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= 0001.4110.p (273 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313159|ref|YP_003777251.1| AraC family transcription regul... 84 8e-18 gi|300313797|ref|YP_003777889.1| AraC family transcription regul... 72 5e-14 gi|300313807|ref|YP_003777899.1| AraC family transcription regul... 71 1e-13 gi|300311760|ref|YP_003775852.1| transcription regulator protein... 68 7e-13 gi|300311726|ref|YP_003775818.1| AraC family transcription regul... 68 8e-13 >gi|300313159|ref|YP_003777251.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 280 Score = 84.3 bits (207), Expect = 8e-18, Method: Compositional matrix adjust. Identities = 67/248 (27%), Positives = 107/248 (43%), Gaps = 15/248 (6%) Query: 12 FGKHTHEQFGVGLILRGAQKSASQCGVVEATAGDIITVNPEEVHDGTPLGEGGRAWQMLY 71 + HTH+ F +G++ G A GD++ V +VH P +++M + Sbjct: 39 YAPHTHDSFSIGIVDAGHSIFALAEHSQPIAPGDVVLVRAGDVHCCNPADLQCWSYRMFH 98 Query: 72 LDVAVVQATVADLNETGPRTCMEFPQPRR----RDPALTRIFRHHVQAVTRSSSDWTLPG 127 ++ + +A+ T P+ R R P ++ A+ +S+ Sbjct: 99 IEHGWLSTLLAETPAT-----RGLPERMRSQVLRSPQAVQLLDRMTLALDHDASERVAEV 153 Query: 128 ----DESLLLLLQALLRPACPKPGYADLRAITRAKSWINEQPAHAWTLAELAREADLSRF 183 E +LL +A A P D + RA + + + + +L ELA A + R+ Sbjct: 154 ITCLQEIMLLCAEACAHDAAPLT--EDAHGLGRAYAHLQQHCRRSVSLDELAEVAGMGRY 211 Query: 184 QFIRHFDRATGLTPHAYIVQRRIHLARQMIRQGCSLRDVAASCGFADQSHMTRQFVRSFG 243 Q IR F R G+TPHA + +I AR +++QG S D A GFADQSH R F Sbjct: 212 QLIRQFRRRYGMTPHALQLDMKIRQARTLLQQGASAADAAYDTGFADQSHFHRAFKSRVA 271 Query: 244 LSPGAYAR 251 +P Y R Sbjct: 272 ATPLQYTR 279 >gi|300313797|ref|YP_003777889.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 294 Score = 72.0 bits (175), Expect = 5e-14, Method: Compositional matrix adjust. Identities = 38/98 (38%), Positives = 62/98 (63%), Gaps = 1/98 (1%) Query: 155 TRAKSWINEQPAHAWTLAELAREADLSRFQFIRHFDRATGLTPHAYIVQRRIHLARQMIR 214 R + ++ A +LAE+A ++ LSR F R F ++ GL+PHA++ Q+RI LA +++ Sbjct: 194 ARVRDFMLSHLAQRLSLAEIAAQSGLSRAHFSRAFKQSFGLSPHAWLQQQRIALACRLLH 253 Query: 215 QGC-SLRDVAASCGFADQSHMTRQFVRSFGLSPGAYAR 251 +G S+ +A CGF+DQSH +R F + G+ P A+ R Sbjct: 254 EGGKSMTTIALECGFSDQSHFSRVFKQVQGMGPAAWLR 291 >gi|300313807|ref|YP_003777899.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 70.9 bits (172), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 36/97 (37%), Positives = 61/97 (62%), Gaps = 1/97 (1%) Query: 156 RAKSWINEQPAHAWTLAELAREADLSRFQFIRHFDRATGLTPHAYIVQRRIHLARQMIRQ 215 RAK + E+ ++ E+ARE ++S F+R F +TG TPH +++ +R+ +A+Q +R Sbjct: 200 RAKMMLLEKVKGNVSIPEIARECNMSASYFLRAFKASTGHTPHQWLMVQRVEMAQQYLRS 259 Query: 216 G-CSLRDVAASCGFADQSHMTRQFVRSFGLSPGAYAR 251 +L ++A +C F DQSH +R F + G +PGA+ R Sbjct: 260 TQLTLAEIALACDFYDQSHFSRVFSQVVGSTPGAWRR 296 >gi|300311760|ref|YP_003775852.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 319 Score = 68.2 bits (165), Expect = 7e-13, Method: Compositional matrix adjust. Identities = 49/150 (32%), Positives = 71/150 (47%), Gaps = 15/150 (10%) Query: 101 RDPALTRIFRHHVQAVTRSSSDWTLPGDESLLLLLQALLRPACPKPGYADLRAITRAKSW 160 R+ L R+ + RSS+D T+ LL G AD+R + +A Sbjct: 166 REVVLARLLEVLLIEALRSSNDPTVAASPGLLR-------------GLADVR-LAQAIRA 211 Query: 161 INEQPAHAWTLAELAREADLSRFQFIRHFDRATGLTPHAYIVQRRIHLA-RQMIRQGCSL 219 ++ QPA W + LAR A LSR F F R GLTP Y++ R+ LA R ++R S+ Sbjct: 212 LHAQPAQDWNVPRLARVAALSRSSFFERFRREVGLTPMDYLLAWRMALAKRLLLRADGSI 271 Query: 220 RDVAASCGFADQSHMTRQFVRSFGLSPGAY 249 +VA G++ S + F R GL P + Sbjct: 272 AEVALQVGYSSASTFSVAFSRHVGLPPSQF 301 >gi|300311726|ref|YP_003775818.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 304 Score = 67.8 bits (164), Expect = 8e-13, Method: Compositional matrix adjust. Identities = 51/168 (30%), Positives = 78/168 (46%), Gaps = 21/168 (12%) Query: 112 HVQAVTRSSSDWTL---------PGDESLL------LLLQALLRPACPKPGYADLRAITR 156 HVQ TR S + PG E +L LL++A+ LR + Sbjct: 135 HVQGSTRLSQLVQMVGEEASGGKPGSEFMLSRLAEMLLVEAMRSSTSTSAPPGLLRGLGD 194 Query: 157 AKSWINEQPAHA-----WTLAELAREADLSRFQFIRHFDRATGLTPHAYIVQRRIHLARQ 211 + + + HA W++A+LAR A LSR F F R G+ P AY++ R+ +AR+ Sbjct: 195 ERLAVALKHMHARIEQRWSVAQLARIAALSRSSFFERFTRTLGVAPMAYLLAWRMEIARE 254 Query: 212 MIRQG-CSLRDVAASCGFADQSHMTRQFVRSFGLSPGAYARAVSGARQ 258 ++R+G S+ ++A G+ S + F R G PG YA S R+ Sbjct: 255 LLRRGELSVSEIAERTGYGSTSAFSVAFTRQVGQPPGLYALYASAERK 302 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 0.324 0.135 0.417 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: 879,179 Number of extensions: 35287 Number of successful extensions: 178 Number of sequences better than 1.0e-08: 9 Number of HSP's gapped: 179 Number of HSP's successfully gapped: 9 Length of query: 273 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 189 Effective length of database: 1,222,130 Effective search space: 230982570 Effective search space used: 230982570 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 130 (54.7 bits)