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= 0001.0299.p (115 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309668|ref|YP_003773760.1| HU histone family DNA-binding p... 224 1e-60 gi|300311300|ref|YP_003775392.1| integration host factor alpha-s... 65 1e-12 gi|300312982|ref|YP_003777074.1| integration host factor subunit... 57 4e-10 >gi|300309668|ref|YP_003773760.1| HU histone family DNA-binding protein [Herbaspirillum seropedicae SmR1] Length = 115 Score = 224 bits (571), Expect = 1e-60, Method: Compositional matrix adjust. Identities = 113/115 (98%), Positives = 115/115 (100%) Query: 1 LRIRLIPVLKSGHLNSERNFKVNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKG 60 +RIRLIPVLKSGHLNSERNF+VNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKG Sbjct: 1 MRIRLIPVLKSGHLNSERNFQVNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKG 60 Query: 61 DTVQLVGFGSFSTGKRAARTGRNPQTGEEIKIAAATTVKFSAGKAFKEAVNKKKK 115 DTVQLVGFGSFSTGKRAARTGRNPQTGEEIKIAAATTVKFSAGKAFKEAVNKKKK Sbjct: 61 DTVQLVGFGSFSTGKRAARTGRNPQTGEEIKIAAATTVKFSAGKAFKEAVNKKKK 115 >gi|300311300|ref|YP_003775392.1| integration host factor alpha-subunit [Herbaspirillum seropedicae SmR1] Length = 104 Score = 65.1 bits (157), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 32/89 (35%), Positives = 52/89 (58%) Query: 22 VNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKGDTVQLVGFGSFSTGKRAARTG 81 + K+EL +++ ++K A+ +++ + I A+ +G+ V+L GFG+F + R G Sbjct: 4 LTKAELAELLFEQVGLNKREAKDMVETFFDEIRNALERGEAVKLSGFGNFQLRDKPQRPG 63 Query: 82 RNPQTGEEIKIAAATTVKFSAGKAFKEAV 110 RNP+TGEEI I A V F A + KE V Sbjct: 64 RNPKTGEEIPITARRVVTFHASQKLKEMV 92 >gi|300312982|ref|YP_003777074.1| integration host factor subunit beta [Herbaspirillum seropedicae SmR1] Length = 101 Score = 57.0 bits (136), Expect = 4e-10, Method: Compositional matrix adjust. Identities = 26/91 (28%), Positives = 52/91 (57%), Gaps = 1/91 (1%) Query: 22 VNKSELVDVIAAD-TEISKAAAQRALDSVIENIIKAVTKGDTVQLVGFGSFSTGKRAART 80 + KSEL+ +A ++ A A+ ++++ ++ A+ G +++ GFGSF+ +R R Sbjct: 1 MTKSELIARLAERYPQLVAKDADYAVKTILDAMVDALATGQRIEIRGFGSFALNRRPPRI 60 Query: 81 GRNPQTGEEIKIAAATTVKFSAGKAFKEAVN 111 GRNP++G+++ + F GK +E V+ Sbjct: 61 GRNPKSGDKVMVPEKRVPHFKPGKELRERVD 91 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.313 0.128 0.331 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 265,170 Number of extensions: 8349 Number of successful extensions: 37 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 37 Number of HSP's successfully gapped: 3 Length of query: 115 Length of database: 1,619,870 Length adjustment: 73 Effective length of query: 42 Effective length of database: 1,274,215 Effective search space: 53517030 Effective search space used: 53517030 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 124 (52.4 bits)