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= 0004.0002.p (90 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 sp|P02346|DBH_BACST DNA-binding protein HU (DNA-binding protein ... 114 5e-25 prf||1702428A DNA binding protein HU 114 6e-25 ref|NP_831289.1| DNA-binding protein HU [Bacillus cereus ATCC 14... 113 1e-24 ref|NP_692713.1| non-specific DNA-binding protein [Oceanobacillu... 113 2e-24 ref|NP_655411.1| Bac_DNA_binding, Bacterial DNA-binding protein ... 113 2e-24 >sp|P02346|DBH_BACST DNA-binding protein HU (DNA-binding protein II) (HB) pir||DNBS2F DNA-binding protein HU - Bacillus stearothermophilus pir||JC1207 DNA-binding protein HU - Bacillus caldolyticus pir||JC1206 DNA-binding protein HU - Bacillus caldotenax pdb|1HUE|A Chain A, Histone-Like Protein pdb|1HUE|B Chain B, Histone-Like Protein pdb|1HUU|A Chain A, Dna-Binding Protein Hu From Bacillus Stearothermophilus pdb|1HUU|B Chain B, Dna-Binding Protein Hu From Bacillus Stearothermophilus pdb|1HUU|C Chain C, Dna-Binding Protein Hu From Bacillus Stearothermophilus gb|AAA22532.1| hubst gb|AAA22533.1| hubcalx gb|AAA22534.1| hubcald dbj|BAA07273.1| DNA binding protein HU [Geobacillus stearothermophilus] Length = 90 Score = 114 bits (286), Expect = 5e-25, Method: Compositional matrix adjust. Identities = 54/89 (60%), Positives = 67/89 (75%) Query: 1 MNKTDLVNNISEKSGLAKKDVETVLNGVLGEITDALAQGDKVQLIGFGTFETRKRSGRSG 60 MNKT+L+N ++E SGL+KKD ++ V IT+AL +GDKVQLIGFG FE R+R+ R G Sbjct: 1 MNKTELINAVAETSGLSKKDATKAVDAVFDSITEALRKGDKVQLIGFGNFEVRERAARKG 60 Query: 61 RNPQTGTPIEIPESTVPAFKAGNKLKEAV 89 RNPQTG +EIP S VPAFK G LK+AV Sbjct: 61 RNPQTGEEMEIPASKVPAFKPGKALKDAV 89 >prf||1702428A DNA binding protein HU Length = 90 Score = 114 bits (285), Expect = 6e-25, Method: Compositional matrix adjust. Identities = 54/89 (60%), Positives = 67/89 (75%) Query: 1 MNKTDLVNNISEKSGLAKKDVETVLNGVLGEITDALAQGDKVQLIGFGTFETRKRSGRSG 60 MNKT+L+N ++E SGL+KKD ++ V IT+AL +GDKVQLIGFG FE R+R+ R G Sbjct: 1 MNKTELINTVAEISGLSKKDATKAVDAVFESITEALKKGDKVQLIGFGNFEVRERAARKG 60 Query: 61 RNPQTGTPIEIPESTVPAFKAGNKLKEAV 89 RNPQTG +EIP S VPAFK G LK+AV Sbjct: 61 RNPQTGEEMEIPASKVPAFKPGKALKDAV 89 >ref|NP_831289.1| DNA-binding protein HU [Bacillus cereus ATCC 14579] gb|AAP08490.1| DNA-binding protein HU [Bacillus cereus ATCC 14579] Length = 114 Score = 113 bits (282), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 54/89 (60%), Positives = 64/89 (71%) Query: 1 MNKTDLVNNISEKSGLAKKDVETVLNGVLGEITDALAQGDKVQLIGFGTFETRKRSGRSG 60 MNKTDL+N ++E S L+KKD ++ V I +AL QGDKVQLIGFG FE R+R+ R G Sbjct: 25 MNKTDLINAVAEASSLSKKDATKAVDAVFDSILEALKQGDKVQLIGFGNFEVRERAARKG 84 Query: 61 RNPQTGTPIEIPESTVPAFKAGNKLKEAV 89 RNPQTG IEI S VPAFK G LK+AV Sbjct: 85 RNPQTGEEIEIAASKVPAFKPGKALKDAV 113 >ref|NP_692713.1| non-specific DNA-binding protein [Oceanobacillus iheyensis HTE831] dbj|BAC13748.1| non-specific DNA-binding protein [Oceanobacillus iheyensis HTE831] Length = 90 Score = 113 bits (282), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 54/89 (60%), Positives = 65/89 (73%) Query: 1 MNKTDLVNNISEKSGLAKKDVETVLNGVLGEITDALAQGDKVQLIGFGTFETRKRSGRSG 60 MNKTDLVN ++EKS L+KKD ++ V + D+L G+KVQLIGFG FE R+RS R G Sbjct: 1 MNKTDLVNAVAEKSELSKKDATKAVDAVFESVMDSLKNGEKVQLIGFGNFEVRERSARKG 60 Query: 61 RNPQTGTPIEIPESTVPAFKAGNKLKEAV 89 RNPQTG IEIP S VPAFK G LK++V Sbjct: 61 RNPQTGEEIEIPASKVPAFKPGKALKDSV 89 >ref|NP_655411.1| Bac_DNA_binding, Bacterial DNA-binding protein [Bacillus anthracis A2012] ref|NP_843982.1| DNA-binding protein HU [Bacillus anthracis str. Ames] ref|NP_977958.1| DNA-binding protein HU [Bacillus cereus ATCC 10987] gb|AAP25468.1| DNA-binding protein HU [Bacillus anthracis str. Ames] gb|AAS40566.1| DNA-binding protein HU [Bacillus cereus ATCC 10987] Length = 90 Score = 113 bits (282), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 54/89 (60%), Positives = 64/89 (71%) Query: 1 MNKTDLVNNISEKSGLAKKDVETVLNGVLGEITDALAQGDKVQLIGFGTFETRKRSGRSG 60 MNKTDL+N ++E S L+KKD ++ V I +AL QGDKVQLIGFG FE R+R+ R G Sbjct: 1 MNKTDLINAVAEASSLSKKDATKAVDAVFDSILEALKQGDKVQLIGFGNFEVRERAARKG 60 Query: 61 RNPQTGTPIEIPESTVPAFKAGNKLKEAV 89 RNPQTG IEI S VPAFK G LK+AV Sbjct: 61 RNPQTGEEIEIAASKVPAFKPGKALKDAV 89 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 0.308 0.130 0.351 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: 135,252,323 Number of extensions: 5214516 Number of successful extensions: 11973 Number of sequences better than 1.0e-05: 914 Number of HSP's gapped: 11984 Number of HSP's successfully gapped: 914 Length of query: 90 Length of database: 757,237,578 Length adjustment: 59 Effective length of query: 31 Effective length of database: 597,046,737 Effective search space: 18508448847 Effective search space used: 18508448847 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.6 bits) S2: 120 (50.8 bits)