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= 0001.4256.p (239 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313671|ref|YP_003777763.1| OmpA family protein [Herbaspiri... 327 4e-91 gi|300312990|ref|YP_003777082.1| signal peptide protein [Herbasp... 82 3e-17 gi|300313316|ref|YP_003777408.1| lipoprotein [Herbaspirillum ser... 79 4e-16 gi|300310091|ref|YP_003774183.1| outer membrane protein and rela... 75 5e-15 gi|300310619|ref|YP_003774711.1| OmpA protein [Herbaspirillum se... 55 4e-09 >gi|300313671|ref|YP_003777763.1| OmpA family protein [Herbaspirillum seropedicae SmR1] Length = 241 Score = 327 bits (839), Expect = 4e-91, Method: Compositional matrix adjust. Identities = 223/242 (92%), Positives = 231/242 (95%), Gaps = 4/242 (1%) Query: 1 MKKLSIAAIAGVLALSGCADMSPTQRGTATGAGIGAGIGGIIGAATGGGGGGRALGGAAI 60 MKKLSIAAIAGVLALSGCADMSPTQRGTATGAGIGAG+GGIIGAATGGGGGGRALGGAAI Sbjct: 1 MKKLSIAAIAGVLALSGCADMSPTQRGTATGAGIGAGLGGIIGAATGGGGGGRALGGAAI 60 Query: 61 GGAIGAVAGNIWSNRMENQKRAMEQATQGTGVQVTQTADNRLKLEIPSDISFDTGRADIK 120 GGAIGAVAGNIWSNRMENQKRAME+ATQGTGVQV+QTADNRLKLEIPSDISFDTGRADIK Sbjct: 61 GGAIGAVAGNIWSNRMENQKRAMEEATQGTGVQVSQTADNRLKLEIPSDISFDTGRADIK 120 Query: 121 PEMRPVLDRFAATLVENPATTVTIVGHTDNTGSDAINDPLSQERAARTRDYLTSRGVAAN 180 PEMRPVLDRFAATLVENPATTVTIVGHTDNTGSDAINDPLS +RA+RTRDYL+SRGVAAN Sbjct: 121 PEMRPVLDRFAATLVENPATTVTIVGHTDNTGSDAINDPLSLQRASRTRDYLSSRGVAAN 180 Query: 181 RFTIMGRGSHEPLVPNTSDANRAKNRRVEIFVAEQQAAAPAQQPPGGYAPGGY---PPPQ 237 RF+I GRGSHEPLV NTSDANRA+NRRVEIFVAEQQAAA QQ P GYAPG Y PPPQ Sbjct: 181 RFSIQGRGSHEPLVANTSDANRARNRRVEIFVAEQQAAA-PQQAPAGYAPGNYPPPPPPQ 239 Query: 238 RY 239 RY Sbjct: 240 RY 241 >gi|300312990|ref|YP_003777082.1| signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 203 Score = 82.4 bits (202), Expect = 3e-17, Method: Compositional matrix adjust. Identities = 46/110 (41%), Positives = 59/110 (53%) Query: 103 KLEIPSDISFDTGRADIKPEMRPVLDRFAATLVENPATTVTIVGHTDNTGSDAINDPLSQ 162 K+ +D FD +A +KP + LD L + VGHTD+ GS A N LS Sbjct: 89 KVTYAADAFFDFDKATLKPAGKAKLDELVGNLKAINLEVIIAVGHTDSIGSVAYNQKLSV 148 Query: 163 ERAARTRDYLTSRGVAANRFTIMGRGSHEPLVPNTSDANRAKNRRVEIFV 212 RA + YL S+GV ANR G+G +P+ N + A RAKNRRVEI V Sbjct: 149 RRAESVKAYLVSKGVEANRVYTEGKGKSQPVADNKTAAGRAKNRRVEIEV 198 >gi|300313316|ref|YP_003777408.1| lipoprotein [Herbaspirillum seropedicae SmR1] Length = 267 Score = 78.6 bits (192), Expect = 4e-16, Method: Compositional matrix adjust. Identities = 41/105 (39%), Positives = 64/105 (60%) Query: 110 ISFDTGRADIKPEMRPVLDRFAATLVENPATTVTIVGHTDNTGSDAINDPLSQERAARTR 169 +SF++GRA + PE + +LD AAT+++ V I+G+TDN G A N LS RA + Sbjct: 163 VSFESGRATLTPEGKRILDEIAATMLQLKGRRVEIIGNTDNEGLRASNISLSLARADAVK 222 Query: 170 DYLTSRGVAANRFTIMGRGSHEPLVPNTSDANRAKNRRVEIFVAE 214 YL+++GV + T G+G P+ N + RA+NRR+E +A+ Sbjct: 223 AYLSTKGVDDSLLTTSGQGPDRPVASNATSEGRARNRRIEFRIAK 267 >gi|300310091|ref|YP_003774183.1| outer membrane protein and related peptidoglycan-associated (lipo)proteins [Herbaspirillum seropedicae SmR1] Length = 271 Score = 75.1 bits (183), Expect = 5e-15, Method: Compositional matrix adjust. Identities = 40/105 (38%), Positives = 63/105 (60%) Query: 110 ISFDTGRADIKPEMRPVLDRFAATLVENPATTVTIVGHTDNTGSDAINDPLSQERAARTR 169 +SF++G+A + PE + +LD AAT+++ V I+G+TDN G A N LS RA + Sbjct: 167 VSFESGQATLTPEGKRILDEIAATMLKLKGRHVEIIGNTDNEGLRASNISLSLARADAVK 226 Query: 170 DYLTSRGVAANRFTIMGRGSHEPLVPNTSDANRAKNRRVEIFVAE 214 YL ++GV + + G+G P+ N + RAKNRR+E +A+ Sbjct: 227 AYLGAKGVDESLLSTSGQGPDRPVASNATAEGRAKNRRIEFRIAK 271 >gi|300310619|ref|YP_003774711.1| OmpA protein [Herbaspirillum seropedicae SmR1] Length = 190 Score = 55.5 bits (132), Expect = 4e-09, Method: Compositional matrix adjust. Identities = 33/104 (31%), Positives = 49/104 (47%) Query: 109 DISFDTGRADIKPEMRPVLDRFAATLVENPATTVTIVGHTDNTGSDAINDPLSQERAART 168 D+ F+ G + P + L + A + + PA + GH DN GS+ ND LS RA Sbjct: 86 DLLFELGTDRLTPASQDALKKAIAEIKDFPAGEFVLTGHADNIGSETNNDALSLRRARLI 145 Query: 169 RDYLTSRGVAANRFTIMGRGSHEPLVPNTSDANRAKNRRVEIFV 212 L V A ++G+G+ +P VP +NR VEI + Sbjct: 146 ERELRRADVKALSIEVIGKGARDPRVPQKRGVAEPRNRFVEIKI 189 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 0.314 0.132 0.380 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: 458,419 Number of extensions: 14731 Number of successful extensions: 53 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 53 Number of HSP's successfully gapped: 5 Length of query: 239 Length of database: 1,619,870 Length adjustment: 82 Effective length of query: 157 Effective length of database: 1,231,600 Effective search space: 193361200 Effective search space used: 193361200 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: 129 (54.3 bits)