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= 0001.4448.p (312 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313854|ref|YP_003777946.1| LysR family transcription regul... 586 e-169 gi|300313153|ref|YP_003777245.1| transcription regulator protein... 296 2e-81 gi|300313102|ref|YP_003777194.1| LysR family transcription regul... 70 2e-13 gi|300312961|ref|YP_003777053.1| transcription regulator protein... 66 4e-12 gi|300312196|ref|YP_003776288.1| LysR family transcription regul... 66 5e-12 >gi|300313854|ref|YP_003777946.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 310 Score = 586 bits (1510), Expect = e-169, Method: Compositional matrix adjust. Identities = 291/310 (93%), Positives = 300/310 (96%) Query: 1 MEIKWVEDFLSVVETLNFSRSAKLRNVTQPAFGRRIRSLETWLGAELFDRSSYPCTLTPA 60 MEIKWVEDFLSVVETLNFSRSAKLRNVTQPAFGRRIRSLETWLGAELFDRSSYPCTLT A Sbjct: 1 MEIKWVEDFLSVVETLNFSRSAKLRNVTQPAFGRRIRSLETWLGAELFDRSSYPCTLTQA 60 Query: 61 GESFVPIAKEMLNQSMQARLVLRGQLAGAQSSLRFAMPHTLLLTVFPKLLSEIEKKIGTI 120 GESFVPIAKEMLNQSMQARLVLRGQLAGAQS++R AMPHTLLLTVFPKLLSEIEK IG I Sbjct: 61 GESFVPIAKEMLNQSMQARLVLRGQLAGAQSAVRLAMPHTLLLTVFPKLLSEIEKSIGAI 120 Query: 121 TTTVMAGNVHDAVMALVERNCDLLLCYDHRQQGIALDTERYAVLSLGKEPLRPYVKALPS 180 +TTVMAGNVHDAVMALVERNCDLLLCYDHRQQGIALDTERY VLSLGKEPLRPYVK LP+ Sbjct: 121 STTVMAGNVHDAVMALVERNCDLLLCYDHRQQGIALDTERYDVLSLGKEPLRPYVKTLPN 180 Query: 181 GLPKYVLPGTPNEPQPLLAYSPYSSLSRIVEKALHSSQRRVHLFRRFETDLAEGLKSMAV 240 GLPKYVLPG PN+PQP L+YSPYSSLSRIVEKALHSS R+VHLFRRFETDLAEGLKSMAV Sbjct: 181 GLPKYVLPGAPNDPQPFLSYSPYSSLSRIVEKALHSSPRQVHLFRRFETDLAEGLKSMAV 240 Query: 241 EGHGIAWLPASAVAREIAEGKLTLAIAPTDSEALAQGLWCDEMDIRIYRRLDGANPDIDR 300 EGHGIAWLPASAVAREIAEGKLTLAIAPTDSEAL QGLWCDEMDIR+YRRLDGANPDIDR Sbjct: 241 EGHGIAWLPASAVAREIAEGKLTLAIAPTDSEALEQGLWCDEMDIRVYRRLDGANPDIDR 300 Query: 301 VWNYLKAEHG 310 +WNYLKAEHG Sbjct: 301 IWNYLKAEHG 310 >gi|300313153|ref|YP_003777245.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 331 Score = 296 bits (757), Expect = 2e-81, Method: Compositional matrix adjust. Identities = 151/309 (48%), Positives = 202/309 (65%), Gaps = 11/309 (3%) Query: 1 MEIKWVEDFLSVVETLNFSRSAKLRNVTQPAFGRRIRSLETWLGAELFDRSSYPCTLTPA 60 ME KW+EDF+S+ ET +FSRSA+LR+VTQPAF RRI+SLE WLG +L DR+SYP LT A Sbjct: 1 MESKWLEDFVSLAETRSFSRSAELRHVTQPAFSRRIQSLEAWLGTDLIDRTSYPTRLTAA 60 Query: 61 GESFVPIAKEMLNQSMQARLVLRGQLAGAQSSLRFAMPHTLLLTVFPKLLSEIEKKIGTI 120 GE F A ML Q R +LRG+ AQ+++ FA+PHTL LT PK LS +E G I Sbjct: 61 GEVFYEQAVAMLGQINNTRALLRGKRPTAQTTIDFAVPHTLSLTYMPKWLSALESGFGAI 120 Query: 121 TTTVMAGNVHDAVMALVERNCDLLLCYDHRQQGIALDTERYAVLSLGKEPLRPYVKALPS 180 T ++A NVHDAVM +VE CDLLLCY H +Q + LD+ RY +L++G E LRPY + + Sbjct: 121 NTRLIALNVHDAVMTIVEGGCDLLLCYHHPRQPVQLDSSRYDMLTMGTETLRPYSRCDRN 180 Query: 181 GLPKYVLPGTPNEPQPLLAYSPYSSLSRIVEKALHSSQRRVHLFRRFETDLAEGLKSMAV 240 G P YV PG+ P P L+Y+ + L R+VE + ++R +HL + +ETD++E LK MA+ Sbjct: 181 GKPDYVFPGSAKAPVPFLSYTSNAYLGRMVELMMADTKRPLHLDKHYETDMSESLKMMAL 240 Query: 241 EGHGIAWLPASAVAREIAEGKLTLAIAPTDSEALAQGLWCDEMDIRIYRRLDGANPD--- 297 EGHG+A+LP S+V RE+ +L P+ G W EM+IR+YR A Sbjct: 241 EGHGVAFLPESSVVREVRNRQLARTDVPS-------GEWEVEMEIRLYRERPTAQRAGKA 293 Query: 298 -IDRVWNYL 305 + R+W YL Sbjct: 294 LVARLWEYL 302 >gi|300313102|ref|YP_003777194.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 70.5 bits (171), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 65/267 (24%), Positives = 119/267 (44%), Gaps = 32/267 (11%) Query: 1 MEIKWVEDFLSVVETLNFSRSAKLRNVTQPAFGRRIRSLETWLGAELFDRSSYPCTLTPA 60 +E++ + F +V ETL+F R+A+L +++QP R+I +LE LGA+LFDRS LT A Sbjct: 2 IELRHLTYFRTVAETLHFGRAAELLHISQPPLTRQIAALEKELGAQLFDRSKRAIQLTAA 61 Query: 61 GESFVPIAKEMLNQSMQARLVLRGQLAGAQSSLRFAMPHTLLLTVFPKL-------LSEI 113 G+ F E+ +A+ + G +L+ + + P + E+ Sbjct: 62 GKYFYRDTTEIFKALERAKRNVSSSSTGKSGALKVGFMMSTAYNILPSVTRHYSAAYPEV 121 Query: 114 EKKIGTITTTVMAGNVHDAVMALVERNCDLLLCYDHRQQGIALDTERYAVLSLGKEPLRP 173 + ++ ++A ++ D D+ + Y D R ++ EPL Sbjct: 122 DMRLTEYVPNLLATDIED-------EKIDVGIMYRPE------DCRRLDSHTIYAEPL-- 166 Query: 174 YVKALPSGLPKYVLPGTPNEPQPLLAYSPYSSLSRIVEKALHS---SQRRVHLFR---RF 227 + LP + L G + LA + S+ R++ ++ ++H FR Sbjct: 167 -LAVLPR---DHRLAGRQSISAAELAEDAFISIPRMIAPVVYDLIQQHCQLHGFRPRIVL 222 Query: 228 ETDLAEGLKSMAVEGHGIAWLPASAVA 254 ET+L + + ++ EG G+A +P S A Sbjct: 223 ETNLQQTIVNLVGEGLGVALVPTSMQA 249 >gi|300312961|ref|YP_003777053.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 65.9 bits (159), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 36/89 (40%), Positives = 56/89 (62%), Gaps = 4/89 (4%) Query: 1 MEIKWVEDFLSVVETLNFSRSAKLRNVTQPAFGRRIRSLETWLGAELFDRSSYPCTLTPA 60 ME++ ++ F +V TL+FSR+A+L ++ QP R+IR LE LG EL DR+S P LT A Sbjct: 1 MELRHLKYFNAVASTLSFSRAAELLHIAQPPLSRQIRQLEEMLGVELIDRASRPIALTMA 60 Query: 61 GESFVPIAKEMLNQSMQ----ARLVLRGQ 85 G+ F ++L++ Q R++ RG+ Sbjct: 61 GKFFYEQTLQVLSRLEQIEEGTRVIARGR 89 >gi|300312196|ref|YP_003776288.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 308 Score = 65.9 bits (159), Expect = 5e-12, Method: Compositional matrix adjust. Identities = 63/265 (23%), Positives = 115/265 (43%), Gaps = 17/265 (6%) Query: 2 EIKWVEDFLSVVETLNFSRSAKLRNVTQPAFGRRIRSLETWLGAELFDRSSYPCTLTPAG 61 +++ ++ F++VVE+ +F + + ++PA R++ LE +LG L R++ +LT G Sbjct: 3 KLQAMQTFVAVVESGSFVAAVDVTGQSKPAVSRQVSELEQFLGIRLLHRTTRRLSLTDEG 62 Query: 62 ESFVPIAKEMLN--QSMQARLVLRGQLAGAQSSLRFAMPHTLLLTVFPKLLSEIEKKIGT 119 + KE+L Q +++ + L A + LR P + L + ++ Sbjct: 63 RVYFARCKELLETIQDVESEVGLNSDQACGR--LRIGAPQDFGVEQLAPLWGKFTEQHPL 120 Query: 120 ITTTVMAGNVHDAVMALVERNCDLLLCYDHRQQGIALDTERYAVLSLGKEPLRPYVKALP 179 IT + + D + L+E D+ + AL R L P+R A P Sbjct: 121 ITLNI---TLSDRTIDLLEEGFDMAIRIS------ALGDSRMVARPLA--PVRMIACAAP 169 Query: 180 SGLPKYVLPGTPNEPQ--PLLAYSPYSSLSRIVEKALHSSQRRVHLFRRFETDLAEGLKS 237 L ++ PGTP E + P ++YS + + +H +V + + ++ Sbjct: 170 EFLARHGTPGTPAELRDYPFISYSYRAGGDDWSFRHVHGDTCQVRVRSTVYVNNGATCRA 229 Query: 238 MAVEGHGIAWLPASAVAREIAEGKL 262 MA+ G GIA P V I G+L Sbjct: 230 MAIAGQGIAIQPDFIVNAAIQAGQL 254 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 0.320 0.134 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: 894,297 Number of extensions: 33026 Number of successful extensions: 222 Number of sequences better than 1.0e-08: 21 Number of HSP's gapped: 218 Number of HSP's successfully gapped: 21 Length of query: 312 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 227 Effective length of database: 1,217,395 Effective search space: 276348665 Effective search space used: 276348665 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)