BLASTP 2.2.18 [Mar-02-2008] 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. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0529.0019.p (174 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KGI8.1 B3KGI8_9BACI 16S rRNA processing protein RimM 211 2e-53 C3HMK3.1 C3HMK3_BACTU Ribosome maturation factor rimM 201 1e-50 C3GMU5.1 C3GMU5_BACTU Ribosome maturation factor rimM 201 1e-50 C3G6W3.1 C3G6W3_BACTU Ribosome maturation factor rimM 201 1e-50 C3F5V3.1 C3F5V3_BACTU Ribosome maturation factor rimM 201 1e-50 >B3KGI8.1 B3KGI8_9BACI 16S rRNA processing protein RimM Length = 173 Score = 211 bits (538), Expect = 2e-53, Method: Compositional matrix adjust. Identities = 107/174 (61%), Positives = 133/174 (76%), Gaps = 2/174 (1%) Query: 1 MTEEL-NVGRLVNTHGIRGEIKILSSTDFPEVRFAPGKKLLVVPADGSQKFEVTVESSRE 59 M+E+L VG++VNTHGIRGE+K++ TDF + RFA KL +VP D K EVTVE+SR Sbjct: 1 MSEKLYTVGKIVNTHGIRGEVKVMPHTDFADQRFAAKSKLYIVP-DKGNKIEVTVETSRF 59 Query: 60 HKGMYIVRLKGYTNINQIEKYKGSLLKVPGDDLVELPENEYYFHQIVGCEVYTDEDDSRP 119 HK MY+++ K IN+ EKYKGSLLK+ D ELPENEYYFH+I+GC+V TDE+ + Sbjct: 60 HKNMYVLKFKELHGINEAEKYKGSLLKITEDLQEELPENEYYFHEIIGCKVMTDEEPAEE 119 Query: 120 LGTIKEILQPGANDVWVVKPVKGQDILIPVINDVVLDVDIQAKKITVHLMEGLL 173 LGTI EIL PGANDVWVVK KG++IL+P I DVVLDVD ++K + VHLMEGLL Sbjct: 120 LGTISEILTPGANDVWVVKTPKGKEILLPAIPDVVLDVDKESKLVRVHLMEGLL 173 >C3HMK3.1 C3HMK3_BACTU Ribosome maturation factor rimM Length = 171 Score = 201 bits (512), Expect = 1e-50, Method: Compositional matrix adjust. Identities = 95/173 (54%), Positives = 131/173 (75%), Gaps = 2/173 (1%) Query: 1 MTEELNVGRLVNTHGIRGEIKILSSTDFPEVRFAPGKKLLVVPADGSQKFEVTVESSREH 60 MT+ NVG++VNTHG++GEI+++S TDFPE R+ G L + G + F V + S R+H Sbjct: 1 MTKWFNVGKIVNTHGVKGEIRVVSRTDFPEERYKVGNTLYISNEKGGEPFPVKITSHRQH 60 Query: 61 KGMYIVRLKGYTNINQIEKYKGSLLKVPGDDLVELPENEYYFHQIVGCEVYTDEDDSRPL 120 K ++ +GY N+N++E++KGSLLKVP D L EL E EYY+H+I+GC V T+E ++ L Sbjct: 61 KTFDLLTFEGYGNVNEVEQFKGSLLKVPEDQLGELAEGEYYYHEIIGCNVVTEEGEA--L 118 Query: 121 GTIKEILQPGANDVWVVKPVKGQDILIPVINDVVLDVDIQAKKITVHLMEGLL 173 GTIKE+L PGANDVWV+K KGQD+LIP I+DVVL V+I+ K +T+H+MEGLL Sbjct: 119 GTIKEVLSPGANDVWVIKRPKGQDLLIPYIDDVVLQVNIENKLVTIHVMEGLL 171 >C3GMU5.1 C3GMU5_BACTU Ribosome maturation factor rimM Length = 171 Score = 201 bits (512), Expect = 1e-50, Method: Compositional matrix adjust. Identities = 95/173 (54%), Positives = 131/173 (75%), Gaps = 2/173 (1%) Query: 1 MTEELNVGRLVNTHGIRGEIKILSSTDFPEVRFAPGKKLLVVPADGSQKFEVTVESSREH 60 MT+ NVG++VNTHG++GEI+++S TDFPE R+ G L + G + F V + S R+H Sbjct: 1 MTKWFNVGKIVNTHGVKGEIRVVSRTDFPEERYKVGNTLYISNEKGGEPFPVKITSHRQH 60 Query: 61 KGMYIVRLKGYTNINQIEKYKGSLLKVPGDDLVELPENEYYFHQIVGCEVYTDEDDSRPL 120 K ++ +GY N+N++E++KGSLLKVP D L EL E EYY+H+I+GC V T+E ++ L Sbjct: 61 KTFDLLTFEGYGNVNEVEQFKGSLLKVPEDQLGELAEGEYYYHEIIGCNVVTEEGEA--L 118 Query: 121 GTIKEILQPGANDVWVVKPVKGQDILIPVINDVVLDVDIQAKKITVHLMEGLL 173 GTIKE+L PGANDVWV+K KGQD+LIP I+DVVL V+I+ K +T+H+MEGLL Sbjct: 119 GTIKEVLSPGANDVWVIKRPKGQDLLIPYIDDVVLQVNIENKLVTIHVMEGLL 171 >C3G6W3.1 C3G6W3_BACTU Ribosome maturation factor rimM Length = 171 Score = 201 bits (512), Expect = 1e-50, Method: Compositional matrix adjust. Identities = 95/173 (54%), Positives = 131/173 (75%), Gaps = 2/173 (1%) Query: 1 MTEELNVGRLVNTHGIRGEIKILSSTDFPEVRFAPGKKLLVVPADGSQKFEVTVESSREH 60 MT+ NVG++VNTHG++GEI+++S TDFPE R+ G L + G + F V + S R+H Sbjct: 1 MTKWFNVGKIVNTHGVKGEIRVVSRTDFPEERYKVGNTLYISNEKGGEPFPVKITSHRQH 60 Query: 61 KGMYIVRLKGYTNINQIEKYKGSLLKVPGDDLVELPENEYYFHQIVGCEVYTDEDDSRPL 120 K ++ +GY N+N++E++KGSLLKVP D L EL E EYY+H+I+GC V T+E ++ L Sbjct: 61 KTFDLLTFEGYGNVNEVEQFKGSLLKVPEDQLGELAEGEYYYHEIIGCNVVTEEGEA--L 118 Query: 121 GTIKEILQPGANDVWVVKPVKGQDILIPVINDVVLDVDIQAKKITVHLMEGLL 173 GTIKE+L PGANDVWV+K KGQD+LIP I+DVVL V+I+ K +T+H+MEGLL Sbjct: 119 GTIKEVLSPGANDVWVIKRPKGQDLLIPYIDDVVLQVNIENKLVTIHVMEGLL 171 >C3F5V3.1 C3F5V3_BACTU Ribosome maturation factor rimM Length = 171 Score = 201 bits (512), Expect = 1e-50, Method: Compositional matrix adjust. Identities = 95/173 (54%), Positives = 131/173 (75%), Gaps = 2/173 (1%) Query: 1 MTEELNVGRLVNTHGIRGEIKILSSTDFPEVRFAPGKKLLVVPADGSQKFEVTVESSREH 60 MT+ NVG++VNTHG++GEI+++S TDFPE R+ G L + G + F V + S R+H Sbjct: 1 MTKWFNVGKIVNTHGVKGEIRVVSRTDFPEERYKVGNTLYISNEKGGEPFPVKITSHRQH 60 Query: 61 KGMYIVRLKGYTNINQIEKYKGSLLKVPGDDLVELPENEYYFHQIVGCEVYTDEDDSRPL 120 K ++ +GY N+N++E++KGSLLKVP D L EL E EYY+H+I+GC V T+E ++ L Sbjct: 61 KTFDLLTFEGYGNVNEVEQFKGSLLKVPEDQLGELAEGEYYYHEIIGCNVVTEEGEA--L 118 Query: 121 GTIKEILQPGANDVWVVKPVKGQDILIPVINDVVLDVDIQAKKITVHLMEGLL 173 GTIKE+L PGANDVWV+K KGQD+LIP I+DVVL V+I+ K +T+H+MEGLL Sbjct: 119 GTIKEVLSPGANDVWVIKRPKGQDLLIPYIDDVVLQVNIENKLVTIHVMEGLL 171 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.317 0.140 0.402 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 1,077,776,907 Number of extensions: 44469522 Number of successful extensions: 99210 Number of sequences better than 1.0e-05: 1119 Number of HSP's gapped: 97611 Number of HSP's successfully gapped: 1119 Length of query: 174 Length of database: 3,060,696,203 Length adjustment: 126 Effective length of query: 48 Effective length of database: 1,873,648,313 Effective search space: 89935119024 Effective search space used: 89935119024 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 126 (53.1 bits)