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= 0012.0007.p (308 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312870|ref|YP_003776962.1| transcription regulator protein... 237 1e-63 gi|300311849|ref|YP_003775941.1| LysR family transcription regul... 107 2e-24 gi|300313810|ref|YP_003777902.1| LysR family transcription regul... 81 9e-17 gi|300313839|ref|YP_003777931.1| MetE/MetH family transcription ... 71 1e-13 gi|300313602|ref|YP_003777694.1| LysR family transcription regul... 67 2e-12 >gi|300312870|ref|YP_003776962.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 312 Score = 237 bits (604), Expect = 1e-63, Method: Compositional matrix adjust. Identities = 130/306 (42%), Positives = 190/306 (62%), Gaps = 4/306 (1%) Query: 2 FRISLDALLILDAIDRRGSFSAAGLELHRVPSTISYTVSKLEQDLGVQVFDRQGPKVVLT 61 ++L++LLILD IDR+GSF+AA + L RVPS ++Y+V KLE DL V +FDR+G + LT Sbjct: 1 MNLTLESLLILDMIDRKGSFAAAAVALDRVPSALTYSVRKLEDDLDVLLFDRRGHRAQLT 60 Query: 62 RAGEELLKEGRYLLKAAEDLEHRVRRVASGWETEFTIGLDSLYSAASLESDIVAFYQVAD 121 AG +LL+EGR+LL AA DLE RV+R A+G ETE I L+SL + I AF + Sbjct: 61 PAGLQLLQEGRHLLLAANDLEQRVKRTATGRETELHIVLNSLIPFDKMLPIIAAFDREQS 120 Query: 122 RTRLRIARESLAGTWEALLDRRVDLLIAAPGEGP----AGGGYVAEQIGTVKFVFVVAPH 177 TRLR L G WE L++ R +L+I +GP G + +++G V +VFVVAP Sbjct: 121 GTRLRFTPGVLTGAWEKLIEGRANLVIGVTLDGPEVVRTSGRFQMQELGAVDWVFVVAPQ 180 Query: 178 HPLAKMDKVLSKADLHPYRAISVADSARKMPPRTVGLLFGQDTLTVPDMRSKYALQLAGV 237 HPLA +++ LS + +RAI+V D+++ +P T+GLL GQ+TLTV + K QLAG+ Sbjct: 181 HPLAGVEEPLSAELVRSHRAIAVGDNSQSLPTLTMGLLSGQETLTVATVADKLQAQLAGL 240 Query: 238 GFGFLPEPCVRKSIASGALVVKEVEQPRAEETFSLAWRVGEDGAALTWWLKRMRETDILN 297 G G LP +ASGALV K+ + + F +AW E G +L W+++ + + + Sbjct: 241 GCGHLPRIWAEPYLASGALVEKQTLAAKPNDNFMVAWPKAEQGKSLKWFIQHLAQPHVRQ 300 Query: 298 RMLSQI 303 ++ + Sbjct: 301 SLIGPV 306 >gi|300311849|ref|YP_003775941.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 309 Score = 107 bits (266), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 87/291 (29%), Positives = 144/291 (49%), Gaps = 10/291 (3%) Query: 3 RISLDALLILDAIDRRGSFSAAGLELHRVPSTISYTVSKLEQDLGVQVFDRQGPKVVLTR 62 R+SLD L + + GSF AA +L R S +SY ++ LE+ LG+ +FDR G + LT Sbjct: 5 RLSLDQLRVFVQVADSGSFLAAARKLARAQSAVSYAIASLEEQLGLLLFDRSGYRPQLTA 64 Query: 63 AGEELLKEGRYLLKAAEDLEHRVRRVASGWETEFTIGLDSLYSAASLESDIVAFYQVADR 122 GE LL + R +L + L+ R A G E E + +D + L + F Sbjct: 65 PGEALLADARQVLDHVDSLQVRASSYARGQELEMALAVDVFFPLDCLVDLLQRFRAAFPA 124 Query: 123 TRLRIARESLAGTWEALLDRR--VDLLIAAPGEGPAGGGYVAEQIGTVKFVFVVAPHHPL 180 +R+ E+L E ++D R + +L P P + + +V+ V VVAPHHPL Sbjct: 125 VTVRLEVEALGAVAERVIDGRAMLGILGTLPTTPP---NLMRITLPSVRLVAVVAPHHPL 181 Query: 181 AKMDKVLSKADLHPYRAISVADSARKMPPRTVGLLFGQDTLTVPDMRSKYALQLAGVGFG 240 AK+ +++ L + ++D + ++ R + + T + D+ +K+AL AG+G+G Sbjct: 182 AKVKGRIAEKMLLQQTQLVLSDRS-ELTARQDFSVHSRLTWRMSDLGTKHALLRAGMGWG 240 Query: 241 FLPEPCVRKSIASGALV-VKEVEQPRAEETFSLAWRVGED---GAALTWWL 287 +P V++ +A+G LV + + P + D G AL+WWL Sbjct: 241 NMPLHVVKEDLAAGRLVSISTIHHPPQGAELPIQCVYKPDHRAGPALSWWL 291 >gi|300313810|ref|YP_003777902.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 301 Score = 81.3 bits (199), Expect = 9e-17, Method: Compositional matrix adjust. Identities = 73/263 (27%), Positives = 114/263 (43%), Gaps = 8/263 (3%) Query: 4 ISLDALLILDAIDRRGSFSAAGLELHRVPSTISYTVSKLEQDLGVQVFDRQGPKVVLTRA 63 S D + + A+ GSFSAA EL RVPS++S T+S+LE +L +Q+FDR T Sbjct: 3 FSSDNVRVFLAVLDSGSFSAAARELGRVPSSVSMTISQLEAELDLQLFDRTARDARPTDM 62 Query: 64 GEELLKEGRYLLKAAEDLEHRVRRVASGWETEFTIGLDSLYSAASLESDIVAFYQVADRT 123 L + R L L+ + G E + T+ + +A + Q Sbjct: 63 ARALEPDARLLASTLRQLDAHALAMHQGLERKLTLAVAPELLSAPWAKPLAVLAQEFPSL 122 Query: 124 RLRIARESLAGTWEALLDRRVDLLIAAPGEGPAGGGYVA-EQIGTVKFVFVVAPHHP-LA 181 + + A L D L + E PAG A ++ + V V+AP HP L Sbjct: 123 EVEVLSSPQADAMRMLYDDTAQLALV--FERPAGNDREAFQEFSSEMLVAVIAPDHPALR 180 Query: 182 KMDKVLSKADLHPYRAISVAD-SARKMPPRTVGLLFGQDTLTVPDMRSKYALQLAGVGFG 240 + + L DL+ R I+VA AR PR + + + +L G+G+ Sbjct: 181 RKKRKLRYEDLYDIRQIAVASRDARVSDPR---FFLARQIWRTDNHLATLSLVREGLGWA 237 Query: 241 FLPEPCVRKSIASGALVVKEVEQ 263 +LP+ V+ I +GAL V + + Sbjct: 238 YLPQSLVQAQIEAGALTVIDFDN 260 >gi|300313839|ref|YP_003777931.1| MetE/MetH family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 295 Score = 70.9 bits (172), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 55/179 (30%), Positives = 87/179 (48%), Gaps = 4/179 (2%) Query: 9 LLILDAIDRRGSFSAAGLELHRVPSTISYTVSKLEQDLGVQVFDRQGPKVVLTRAGEELL 68 L I+ ++R+GS +AA LH S +S+++ KLEQ LG ++ R+G + LT+AG+ LL Sbjct: 7 LSIVQEVERQGSLTAAAGVLHVTQSALSHSMKKLEQQLGTDIWLREGRHLRLTQAGQYLL 66 Query: 69 KEGRYLLKAAEDLEHRVRRVASGWETEFTIGLDSLYSAASLESDIVAFYQVADRTRLRIA 128 +L E R+R+ A G IG++ L + + + + Sbjct: 67 AVANRVLPQLSLAEERLRQFAQGERGALRIGMECHPCYQWLLKVVSPYLAAWPDVDVDVK 126 Query: 129 RESLAGTWEALLDRRVDLLIAA-PGEGPAGGGYVAEQIGTVKFVFVVAPHHPLAKMDKV 186 ++ G AL +DLL+ P + P G V E + + V VVA HPLA +D V Sbjct: 127 QKFQFGGIGALFGYEIDLLVTPDPLDKP---GLVFEPVFDYEQVLVVASDHPLADVDYV 182 >gi|300313602|ref|YP_003777694.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 67.0 bits (162), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 57/182 (31%), Positives = 92/182 (50%), Gaps = 6/182 (3%) Query: 2 FRISLDALLILDAIDRRGSFSAAGLELHRVPSTISYTVSKLEQDLGVQVFDRQGPKVVLT 61 +I+L L I A+ + GS +AA + S S +++LE LGVQ+FDR G ++VL Sbjct: 1 MKITLRQLQIFLAVAQSGSTTAAADLVALSQSAASAALNELEHLLGVQLFDRVGKRLVLN 60 Query: 62 RAGEELLKEGRYLLKAAEDLEHRVRRVASGWETEFTIGLDSLYSAASLESDIVAFYQVAD 121 +G +LL + R++L AA+ +E + +G +E IG + + L + I A+ + Sbjct: 61 DSGRQLLPQARHMLDAAQTIERQFSDPEAG--SELHIGASTTIGSYMLPAMIAAYRKDHA 118 Query: 122 RTRLRIARESLAGTWEALLDRRVDLLIAAPGEGPAGGGYV-AEQIGTVKFVFVVAPHHPL 180 R+R + A +A+++ VD A EGP V E + + V AP HPL Sbjct: 119 GARVRALVANTADIVDAVVNFEVD---AGLIEGPCHADDVEVEPWMMDELIVVAAPRHPL 175 Query: 181 AK 182 K Sbjct: 176 VK 177 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 0.321 0.137 0.398 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: 846,969 Number of extensions: 32870 Number of successful extensions: 207 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 204 Number of HSP's successfully gapped: 12 Length of query: 308 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 223 Effective length of database: 1,217,395 Effective search space: 271479085 Effective search space used: 271479085 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 (21.8 bits) S2: 130 (54.7 bits)