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: pm 204 sequences; 2,269,587 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value embl|AE006229|AE006229 Pasteurella multocida subsp. multocida st... 718 0.0 embl|AE006185|AE006185 Pasteurella multocida subsp. multocida st... 47 2e-06 embl|AE006234|AE006234 Pasteurella multocida subsp. multocida st... 25 8.1 >embl|AE006229|AE006229 Pasteurella multocida subsp. multocida str. Pm70 section 196 of 204 of the complete genome. Length = 11895 Score = 718 bits (1854), Expect = 0.0 Identities = 363/420 (86%), Positives = 392/420 (93%), Gaps = 1/420 (0%) Frame = -2 Query: 1 MNLTELKNTPVSELITLGEN-MGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQ 59 M+LTELKN PVSEL+ LGE MGLENLAR+RKQDI+FAILKQHAKSGEDIFG GVLEIL Sbjct: 4283 MHLTELKNRPVSELVELGEGQMGLENLARLRKQDIVFAILKQHAKSGEDIFGGGVLEILP 4104 Query: 60 DGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEV 119 DGFGFLRSADSSYLAGPDDIYVSPSQIRRFNL+TGD I GKIRPPKEGERYFALLKV++V Sbjct: 4103 DGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLQTGDKIEGKIRPPKEGERYFALLKVDQV 3924 Query: 120 NFDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAP 179 N D+PE +R+KILFENLTPLHANSRLRMERGNGSTEDLTAR+LDLASPIG+GQRGLIVAP Sbjct: 3923 NDDRPEVSRSKILFENLTPLHANSRLRMERGNGSTEDLTARILDLASPIGKGQRGLIVAP 3744 Query: 180 PKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRH 239 PKAGKTMLLQNIAQSI YN+P+C L+VLLIDERPEEVTEMQR VKGEV+ASTFDEPA+RH Sbjct: 3743 PKAGKTMLLQNIAQSITYNYPECELIVLLIDERPEEVTEMQRSVKGEVIASTFDEPATRH 3564 Query: 240 VQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKR 299 VQVAEMVIEKAKR VEHKKDV+ILLDSITRLARAYNTV PASGK+L+GGVDANALHRPKR Sbjct: 3563 VQVAEMVIEKAKRSVEHKKDVVILLDSITRLARAYNTVTPASGKILSGGVDANALHRPKR 3384 Query: 300 FFGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAID 359 FFGAARNVEEGGSLTIIATAL+DTGSKMDEVI+EEFKGTGNMELHLSRKIAEKRVFPAID Sbjct: 3383 FFGAARNVEEGGSLTIIATALVDTGSKMDEVIFEEFKGTGNMELHLSRKIAEKRVFPAID 3204 Query: 360 YNRSGTRKXXXXXXXXXXXKMWILRKIIHPMGEIDAMEFLINKLAMTKTNDDFFEMMKRS 419 +NRSGTRK KMWILRKI+HPMGE++AMEFLI+KL + KTND+FFEMMKRS Sbjct: 3203 FNRSGTRKEDLLTSPDELQKMWILRKILHPMGEVEAMEFLIDKLMVAKTNDEFFEMMKRS 3024 >embl|AE006185|AE006185 Pasteurella multocida subsp. multocida str. Pm70 section 152 of 204 of the complete genome. Length = 10229 Score = 47.4 bits (111), Expect = 2e-06 Identities = 50/228 (21%), Positives = 93/228 (40%), Gaps = 8/228 (3%) Frame = +3 Query: 148 ERGNGSTEDLTA--RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLM 205 E + STE L +V+DL P +G + + GKT+ + + ++IA H + Sbjct: 8364 EEQSNSTELLETGIKVIDLVCPFAKGGKVGLFGGAGVGKTVNMMELIRNIAIEHSGYSVF 8543 Query: 206 VLLIDERPE------EVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKD 259 + + E E+ + L K +V +EP ++VA + A++ + +D Sbjct: 8544 AGVGERTREGNDFYHEMKDSNVLDKVSLVYGQMNEPPGNRLRVALTGLTMAEKFRDEGRD 8723 Query: 260 VIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATA 319 V+ +D+I R A V G++ + L + GS+T + Sbjct: 8724 VLFFVDNIYRYTLAGTEVSALLGRMPSAVGYQPTLAEEMGVLQERITSTKTGSITSVQAV 8903 Query: 320 LIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDYNRSGTRK 367 + D F + + LSR+IA ++PA+D S +R+ Sbjct: 8904 YVPADDLTDPSPATTFAHLDSTVV-LSRQIASLGIYPAVDPLESTSRQ 9044 Score = 35.4 bits (80), Expect = 0.006 Identities = 56/292 (19%), Positives = 111/292 (38%), Gaps = 19/292 (6%) Frame = +2 Query: 5 ELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDI-FGDGVLEILQDGFG 63 +L +T +SELI +K+ F ++ + +G + DG++ I G Sbjct: 5570 QLNSTEISELI--------------KKRIAQFDVVSEARNTGTIVSVSDGIIRI----HG 5695 Query: 64 FLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEV---- 119 +A P + Y + R ++ G + G EG ++ EV Sbjct: 5696 LSEVMQGEMIALPGNRYAMALNLERDSV--GAVVMGPYADLAEGMEVQCTGRILEVPVGR 5869 Query: 120 --------NFDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTA-RVLDLASPIGR 170 +P + + +I + +P+ + ++R + T + +D PIGR Sbjct: 5870 GLLGRVVNTLGEPIDGKGEIENDGFSPVEVIAPGVIDRKSVDQPVQTGYKAVDSMVPIGR 6049 Query: 171 GQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVL-----LIDERPEEVTEMQRLVKG 225 GQR LI+ + GKT L + + + C+ + + I ++ E L Sbjct: 6050 GQRELIIGDRQTGKTALAIDAIINQRDSGIKCIYVAIGQKASTIANVVRKLEEHSALQNT 6229 Query: 226 EVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTV 277 VV ++ E A+ + + +D +I+ D +++ A AY + Sbjct: 6230 IVVVASASESAALQYLAPYSGCAMGEYFRDRGEDALIIYDDLSKQAVAYRQI 6385 >embl|AE006234|AE006234 Pasteurella multocida subsp. multocida str. Pm70 section 201 of 204 of the complete genome. Length = 14505 Score = 25.0 bits (53), Expect = 8.1 Identities = 11/19 (57%), Positives = 14/19 (73%) Frame = +2 Query: 176 IVAPPKAGKTMLLQNIAQS 194 +V PP GKT L Q+IAQ+ Sbjct: 4613 LVGPPGVGKTSLGQSIAQA 4669 Database: pm Posted date: Sep 25, 2007 7:19 PM Number of letters in database: 2,269,587 Number of sequences in database: 204 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: 204 Number of Hits to DB: 729,906 Number of extensions: 8211 Number of successful extensions: 42 Number of sequences better than 10.0: 3 Number of HSP's gapped: 41 Number of HSP's successfully gapped: 4 Length of query: 419 Length of database: 756,529 Length adjustment: 84 Effective length of query: 335 Effective length of database: 739,393 Effective search space: 247696655 Effective search space used: 247696655 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: 46 (22.3 bits)