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= 0025.0012.p (139 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311850|ref|YP_003775942.1| AraC family transcription regul... 92 2e-20 gi|300313912|ref|YP_003778004.1| AraC family transcription regul... 82 1e-17 gi|300313081|ref|YP_003777173.1| transcription regulator protein... 77 7e-16 gi|300312798|ref|YP_003776890.1| AraC family transcription regul... 72 2e-14 gi|300313797|ref|YP_003777889.1| AraC family transcription regul... 63 8e-12 >gi|300311850|ref|YP_003775942.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 343 Score = 91.7 bits (226), Expect = 2e-20, Method: Compositional matrix adjust. Identities = 48/136 (35%), Positives = 81/136 (59%), Gaps = 4/136 (2%) Query: 2 AKRLIVYIRREGGQSQYSPYLAVGPGEDSLVAKVLKYVTDHISDALTIEEIAAFAKHANV 61 A++L+++I+R GGQSQ+S LA A++ ++ H++D L +E +A A + Sbjct: 196 ARQLVMFIKRPGGQSQFSTPLATQSTGAGRFAELHAWIAAHLADDLHVENLA---HRAGM 252 Query: 62 TP-SFSRAFAKHANVTPSVFVEQVRIDFARKLLEETDVPLKTVAFRCGFSNATQMRMIFS 120 +P +F+R + TP+ VE +R++ AR+ LEET +PLK +A + G+ +R +F Sbjct: 253 SPRTFARLYVAETGRTPARTVELMRLEAARRALEETRLPLKRIASQAGYGEEQNLRRVFL 312 Query: 121 RQLNTTPKAYRDGFRA 136 RQL +P YR+ F A Sbjct: 313 RQLGVSPGQYRERFAA 328 >gi|300313912|ref|YP_003778004.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 313 Score = 82.4 bits (202), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 46/137 (33%), Positives = 77/137 (56%), Gaps = 5/137 (3%) Query: 1 VAKRLIVYIRREGGQSQYSPYLAVGPGEDSLVAKVLKYVTDHISDALTIEEIAAFAKHAN 60 VA++L+++ R GGQSQ+S L + P D + L Y ++ ALT+EE+A + AN Sbjct: 181 VARKLVMHQHRAGGQSQHSEMLELAPKTDR-IQDALNYARRNLKRALTVEELA---EQAN 236 Query: 61 VTP-SFSRAFAKHANVTPSVFVEQVRIDFARKLLEETDVPLKTVAFRCGFSNATQMRMIF 119 ++ F+R F +P+ +E +R++ AR ++E++ PL+ VA GF + MR +F Sbjct: 237 LSARQFTRVFTSETGQSPAKAIEGLRLEAARLMIEQSRHPLEVVARETGFRDRRHMREVF 296 Query: 120 SRQLNTTPKAYRDGFRA 136 R P++ R RA Sbjct: 297 LRGFGVAPQSMRREGRA 313 >gi|300313081|ref|YP_003777173.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 330 Score = 76.6 bits (187), Expect = 7e-16, Method: Compositional matrix adjust. Identities = 48/142 (33%), Positives = 76/142 (53%), Gaps = 9/142 (6%) Query: 1 VAKRLIVYIRREGGQSQYSPYLAVGPGEDSLVAKVLKYVTDHISDALTIE---EIAAFAK 57 VA+ L+VY RR GGQSQ+S + G + + + L + +H+ ALT++ E+A ++ Sbjct: 183 VARELVVYHRRPGGQSQFSALQEMDGGSER-IRRALGFAREHLHQALTVDLLAEVACLSR 241 Query: 58 HANVTPSFSRAFAKHANVTPSVFVEQVRIDFARKLLEETDVPLKTVAFRCGFSNATQMRM 117 F RAFA TP+ +EQ+R + AR +E++ L+++A GF +A +MR Sbjct: 242 R-----QFDRAFAAETGQTPARAIEQMRAEAARLRIEQSQDTLESIARATGFGDADRMRR 296 Query: 118 IFSRQLNTTPKAYRDGFRAGRD 139 R P+A R RA D Sbjct: 297 ACLRLFGQPPQAMRRLARAEDD 318 >gi|300312798|ref|YP_003776890.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 335 Score = 71.6 bits (174), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 39/132 (29%), Positives = 70/132 (53%), Gaps = 4/132 (3%) Query: 1 VAKRLIVYIRREGGQSQYSPYLAVGPGEDSLVAKVLKYVTDHISDALTIEEIAAFAKHAN 60 +A+ L++++ R G Q Q S L L + +L ++ DH + +++ A A+ A Sbjct: 201 IARDLVLFLHRPGRQQQISATLVAQQSAGDLFSALLVWMLDHPQEDMSVN---ALAERAA 257 Query: 61 VTP-SFSRAFAKHANVTPSVFVEQVRIDFARKLLEETDVPLKTVAFRCGFSNATQMRMIF 119 ++P +F+R F + P +V ++RID A + LE+T ++ +A R G NA + +F Sbjct: 258 MSPRNFARRFLREVGKPPGQYVLELRIDHACRHLEKTGWSIERIAERSGLKNADTLHRVF 317 Query: 120 SRQLNTTPKAYR 131 + L TP YR Sbjct: 318 RQHLGMTPAQYR 329 >gi|300313797|ref|YP_003777889.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 294 Score = 63.2 bits (152), Expect = 8e-12, Method: Compositional matrix adjust. Identities = 36/126 (28%), Positives = 62/126 (49%), Gaps = 2/126 (1%) Query: 5 LIVYIRREGGQSQYSPYLAVGPGEDSLVAKVLKYVTDHISDALTIEEIAAFAKHANVTPS 64 L ++ + GQ P A G A+V ++ H++ L++ EIAA + + Sbjct: 166 LTTHLWQRYGQQSSRPASAAGRLAGWQEARVRDFMLSHLAQRLSLAEIAAQSGLSRA--H 223 Query: 65 FSRAFAKHANVTPSVFVEQVRIDFARKLLEETDVPLKTVAFRCGFSNATQMRMIFSRQLN 124 FSRAF + ++P +++Q RI A +LL E + T+A CGFS+ + +F + Sbjct: 224 FSRAFKQSFGLSPHAWLQQQRIALACRLLHEGGKSMTTIALECGFSDQSHFSRVFKQVQG 283 Query: 125 TTPKAY 130 P A+ Sbjct: 284 MGPAAW 289 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 0.322 0.134 0.382 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: 399,627 Number of extensions: 13615 Number of successful extensions: 66 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 63 Number of HSP's successfully gapped: 6 Length of query: 139 Length of database: 1,619,870 Length adjustment: 76 Effective length of query: 63 Effective length of database: 1,260,010 Effective search space: 79380630 Effective search space used: 79380630 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 126 (53.1 bits)