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= 0001.1100.p (307 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311165|ref|YP_003775257.1| transcription regulator protein... 94 1e-20 gi|300312614|ref|YP_003776706.1| LysR family transcription regul... 86 5e-18 gi|300313217|ref|YP_003777309.1| LysR family transcription regul... 80 3e-16 gi|300309386|ref|YP_003773478.1| LysR family transcription regul... 79 5e-16 gi|300309859|ref|YP_003773951.1| LysR family transcription regul... 77 3e-15 >gi|300311165|ref|YP_003775257.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 311 Score = 94.4 bits (233), Expect = 1e-20, Method: Compositional matrix adjust. Identities = 81/310 (26%), Positives = 141/310 (45%), Gaps = 22/310 (7%) Query: 1 MTLKQLEAFYWAATCANFGIASERLHLSISSLSKRISELELSLGISLFDRSGHRAMLSEA 60 M ++ LE F W A NF + +ERLH + +++S RI+ LE G+ LFDRS L+ Sbjct: 1 MNIRFLETFVWLARLRNFRLTAERLHTTQAAVSSRIASLEQDFGVRLFDRSAREVALTAD 60 Query: 61 GQALLPQAQALLDNAARVRATFAPSVGLVGRCAFGVGELSALTWLPQFMVQVRARHPKLV 120 G L A+ ++ ++ + G GV E +W P F+ ++ P+L Sbjct: 61 GSKALVHAERMVKLMREMKEDMSDREVYAGVIRIGVIESIVHSWFPDFLGRLHKTFPRLQ 120 Query: 121 LEPYVDVGAVLESRVAKGELDF-----AIIAGRSSHYDILSQPLSQEQFIWVAAPALAVS 175 +E D L + +KG LD A+I + S+ + P+ WV +P L + Sbjct: 121 IEIVSDTTIHLHEQFSKGNLDLVLQAEAVIGPQVSNLALCEFPMR-----WVGSPKLDIG 175 Query: 176 DDSQRVYSAVDLLQAGQPMIVLPPSAGSTRLIDDWLLEHGITAVERINCNNWGAIAGML- 234 ++ S DL A P+I ++G +I+ L + ++ N ++A M+ Sbjct: 176 SET---LSLADL--AAFPIISFARNSGPHAVIER-LFSDSQRSERTLHINCIASVATMIR 229 Query: 235 IASVGIGI--LPAGWSQKLLDQNLLRPL-AGGELPTSLTYSFQWRRGDNRPLLDPLRRLS 291 +A+ G GI +P Q+ L++ L L E P +L +R PL + + R++ Sbjct: 230 LATDGFGITAVPPAIIQRELNEESLHLLRVDTEFP-ALVLIASFRSDHENPLTETVARIA 288 Query: 292 TQ-CVDFTID 300 + DF ++ Sbjct: 289 QETAADFALN 298 >gi|300312614|ref|YP_003776706.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 301 Score = 85.5 bits (210), Expect = 5e-18, Method: Compositional matrix adjust. Identities = 72/266 (27%), Positives = 127/266 (47%), Gaps = 18/266 (6%) Query: 1 MTLKQLEAFYWAATCANFGIASERLHLSISSLSKRISELELSLGISLFDRSGHRAMLSEA 60 M L+ +EAF+WAA+ + A+E+LH++ S++S RI+ LE LG+ L DR + L+ A Sbjct: 1 MNLRFVEAFHWAASLKSITRAAEKLHITQSTMSSRIASLEEELGVVLLDRREKQFRLTVA 60 Query: 61 GQALLPQAQALLDNAARVRATFAPSVGLVGRCAFGVGELSAL--TWLPQFMVQVRARHPK 118 GQ A LLD ++R G A +G + ++ +WLP ++ ++R R+P Sbjct: 61 GQRFQRLAVKLLDMQRQIRQELGGHSA--GPLALRIGSIESVVHSWLPAWLQEIRCRYPD 118 Query: 119 LVLEPYVDVGAVLESRVAKGELDFAIIAGRSSHYDILSQPLSQEQFIWVAA-PALAVSDD 177 LE V+ VL ++ +G D + S + S+ ++ + ++V Sbjct: 119 FALELTVETSPVLTEQIRRGAQDLVFTSTVGSDTAVRSRLMTPMEMVFVGHRERFGTRSH 178 Query: 178 SQRVYSAVDLL--QAGQPMIVLPPSAGSTRLIDDWLLEHGITAVERINC-NNWGAIAGML 234 + +A DL+ Q G P G +L +W G+ A RI+ ++ A+ ++ Sbjct: 179 TLEELAAHDLITFQRGS-----QPHQGLLQLCQEW----GV-ANPRIHAISSISAMVQLV 228 Query: 235 IASVGIGILPAGWSQKLLDQNLLRPL 260 G+ LP ++L + LR L Sbjct: 229 EGGFGVATLPRASVRQLTRRLPLRIL 254 >gi|300313217|ref|YP_003777309.1| LysR family transcription regulator [Herbaspirillum seropedicae SmR1] Length = 296 Score = 79.7 bits (195), Expect = 3e-16, Method: Compositional matrix adjust. Identities = 70/246 (28%), Positives = 113/246 (45%), Gaps = 11/246 (4%) Query: 1 MTLKQLEAFYWAATCANFGIASERLHLSISSLSKRISELELSLGISLFDRSGHRAMLSEA 60 M L +LE F A+ERL+ S+++ RI +LE S+G+ LF R R +L+ A Sbjct: 10 MELAELEIFRTVVAEGGVTRAAERLNRVQSNVTTRIKQLEQSMGVPLFVRDRRRMVLTAA 69 Query: 61 GQALLPQAQALLDNAARVRATFAPSVGLVGRCAFGVGELSALTWLPQFMVQVRARHPKLV 120 G+ALL A+ +LD A R AP GR G E +A + LP + + R P++ Sbjct: 70 GEALLDYAERILDLAQEARQAVAPQ-SPRGRLRIGSMESAAASRLPGPLAEFHQRWPEVR 128 Query: 121 LEPYVDVGAVLESRVAKGELDFAIIAGRSSHYDILSQPLSQEQFIWVAAPALAVSDDSQR 180 LE VL ++V +LD A++AG S + PL +E+ + V +R Sbjct: 129 LELSTAPTDVLMAQVRACKLDAALVAGPVSDPAFDATPLFREELLLV------TPRSHRR 182 Query: 181 VYSAVDLLQAGQPMIVLPPSAGSTRLIDDWLLEHGI--TAVERINCNNWGAIAGMLIASV 238 V + +++ +IV R + W HG + ++ AI + A Sbjct: 183 VRAPEEVML--DTLIVFEQGCAYRRHAEAWFAGHGAGRQLPRTLELASYHAILACVSAGA 240 Query: 239 GIGILP 244 G+ ++P Sbjct: 241 GVAVVP 246 >gi|300309386|ref|YP_003773478.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 301 Score = 78.6 bits (192), Expect = 5e-16, Method: Compositional matrix adjust. Identities = 66/259 (25%), Positives = 115/259 (44%), Gaps = 9/259 (3%) Query: 1 MTLKQLEAFYWAATCANFGIASERLHLSISSLSKRISELELSLGISLFDRSGHRAMLSEA 60 M ++ L F ++F A++ LH++ S++SK + +LE + L R G R L++ Sbjct: 1 MDIRALRYFTETVRHSSFSRAADALHVTQSTVSKMVRQLEEEVDAPLLIRDGRRLQLTDT 60 Query: 61 GQALLPQAQALLDNAARVRATFAPSVGL-VGRCAFGVGELSALTWLPQFMVQVRARHPKL 119 G+ + Q Q +L R+ A + L GR G+ + + P + R RHP + Sbjct: 61 GRVVYEQGQQILAAMQRLHAEVRDTKALRSGRLEIGIPPMINILCTP-VLKAFRERHPDI 119 Query: 120 VLEPYVDVGAVLESRVAKGELDFAI-IAGRSSHYDILSQPLSQEQFIWVAAPALAVSDDS 178 + D G +E RVA GEL+ + + + + P++ +W A A + + Sbjct: 120 AVVLQEDTGPQIEQRVANGELEIGMTVLPADPELGLETLPVASYP-MWAVAQAGSFQKNR 178 Query: 179 QRVYSA-VDLLQAGQPMIVLPPSAGSTRLIDDWLLEHGITAVERINCNNWGAIAGMLIAS 237 + A +D G P+++L G TR + EHGI W + M +A Sbjct: 179 ASLRCAQLD----GMPLVLLNNEFGLTRSLRGVFREHGIKPEIVAQSAQWDWLVAMALAG 234 Query: 238 VGIGILPAGWSQKLLDQNL 256 +G +LP + +L Q L Sbjct: 235 MGTALLPEPFIHRLATQQL 253 >gi|300309859|ref|YP_003773951.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 297 Score = 76.6 bits (187), Expect = 3e-15, Method: Compositional matrix adjust. Identities = 56/169 (33%), Positives = 88/169 (52%), Gaps = 11/169 (6%) Query: 6 LEAFYWAATCANFGIASERLHLSISSLSKRISELELSLGISLFDRSGHRAMLSEAGQALL 65 L+ F AA+ A+F A +L L+ S++S I LE SLG LF R H L+ G++LL Sbjct: 22 LQTFSTAASSASFTEAGRQLGLTQSTVSDHIRRLEESLGRRLFVRDTHSLALTADGESLL 81 Query: 66 PQAQALLDNAARVRATF-APSVGLVGRCAFGVGELSALTWLPQFMVQVRARHPKLVLEPY 124 A+ +L AR A F AP L GR FG + A+ LP + R++HP++ LE Sbjct: 82 VHARLILQAHARAEAQFSAPR--LRGRVRFGTSDDLAMGPLPDMLAAFRSQHPEVELEIT 139 Query: 125 VDVGAVLESRVAKGELDFAI---IAGRSSHYDILSQPLSQEQFIWVAAP 170 + + + L + + +G+LD + +G S + + S P+ W+ P Sbjct: 140 IGLTSDLYASLDQGKLDLLVGKRRSGESRGHSMFSTPMQ-----WLTRP 183 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 0.322 0.136 0.407 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: 840,433 Number of extensions: 33179 Number of successful extensions: 194 Number of sequences better than 1.0e-08: 27 Number of HSP's gapped: 184 Number of HSP's successfully gapped: 27 Length of query: 307 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 222 Effective length of database: 1,217,395 Effective search space: 270261690 Effective search space used: 270261690 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 (21.9 bits) S2: 130 (54.7 bits)