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= 0002.0308.p (293 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310059|ref|YP_003774151.1| LysR family transcription regul... 124 9e-30 gi|300310322|ref|YP_003774414.1| LysR family transcription regul... 120 1e-28 gi|300312300|ref|YP_003776392.1| LysR family transcription regul... 110 1e-25 gi|300312373|ref|YP_003776465.1| LysR family transcription regul... 105 5e-24 gi|300312785|ref|YP_003776877.1| transcription regulator protein... 100 2e-22 >gi|300310059|ref|YP_003774151.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 283 Score = 124 bits (311), Expect = 9e-30, Method: Compositional matrix adjust. Identities = 90/284 (31%), Positives = 137/284 (48%), Gaps = 23/284 (8%) Query: 2 EWSDVRIFLAVARTGTLGAAARLLHVSHPTIGRRLRALEEATGQVLFQRTADGFVLTEEG 61 +W +R F A G+ AAR+L V+H TIGRRL+ LE+ LF R AD LT G Sbjct: 4 DWESLRSFAAFVDAGSFSGAARVLGVTHATIGRRLQQLEQTLAAPLFIRRADDIELTRLG 63 Query: 62 MGVLPLAEQIEEGALAMERRLAGKQRTLDGILRITSADWFGAYVLPPVLAEYAASYPLVE 121 VL A +++ + R LAG+ ++G LR+ D G L P L +P ++ Sbjct: 64 ESVLAAARAMQDQTRQLARTLAGEDLRMEGKLRLACTDAMGTLFLAPRLPSLLQQWPALD 123 Query: 122 IEVLTGTRLFNLAQREADIAFRIVPFEEQDIVQRRLLRMRY---------GVYVATASPD 172 IE+ G + +LA+READ+A R ++ +++ RRL +R+ + Sbjct: 124 IELAMGHQTLSLARREADLALRFARPQDGELIARRLGVVRFYLCGTADQVAAWRHQRGSA 183 Query: 173 PVIGDGSGIRLITPDTFSGTFPDTAWLKEMFPNAGVVLQSNNRSIKAQMCAMGMGIAVLP 232 PVIG + PD P+T WL V L+S + + G+G+A+LP Sbjct: 184 PVIGYDDSV----PD-----IPETRWLAAHADGNPVRLRSASLVAQCMAARAGVGLALLP 234 Query: 233 RP-LGDQVNGIRLLELGVEPSHREIWMGYHRDLRRLNRLRAFVD 275 L ++ + V RE+W +HRDL+ L RLRA ++ Sbjct: 235 SYLLAPELQTVESTPQLV----RELWAVFHRDLKALPRLRAVLE 274 >gi|300310322|ref|YP_003774414.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 288 Score = 120 bits (301), Expect = 1e-28, Method: Compositional matrix adjust. Identities = 89/282 (31%), Positives = 142/282 (50%), Gaps = 10/282 (3%) Query: 1 MEWSDVRIFLAVARTGTLGAAARLLHVSHPTIGRRLRALEEATGQVLFQRTADGFVLTEE 60 M+W + RIFLA+ R GTL AA L + T+GRRL ALE + G LF RT +G+V T Sbjct: 1 MDWDNARIFLAIYRVGTLRGAAETLELDQATVGRRLAALERSLGARLFLRTPNGYVPTPA 60 Query: 61 GMGVLPLAEQIEEGALAMERRLAGKQRTLDGILRITSADWFGAYVLPPVLAEYAASYPLV 120 G A+Q+E+GA ++R++ G L G++R+ + D + L P L +P + Sbjct: 61 GEMAAAAAQQMEQGAEQLQRQMQGIDERLCGVVRLAATDVTARHFLIPALHRLRQEHPHI 120 Query: 121 EIEVLTGTRLFNLAQREADIAFRIVPFEEQDIVQRRLLRMRYGVYVATAS------PDPV 174 + + T T++ NL +READIA R + + D++ R L R+ +Y + + P+P Sbjct: 121 RVVLSTSTQITNLTKREADIAVRTLRPDAPDLIARHLKRLHTAIYASRSYVKKRGLPEPG 180 Query: 175 IGDGSGIRLITPDTFSGTFPDTAWLKEMFPNAGVVLQSNNRSIKAQMCAMGMGIAVLPRP 234 G +I + S + E NA V ++ + + G G+ LP Sbjct: 181 TGLKGHDVVIYQRSVSPAKSEQI-CGESIINAQVAMEVSTGLVMYDCLQAGFGLGELPTH 239 Query: 235 LGDQVNG-IRLLELGVEPSHREIWMGYHRDLRRLNRLRAFVD 275 +GD+ +G +R+ P ++W+ H DL R R+RA D Sbjct: 240 VGDKASGLVRVWPQRETPY--DMWLVLHSDLNRTARVRAVAD 279 >gi|300312300|ref|YP_003776392.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 305 Score = 110 bits (276), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 87/278 (31%), Positives = 136/278 (48%), Gaps = 5/278 (1%) Query: 1 MEWSDVRIFLAVARTGTLGAAARLLHVSHPTIGRRLRALEEATGQVLFQRTADGFVLTEE 60 ++W DVR FL ++R G+L A+AR+L V H T+ R + LE+ LF R A G+VLT E Sbjct: 23 LQWDDVRYFLTLSREGSLSASARVLKVEHSTVARHVGNLEKTLRVKLFDRLARGWVLTTE 82 Query: 61 GMGVLPLAEQIEEGALAMERRLAGKQRTLDGILRITSADWFGAYVLPPVLAEYAASYPLV 120 G + AEQ+E ++ R A TL G +R+++ + L P L + YP + Sbjct: 83 GAELSKQAEQLEVEMHSLW-RAALANTTLSGKVRVSAPPILMSDFLVPRLPAFQEKYPDI 141 Query: 121 EIEVLTGTRLFNLAQREADIAFRIVPFEEQDIVQRRLLRMRYGVYVATASPDPVIGDGSG 180 E+EV+ R +L + EADIA R+ +V R L + Y VY A + + S Sbjct: 142 ELEVIGEARGVDLTRGEADIALRMGEPVSPLLVARMLCNVSYSVYGIPAWLERPESERSF 201 Query: 181 IRLITPDTFSGTFPDTAWLKEMFPNAGVVLQSNNRSIKAQMCAMGMGIAVLPRPLGDQVN 240 I L D S AWL+ L++N+ G+G+A+LPR + + Sbjct: 202 IGL---DQESPC-RQKAWLESQVDQRRYALRTNDIRAMCHAAMSGIGLALLPRFMVAEDT 257 Query: 241 GIRLLELGVEPSHREIWMGYHRDLRRLNRLRAFVDLAV 278 + + + P +++ H D+RR R+RA D + Sbjct: 258 RLVAIPMPETPPPCPLYLVMHSDVRRAPRIRATADFLI 295 >gi|300312373|ref|YP_003776465.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 305 Score = 105 bits (261), Expect = 5e-24, Method: Compositional matrix adjust. Identities = 71/249 (28%), Positives = 118/249 (47%), Gaps = 17/249 (6%) Query: 1 MEWSDVRIFLAVARTGTLGAAARLLHVSHPTIGRRLRALEEATGQVLFQRTADGFVLTEE 60 ++W ++RIFL + R+ L AA+ L + H T+ RR++ EE G LF R G+ LT + Sbjct: 2 LDWDNLRIFLELTRSQGLVDAAKKLGIDHSTVSRRMKRFEEQVGSQLFDRNNHGYKLTAD 61 Query: 61 GMGVLPLAEQIEEGALAMERRLAGKQRTLDGILRITSADWFGAYVLPPVLAEYAASYPLV 120 G ++ AEQ+E A L G L G +R+ + + FG +VL P +A + A P + Sbjct: 62 GYRLVEYAEQVESTLYAATEELGGHNSKLSGQVRLGATEGFGTFVLAPHIAHFCARNPHI 121 Query: 121 EIEVLTGTRLFNLAQREADIAFRIV-PFEEQDIVQR---RLLRMRYGV-YVATASPDPVI 175 +++L R NL++ EADI+ I P +V + +L++ Y+A P + Sbjct: 122 TVDMLPMPRFVNLSKHEADISVSIERPLSGNYVVTKLSDYVLKLYASRDYLAQHPPIHTM 181 Query: 176 GDGSGIRLITPDTFSGTFPDTAWLKEM------FPNAGVVLQSNNRSIKAQMCAMGMGIA 229 D + F G D + +E+ P+A +S + + G +A Sbjct: 182 DD------LAQHHFIGYIDDLVFSEELRYKDTVAPDAFRAFRSTSVVAQYTAACAGRALA 235 Query: 230 VLPRPLGDQ 238 +LP L Q Sbjct: 236 ILPCFLAQQ 244 >gi|300312785|ref|YP_003776877.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 297 Score = 100 bits (248), Expect = 2e-22, Method: Compositional matrix adjust. Identities = 81/275 (29%), Positives = 138/275 (50%), Gaps = 17/275 (6%) Query: 2 EWSDVRIFLAVARTGTLGAAARLLHVSHPTIGRRLRALEEATGQVLFQRTADGFVLTEEG 61 W R FL V TG+L AA R + ++ PT+GR + LE G LF R+ DGF T+ Sbjct: 7 NWEWYRSFLKVLETGSLSAAGREMGLTQPTVGRHIENLESTLGLKLFVRSFDGFSPTDAA 66 Query: 62 MGVLPLAEQIEEGALAMERRLAGKQRTLDGILRITSADWFGAYVLPPVLAEYAASYPLVE 121 + + P A I + A+ R + + + + G +R+T+++ VLPP+LA +P + Sbjct: 67 LELKPYAAAIAANSAALRRAASSQGKEVRGTVRLTASEVISVEVLPPILAALRHRHPELR 126 Query: 122 IEVLTGTRLFNLAQREADIAFRIVPFEEQDIVQRRLLRMRYGVYVATASPDPVIGDGSGI 181 +E++ + +L QREADIA R+ + +V +RL + G++ A S V G + Sbjct: 127 VELVLSNKADDLLQREADIAVRMFRPAQDALVAKRLGSIELGLH-AHQSYLTVHGAPKSV 185 Query: 182 RLITPDTFSGTFPDTAWLKEMFPN------AGVVLQSNNRSIKAQMCAM--GMGIAVLPR 233 + T G ++A+++ + A + L+++ S AQ+ A+ G GI + Sbjct: 186 DALADHTLIGFDQESAYVRNVLKQIPWLSRAALALRTD--SDLAQLAAIRAGFGIGICQV 243 Query: 234 PLGDQ-VNGIRLL--ELGVEPSHREIWMGYHRDLR 265 L + V +RLL + ++ E W+ H DLR Sbjct: 244 ALAARDVALVRLLPRQFALK---METWVAMHEDLR 275 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 0.323 0.139 0.411 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: 982,124 Number of extensions: 43581 Number of successful extensions: 256 Number of sequences better than 1.0e-08: 44 Number of HSP's gapped: 248 Number of HSP's successfully gapped: 44 Length of query: 293 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 209 Effective length of database: 1,222,130 Effective search space: 255425170 Effective search space used: 255425170 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 130 (54.7 bits)