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= 0476.0004.p (99 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_243231.1| host factor-1 protein [Bacillus halodurans] >gi... 116 2e-25 ref|NP_657675.1| hypothetical protein predicted by GeneMark [Bac... 111 6e-24 ref|NP_692556.1| host factor-1 protein [Oceanobacillus iheyensis... 109 2e-23 ref|NP_389616.1| similar to host factor-1 protein [Bacillus subt... 105 4e-22 ref|ZP_00182651.1| hypothetical protein Exigu200301 [Exiguobacte... 101 7e-21 >ref|NP_243231.1| host factor-1 protein [Bacillus halodurans] sp|Q9KAC4|HFQ_BACHD Hfq protein pir||E83945 host factor-1 protein BH2365 [imported] - Bacillus halodurans (strain C-125) dbj|BAB06084.1| host factor-1 protein [Bacillus halodurans] Length = 78 Score = 116 bits (291), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 48/71 (67%), Positives = 63/71 (88%) Query: 1 MNKSINIQDTFLNQLRKENIPATVYLTNGFQIRGIIKAFDNFTIVIDSDGRQQMVYKHAI 60 M S+NIQD FLNQLRKENIP TV+L NGFQ+RG++K FDNFT++++++G+QQ+VYKHAI Sbjct: 1 MKSSVNIQDHFLNQLRKENIPVTVFLLNGFQLRGLVKGFDNFTVILETEGKQQLVYKHAI 60 Query: 61 STFTPQRSVSL 71 STF PQR+V + Sbjct: 61 STFAPQRNVQM 71 >ref|NP_657675.1| hypothetical protein predicted by GeneMark [Bacillus anthracis A2012] ref|NP_833439.1| Hfq protein [Bacillus cereus ATCC 14579] ref|NP_846093.1| host factor-I protein [Bacillus anthracis str. Ames] ref|NP_980037.1| host factor-I protein [Bacillus cereus ATCC 10987] gb|AAP10640.1| Hfq protein [Bacillus cereus ATCC 14579] gb|AAP27579.1| host factor-I protein [Bacillus anthracis str. Ames] gb|AAS42645.1| host factor-I protein [Bacillus cereus ATCC 10987] Length = 74 Score = 111 bits (277), Expect = 6e-24, Method: Compositional matrix adjust. Identities = 47/71 (66%), Positives = 63/71 (88%) Query: 1 MNKSINIQDTFLNQLRKENIPATVYLTNGFQIRGIIKAFDNFTIVIDSDGRQQMVYKHAI 60 M +SINIQD FLNQLRKEN T+YL NGFQ+RG+IK FDNFT++++++G+QQ++YKHAI Sbjct: 1 MKQSINIQDQFLNQLRKENTFVTLYLLNGFQLRGLIKGFDNFTVLLETEGKQQLIYKHAI 60 Query: 61 STFTPQRSVSL 71 STF PQ++VS+ Sbjct: 61 STFVPQKNVSI 71 >ref|NP_692556.1| host factor-1 protein [Oceanobacillus iheyensis HTE831] dbj|BAC13591.1| host factor-1 protein [Oceanobacillus iheyensis HTE831] Length = 74 Score = 109 bits (272), Expect = 2e-23, Method: Compositional matrix adjust. Identities = 45/71 (63%), Positives = 65/71 (91%) Query: 1 MNKSINIQDTFLNQLRKENIPATVYLTNGFQIRGIIKAFDNFTIVIDSDGRQQMVYKHAI 60 M +S+NIQD +LNQLRK +I TV+LTNGFQ+RG++KAFDNFT+++++DG+QQ+++KHAI Sbjct: 1 MAQSVNIQDQYLNQLRKNHISVTVFLTNGFQLRGLVKAFDNFTVLLETDGKQQLIFKHAI 60 Query: 61 STFTPQRSVSL 71 STF+P ++VSL Sbjct: 61 STFSPVKNVSL 71 >ref|NP_389616.1| similar to host factor-1 protein [Bacillus subtilis] sp|O31796|HFQ_BACSU Hfq protein pir||B69884 host factor-1 protein homolog ymaH - Bacillus subtilis emb|CAB13618.1| ymaH [Bacillus subtilis subsp. subtilis str. 168] Length = 73 Score = 105 bits (261), Expect = 4e-22, Method: Compositional matrix adjust. Identities = 45/69 (65%), Positives = 59/69 (85%) Query: 3 KSINIQDTFLNQLRKENIPATVYLTNGFQIRGIIKAFDNFTIVIDSDGRQQMVYKHAIST 62 K INIQD FLNQ+RKEN TV+L NGFQ+RG +K FDNFT++++S+G+QQ++YKHAIST Sbjct: 2 KPINIQDQFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLLESEGKQQLIYKHAIST 61 Query: 63 FTPQRSVSL 71 F PQ++V L Sbjct: 62 FAPQKNVQL 70 >ref|ZP_00182651.1| hypothetical protein Exigu200301 [Exiguobacterium sp. 255-15] Length = 66 Score = 101 bits (251), Expect = 7e-21, Method: Compositional matrix adjust. Identities = 40/65 (61%), Positives = 58/65 (89%) Query: 1 MNKSINIQDTFLNQLRKENIPATVYLTNGFQIRGIIKAFDNFTIVIDSDGRQQMVYKHAI 60 M + NIQD FLNQLRK+++P TV+L +G+Q+RG+IK+FDNFT++++S+G+QQ++YKHAI Sbjct: 1 MKATYNIQDYFLNQLRKDSVPTTVFLISGYQLRGLIKSFDNFTVILESEGKQQLIYKHAI 60 Query: 61 STFTP 65 STF P Sbjct: 61 STFAP 65 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.323 0.136 0.375 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 124,923,425 Number of extensions: 4161467 Number of successful extensions: 8292 Number of sequences better than 1.0e-05: 113 Number of HSP's gapped: 8232 Number of HSP's successfully gapped: 114 Length of query: 99 Length of database: 757,237,578 Length adjustment: 66 Effective length of query: 33 Effective length of database: 578,041,044 Effective search space: 19075354452 Effective search space used: 19075354452 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 120 (50.8 bits)