AE008754 AE006468 |AE008754| Salmonella typhimurium LT2, section... 26 7.7 >AE008883 AE006468 |AE008883| Salmonella typhimurium LT2, section 187 of 220 of the complete genome. Length = 20621 Score = 791 bits (2043), Expect = 0.0 Identities = 406/419 (96%), Positives = 408/419 (97%) Frame = +3 Query: 1 MNLTELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQD 60 MNLTELKNTPVSELITLGE+MGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQD Sbjct: 75 MNLTELKNTPVSELITLGESMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQD 254 Query: 61 GFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVN 120 GFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVN Sbjct: 255 GFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVN 434 Query: 121 FDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPP 180 +DKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPP Sbjct: 435 YDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPP 614 Query: 181 KAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHV 240 KAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHV Sbjct: 615 KAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHV 794 Query: 241 QVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRF 300 QVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRF Sbjct: 795 QVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRF 974 Query: 301 FGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDY 360 FGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDY Sbjct: 975 FGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDY 1154 Query: 361 NRSGTRKXXXXXXXXXXXKMWILRKIIHPMGEIDAMEFLINKLAMTKTNDDFFEMMKRS 419 NRSGTRK KMWILRKIIHPMGEIDAMEFLINKLAMTKTNDDFFEMMKRS Sbjct: 1155NRSGTRKEELLTTQEELQKMWILRKIIHPMGEIDAMEFLINKLAMTKTNDDFFEMMKRS 1331 >AE008761 AE006468 |AE008761| Salmonella typhimurium LT2, section 65 of 220 of the complete genome. Length = 27863 Score = 79.0 bits (193), Expect = 1e-15 Identities = 68/213 (31%), Positives = 101/213 (47%), Gaps = 13/213 (6%) Frame = +3 Query: 160 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVL-LIDERPEEVTE 218 R +D + G GQR I + P GK+ LL + N PD VL LI ER EV E Sbjct: 22389 RAIDSVATCGEGQRVGIFSAPGVGKSTLLAMLC-----NAPDADSNVLVLIGERGREVRE 22553 Query: 219 MQRLVKGE-------VVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLA 271 E +V +T D PA V+ + A+ ++ K V++L DS+TR A Sbjct: 22554 FIDFTLSEETRKRCVIVVATSDRPALERVRALFVATTIAEFFRDNGKRVVLLADSLTRYA 22733 Query: 272 RAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVE-----EGGSLTIIATALIDTGSK 326 RA + A+G+ G + P F R +E E GS+T T L++ G Sbjct: 22734 RAAREIALAAGETAVSGE-----YPPGVFSALPRLLERTGMGEKGSITAFYTVLVE-GDD 22895 Query: 327 MDEVIYEEFKGTGNMELHLSRKIAEKRVFPAID 359 M+E + +E + + + LSR++AE+ +PAID Sbjct: 22896 MNEPLADEVRSLLDGHIVLSRRLAERGHYPAID 22994 >AE008832 AE006468 |AE008832| Salmonella typhimurium LT2, section 136 of 220 of the complete genome. Length = 23125 Score = 73.6 bits (179), Expect = 4e-14 Identities = 64/215 (29%), Positives = 102/215 (47%), Gaps = 8/215 (3%) Frame = -3 Query: 160 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEM 219 R +D G GQR I A GKTML+ + + + V ++ LI ER EVTE Sbjct: 6113 RAIDGLLTCGVGQRMGIFASAGCGKTMLMHMLIEQTEAD----VFVIGLIGERGREVTEF 5946 Query: 220 QRLVKGE-------VVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLAR 272 +++ +V +T D P+ A++ A+ + K V++ +DS+TR AR Sbjct: 5945 VDMLRASHKKEKCVLVFATSDFPSVDRCNAAQLATTVAEYFRDQGKRVVLFIDSMTRYAR 5766 Query: 273 AYNTVVPASG-KVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVI 331 A V ASG + G A+ R E GS+T T L+++ + D + Sbjct: 5765 ALRDVALASGERPARRGYPASVFDNLPRLLERPGATSE-GSITAFYTVLLESEEEADPMA 5589 Query: 332 YEEFKGTGNMELHLSRKIAEKRVFPAIDYNRSGTR 366 +E + + L+LSRK+A + +PAID +S +R Sbjct: 5588 -DEIRSILDGHLYLSRKLAGQGHYPAIDVLKSVSR 5487 >AE008787 AE006468 |AE008787| Salmonella typhimurium LT2, section 91 of 220 of the complete genome. Length = 24186 Score = 65.1 bits (157), Expect = 1e-11 Identities = 62/220 (28%), Positives = 101/220 (45%), Gaps = 9/220 (4%) Frame = +3 Query: 156 DLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEE 215 D R ++ +GRGQR + A GK++LL +A+ Y D V++V LI ER E Sbjct: 17298 DTGVRAINALLTVGRGQRMGLFAGSGVGKSVLLGMMAR---YTRAD-VIVVGLIGERGRE 17465 Query: 216 VTEMQRLVKGE-------VVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSIT 268 V + + G V+A+ D +Q A A+ + + V++++DS+T Sbjct: 17466 VKDFIENILGPDGRARSVVIAAPADVSPLLRMQGAAYATRIAEDFRDRGQHVLLIMDSLT 17645 Query: 269 RLARAYNTVVPASGKV-LTGGVDANALHR-PKRFFGAARNVEEGGSLTIIATALIDTGSK 326 R A A + A G+ T G + + P A + GGS+T T L + G Sbjct: 17646 RYAMAQREIALAIGEPPATKGYPPSVFAKLPALVERAGNGIHGGGSITAFYTVLTE-GDD 17822 Query: 327 MDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDYNRSGTR 366 + I + + + + LSR++AE +PAID S +R Sbjct: 17823 QQDPIADSARAILDGHIVLSRRLAEAGHYPAIDIEASISR 17942 >AE008880 AE006468 |AE008880| Salmonella typhimurium LT2, section 184 of 220 of the complete genome. Length = 20518 Score = 46.6 bits (109), Expect = 6e-06 Identities = 45/214 (21%), Positives = 89/214 (41%), Gaps = 6/214 (2%) Frame = -3 Query: 160 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPE----- 214 +V+DL P +G + + GKT+ + + ++IA H + + + E Sbjct: 11606 KVIDLMCPFAKGGKVGLFGGAGVGKTVNMMELIRNIAIEHSGYSVFAGVGERTREGNDFY 11427 Query: 215 -EVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARA 273 E+T+ + K +V +EP ++VA + A++ + +DV++ +D+I R A Sbjct: 11426 HEMTDSNVIDKVSLVYGQMNEPPGNRLRVALTGLTMAEKFRDEGRDVLLFVDNIYRYTLA 11247 Query: 274 YNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVIYE 333 V G++ + L + GS+T + + D Sbjct: 11246 GTEVSALLGRMPSAVGYQPTLAEEMGVLQERITSTKTGSITSVQAVYVPADDLTDPSPAT 11067 Query: 334 EFKGTGNMELHLSRKIAEKRVFPAIDYNRSGTRK 367 F + + LSR+IA ++PA+D S +R+ Sbjct: 11066 TFAHL-DATVVLSRQIASLGIYPAVDPLDSTSRQ 10968 Score = 37.0 bits (84), Expect = 0.004 Identities = 29/123 (23%), Positives = 52/123 (42%), Gaps = 5/123 (4%) Frame = -2 Query: 160 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVL-----LIDERPE 214 + +D PIGRGQR LI+ + GKT L + + + C+ + + I Sbjct: 14031 KAVDSMIPIGRGQRELIIGDRQTGKTALAIDAIINQRDSGIKCIYVAIGQKASTISNVVR 13852 Query: 215 EVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAY 274 ++ E L VV +T E A+ + + +D +I+ D +++ A AY Sbjct: 13851 KLEEHGALANTIVVVATASESAALQYLAPYAGCAMGEYFRDRGEDALIIYDDLSKQAVAY 13672 Query: 275 NTV 277 + Sbjct: 13671 RQI 13663 >AE008878 AE006468 |AE008878| Salmonella typhimurium LT2, section 182 of 220 of the complete genome. Length = 22418 Score = 27.7 bits (60), Expect = 2.7 Identities = 29/122 (23%), Positives = 51/122 (41%), Gaps = 5/122 (4%) Frame = -2 Query: 9 TPVSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDIF-GDGVLEILQDGFGFLRS 67 TPV +G N+G +N + + AI +Q G++I+ G+ +D +R Sbjct: 13018 TPVVMAGMIGSNVGWQNAPYLPVPALFSAIGEQLTAVGDNIWIIPGLCVSREDNHNVMRG 12839 Query: 68 ADSSYLA----GPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDK 123 ++ L P +YV P ++ ++T R GE + LL+ + V Sbjct: 12838 EETQLLGACELSPSSVYVMPGTHCKW-VQTDTQQIHDFRTVMTGELHHLLLRHSLVGAGL 12662 Query: 124 PE 125 PE Sbjct: 12661 PE 12656 >AE008719 AE006468 |AE008719| Salmonella typhimurium LT2, section 27 of 220 of the complete genome. Length = 20607 Score = 27.3 bits (59), Expect = 3.5 Identities = 12/36 (33%), Positives = 20/36 (55%) Frame = +3 Query: 62 FGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTI 97 +G L++ A P + ++P + NL+TGDTI Sbjct: 12132 YGELQTRPGGVKAQPGSVLLAPRLMALLNLKTGDTI 12239 >AE008850 AE006468 |AE008850| Salmonella typhimurium LT2, section 154 of 220 of the complete genome. Length = 21944 Score = 26.9 bits (58), Expect = 4.5 Identities = 13/31 (41%), Positives = 16/31 (51%) Frame = -1 Query: 275 NTVVPASGKVLTGGVDANALHRPKRFFGAAR 305 N VPA G+ +NALHRP F + R Sbjct: 7322 NDRVPAHGRPAASDNQSNALHRPSAFLLSMR 7230 >AE008898 AE006468 |AE008898| Salmonella typhimurium LT2, section 202 of 220 of the complete genome. Length = 23880 Score = 26.6 bits (57), Expect = 5.9 Identities = 11/39 (28%), Positives = 22/39 (56%) Frame = +2 Query: 265 DSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGA 303 + + RL + + ASG++ G++A+ +HR + F A Sbjct: 16889 EQVDRLRDEFGVYLIASGRMCVAGLNASNVHRVAKAFAA 17005 >AE008872 AE006468 |AE008872| Salmonella typhimurium LT2, section 176 of 220 of the complete genome. Length = 20456 Score = 26.2 bits (56), Expect = 7.7 Identities = 16/28 (57%), Positives = 18/28 (64%) Frame = -1 Query: 288 GVDANALHRPKRFFGAARNVEEGGSLTI 315 GVD NAL KRFF AA V+E G + I Sbjct: 7385 GVDQNALFTSKRFFYAA--VKEKGYVRI 7308 >AE008754 AE006468 |AE008754| Salmonella typhimurium LT2, section 58 of 220 of the complete genome. Length = 24578 Score = 26.2 bits (56), Expect = 7.7 Identities = 11/28 (39%), Positives = 16/28 (57%) Frame = +1 Query: 272 RAYNTVVPASGKVLTGGVDANALHRPKR 299 R Y VPA+ V +GG+ L+ P+R Sbjct: 5818 RRYRRCVPATNPVASGGIRRYRLYEPER 5901 Database: st Posted date: Sep 25, 2007 7:19 PM Number of letters in database: 4,870,572 Number of sequences in database: 220 Lambda K H 0.319 0.136 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 220 Number of Hits to DB: 1,750,361 Number of extensions: 22160 Number of successful extensions: 128 Number of sequences better than 10.0: 11 Number of HSP's gapped: 124 Number of HSP's successfully gapped: 12 Length of query: 419 Length of database: 1,623,524 Length adjustment: 90 Effective length of query: 329 Effective length of database: 1,603,724 Effective search space: 527625196 Effective search space used: 527625196 Neighboring words threshold: 13 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)