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= 0028.0055.p (313 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311571|ref|YP_003775663.1| LysR family transcription regul... 534 e-153 gi|300309386|ref|YP_003773478.1| LysR family transcription regul... 108 6e-25 gi|300310637|ref|YP_003774729.1| LysR family transcription regul... 102 5e-23 gi|300312961|ref|YP_003777053.1| transcription regulator protein... 97 2e-21 gi|300313102|ref|YP_003777194.1| LysR family transcription regul... 96 4e-21 >gi|300311571|ref|YP_003775663.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 313 Score = 534 bits (1375), Expect = e-153, Method: Compositional matrix adjust. Identities = 266/313 (84%), Positives = 286/313 (91%) Query: 1 MELRQLRYFVAIVDHGSLSRAARVLHIAQPALTQQVRQLEEELEAQLLHRSAQGVIATDA 60 MELRQLRYFVAIVDHGSLSRAAR LHIAQPALTQQ+RQLE+EL AQLLHRSAQGVIATDA Sbjct: 1 MELRQLRYFVAIVDHGSLSRAARALHIAQPALTQQIRQLEDELAAQLLHRSAQGVIATDA 60 Query: 61 GKTFYEHAQAILKQVIDAKSAVAQSNDKPSGTVALGIPQSVSGALALPLLTAIRATYPEI 120 GK FYEHA AILKQV DAK AV QS DKPSGTVALGIPQSVS ALALPLL A+R+TYPEI Sbjct: 61 GKVFYEHALAILKQVQDAKQAVGQSADKPSGTVALGIPQSVSNALALPLLNAVRSTYPEI 120 Query: 121 TLLLTEELTGNLIVQLKSGRINLAVLFDDGQLSPFASTPMVEEEMMYITRADSQYGAGKK 180 TL LTEELTGNLI QLKSGRINLAVLFDDGQLS FA+TPM+EEEMMYITRA SQYG + Sbjct: 121 TLQLTEELTGNLITQLKSGRINLAVLFDDGQLSSFAATPMIEEEMMYITRAKSQYGVAGR 180 Query: 181 KSVTLAQAIKAPLILPGLQHGVRPRIENIVRSQGMSLANVIEINSVAILKSAILADIGAT 240 KSV LA+AI+APLILPGL HGVRPRIEN+VRSQGMSL NVIEINSVAILKSAILADIGAT Sbjct: 181 KSVPLARAIQAPLILPGLAHGVRPRIENLVRSQGMSLDNVIEINSVAILKSAILADIGAT 240 Query: 241 ILPVAPLLSEIERGDMVALPISGERMARTLALCASKNIPLTNAAAAVERLVLDVTDDLCR 300 ILPVAPLL++IERG+MVA I+GER++RTLALCAS+NIPLT AAAAVE+LVLDVTD+LCR Sbjct: 241 ILPVAPLLADIERGEMVAHRIAGERISRTLALCASRNIPLTTAAAAVEQLVLDVTDELCR 300 Query: 301 KGKWLHTEGLARE 313 G+W HTE L RE Sbjct: 301 SGRWGHTELLERE 313 >gi|300309386|ref|YP_003773478.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 301 Score = 108 bits (270), Expect = 6e-25, Method: Compositional matrix adjust. Identities = 81/251 (32%), Positives = 125/251 (49%), Gaps = 18/251 (7%) Query: 1 MELRQLRYFVAIVDHGSLSRAARVLHIAQPALTQQVRQLEEELEAQLLHRSAQGVIATDA 60 M++R LRYF V H S SRAA LH+ Q +++ VRQLEEE++A LL R + + TD Sbjct: 1 MDIRALRYFTETVRHSSFSRAADALHVTQSTVSKMVRQLEEEVDAPLLIRDGRRLQLTDT 60 Query: 61 GKTFYEHAQAILKQVIDAKSAVAQSNDKPSGTVALGIPQSVSGALALPLLTAIRATYPEI 120 G+ YE Q IL + + V + SG + +GIP ++ L P+L A R +P+I Sbjct: 61 GRVVYEQGQQILAAMQRLHAEVRDTKALRSGRLEIGIPPMIN-ILCTPVLKAFRERHPDI 119 Query: 121 TLLLTEELTGNLIVQLKSG--RINLAVLFDDGQLS----PFASTPMVEEEMMYITRADSQ 174 ++L E+ + ++ +G I + VL D +L P AS PM A +Q Sbjct: 120 AVVLQEDTGPQIEQRVANGELEIGMTVLPADPELGLETLPVASYPMW---------AVAQ 170 Query: 175 YGAGKKKSVTL--AQAIKAPLILPGLQHGVRPRIENIVRSQGMSLANVIEINSVAILKSA 232 G+ +K +L AQ PL+L + G+ + + R G+ V + L + Sbjct: 171 AGSFQKNRASLRCAQLDGMPLVLLNNEFGLTRSLRGVFREHGIKPEIVAQSAQWDWLVAM 230 Query: 233 ILADIGATILP 243 LA +G +LP Sbjct: 231 ALAGMGTALLP 241 >gi|300310637|ref|YP_003774729.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 326 Score = 102 bits (253), Expect = 5e-23, Method: Compositional matrix adjust. Identities = 92/306 (30%), Positives = 154/306 (50%), Gaps = 28/306 (9%) Query: 1 MELRQLRYFVAIVDHGSLSRAARVLHIAQPALTQQVRQLEEELEAQLLHRSAQGVIATDA 60 M++RQL+YFVA+ + + +RA+ LHIAQP L++Q++ LEEEL QLL R+++ + T+A Sbjct: 1 MDIRQLKYFVAVANTRNFTRASEQLHIAQPPLSRQIQLLEEELGVQLLLRNSRPLRLTEA 60 Query: 61 GKTFYEHAQAILKQVIDAKSAVAQSNDKPSGTVALG-IPQSVSGALALPLLTAIRATYPE 119 G+ FYE A IL ++ K+A Q T+++G + ++ G L + L+ +R YPE Sbjct: 61 GRVFYEQALQILNRLDQLKNATQQIGLNQRQTLSIGFVASTLYGGLPM-LVRKLRQHYPE 119 Query: 120 ITLLLTEELTGNLIVQLKSGRINLAVLFDDGQLSPFASTP---MVEEEMMYITRADSQYG 176 + + L E + LKSGRI++ G++ +T ++ EE + + S Sbjct: 120 VDIQLLELTSMQQFAALKSGRIDVGF----GRIRSNDATVARIVLREEKLVLAIPPSFAL 175 Query: 177 AGKKKSVTLAQAIKAPLILPGLQHGVRPR------IENIVRSQGMSLANVIEINSVAILK 230 AG + V+L + LI+ + PR I +++ Q + A V E+ + Sbjct: 176 AGSNQRVSLKEVHGQKLIV----YPKEPRPSFADHILSLLNDQDIHPAEVHEVREIQTAL 231 Query: 231 SAILADIGATILPVAPLLSEIERGDMVALPISGERMARTLALCASKNIPLTNAA--AAVE 288 + A+ G ++P + L R D+ I R + L N NA AV+ Sbjct: 232 GLVAAESGICLIPASARL----RNDLHYRLIDDARATSPIILTHRIN---DNAWYIEAVK 284 Query: 289 RLVLDV 294 RLV D+ Sbjct: 285 RLVADM 290 >gi|300312961|ref|YP_003777053.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 97.1 bits (240), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 87/278 (31%), Positives = 139/278 (50%), Gaps = 30/278 (10%) Query: 1 MELRQLRYFVAIVDHGSLSRAARVLHIAQPALTQQVRQLEEELEAQLLHRSAQGVIATDA 60 MELR L+YF A+ S SRAA +LHIAQP L++Q+RQLEE L +L+ R+++ + T A Sbjct: 1 MELRHLKYFNAVASTLSFSRAAELLHIAQPPLSRQIRQLEEMLGVELIDRASRPIALTMA 60 Query: 61 GKTFYEHAQAILKQV--IDAKSAVAQSNDKPSGTVALGIPQSVSGALALPLLTAIRATYP 118 GK FYE +L ++ I+ + V + + +P ++ G L ++ R P Sbjct: 61 GKFFYEQTLQVLSRLEQIEEGTRVIARGRQHWFNIGF-VPSALYGLLP-EMIKRFRTEMP 118 Query: 119 EITLLLTEELTGNLIVQLKSGRINLAVLFDDGQLSPFASTP------MVEEEMMYITRAD 172 EI + +E +T + LKSGRI++ G+L S P +VEE ++ + Sbjct: 119 EIEIGFSEIVTMEQVEALKSGRIDVGF----GRLP--ISDPDIVCETIVEEPLVAVFPLG 172 Query: 173 SQYGAGKKKSVTLAQAIKAPLILPGLQHGVRPR------IENIVRSQGMSLANVIEINSV 226 A K VTLAQ IL + RPR + +I S+ + + V E N + Sbjct: 173 HPLLARNK--VTLAQLAAQRFIL----YPARPRPSYADQVLDIFSSRALRPSIVKEANEM 226 Query: 227 AILKSAILADIGATILPVAPLLSEIERGDMVALPISGE 264 + A +G T++P + + + R D+V P+S + Sbjct: 227 QTAIGLVAAGVGVTLVPRS--VQGLHRSDVVYRPLSNK 262 >gi|300313102|ref|YP_003777194.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 300 Score = 95.9 bits (237), Expect = 4e-21, Method: Compositional matrix adjust. Identities = 65/221 (29%), Positives = 108/221 (48%), Gaps = 17/221 (7%) Query: 1 MELRQLRYFVAIVDHGSLSRAARVLHIAQPALTQQVRQLEEELEAQLLHRSAQGVIATDA 60 +ELR L YF + + RAA +LHI+QP LT+Q+ LE+EL AQL RS + + T A Sbjct: 2 IELRHLTYFRTVAETLHFGRAAELLHISQPPLTRQIAALEKELGAQLFDRSKRAIQLTAA 61 Query: 61 GKTFYEHAQAILKQVIDAKSAVAQSNDKPSGTVALGIPQSVSGALALPLLTAIRATYPEI 120 GK FY I K + AK V+ S+ SG + +G S + + + A YPE+ Sbjct: 62 GKYFYRDTTEIFKALERAKRNVSSSSTGKSGALKVGFMMSTAYNILPSVTRHYSAAYPEV 121 Query: 121 TLLLTEELTGNLIVQLKSGRINLAVLFDDGQLSPFASTPMVEEEMMYITRADSQYGAGKK 180 + LTE + L ++ +I++ +++ S + E ++ + D + + Sbjct: 122 DMRLTEYVPNLLATDIEDEKIDVGIMYRPEDCRRLDSHTIYAEPLLAVLPRDHRLAG--R 179 Query: 181 KSVTLAQAIK----------APLILPGLQ-----HGVRPRI 206 +S++ A+ + AP++ +Q HG RPRI Sbjct: 180 QSISAAELAEDAFISIPRMIAPVVYDLIQQHCQLHGFRPRI 220 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 0.318 0.133 0.360 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: 842,545 Number of extensions: 30440 Number of successful extensions: 231 Number of sequences better than 1.0e-08: 70 Number of HSP's gapped: 223 Number of HSP's successfully gapped: 70 Length of query: 313 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 228 Effective length of database: 1,217,395 Effective search space: 277566060 Effective search space used: 277566060 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 130 (54.7 bits)