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= 0007.0058.p (379 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311586|ref|YP_003775678.1| ATP-dependent DNA ligase [Herba... 255 3e-69 gi|300309639|ref|YP_003773731.1| LysR family transcription regul... 151 7e-38 gi|300309921|ref|YP_003774013.1| LysR family transcription regul... 75 1e-14 gi|300311929|ref|YP_003776021.1| LysR family transcription regul... 73 5e-14 gi|300311233|ref|YP_003775325.1| LysR family transcription regul... 72 6e-14 >gi|300311586|ref|YP_003775678.1| ATP-dependent DNA ligase [Herbaspirillum seropedicae SmR1] Length = 856 Score = 255 bits (652), Expect = 3e-69, Method: Compositional matrix adjust. Identities = 129/195 (66%), Positives = 149/195 (76%), Gaps = 6/195 (3%) Query: 165 DGEVVAVLDDGSISFEALQ-----DPTGYDGVTLAIYVFDLLWLNGKDLRDTPLLERKRL 219 DGEVVA+ G ISFEALQ D DG+ LA+Y FDLL+LNG DLRD PL +RK L Sbjct: 284 DGEVVALDAQGQISFEALQNLARGDRQQADGIRLALYAFDLLYLNGHDLRDIPLRQRKAL 343 Query: 220 LREVVPGVDHSGLIRFSEHVVGDAAEVYRHACLHGMEGTVVKRADAAYAGRRDRSWVKLK 279 LRE++PG D GL+ +SEH+ G AAEV+RHAC HGMEG V+KRADA Y GRRDR W+KLK Sbjct: 344 LRELIPGSDPEGLLLYSEHIEGHAAEVFRHACQHGMEGIVLKRADAPYTGRRDRYWLKLK 403 Query: 280 CAMRQEFVIAGYTDPAGSRVGFGALLVGVYDAASGELHYAGRVGTGFDDRKLTQLLKRFK 339 C RQEFVIAGYT+PAG R GFGA+LVGVYD +L YAGRVGTGFDD+ L LLK+F Sbjct: 404 CEHRQEFVIAGYTEPAGQRSGFGAILVGVYDEHE-QLRYAGRVGTGFDDKLLETLLKQFG 462 Query: 340 TLERDQPAFVDPPRG 354 LE+DQPAF +PP G Sbjct: 463 PLEQDQPAFANPPTG 477 >gi|300309639|ref|YP_003773731.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 296 Score = 151 bits (382), Expect = 7e-38, Method: Compositional matrix adjust. Identities = 75/137 (54%), Positives = 102/137 (74%), Gaps = 1/137 (0%) Query: 24 LNRIEQLRIFCMAAESANFREAAVRLGISPQVVTRAVKELEAAFGEVLFHRNTRQVRITA 83 LNR+E LRIFC AA++ +F++AA+RLGISPQ VTRA++ELE GE+LFHRNTRQVRIT+ Sbjct: 2 LNRLEMLRIFCAAADTGSFKDAAIRLGISPQAVTRAIQELERLQGEMLFHRNTRQVRITS 61 Query: 84 FGERLMHRARLSINALDDLFLDNNHRNDEILSGVVRITAPSTLAHTYLLPVINRIARQHP 143 FGE L RAR S+ LD LF + + +SG+VR+ APS+L + LLP++ R+A+ HP Sbjct: 62 FGEALAERARASLRDLDGLFETDTASPADEMSGLVRLAAPSSLGRSRLLPIVERLAQAHP 121 Query: 144 DITLDLRLSEXQHPDIT 160 + DLRL++ Q D+ Sbjct: 122 GLRFDLRLTD-QRADVV 137 >gi|300309921|ref|YP_003774013.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 74.7 bits (182), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 45/133 (33%), Positives = 72/133 (54%), Gaps = 7/133 (5%) Query: 24 LNRIEQLRIFCMAAESANFREAAVRLGISPQVVTRAVKELEAAFGEVLFHRNTRQVRITA 83 +N++ ++ F A+ +F +AA LGIS V+R V ELEA G L R TR++ +T Sbjct: 1 MNKLREIECFIAVADLGSFVKAAEALGISKAAVSRTVLELEARLGSRLMQRTTRRLSLTE 60 Query: 84 FGERLMHRARLSINAL---DDLFLDNNHRNDEILSGVVRITAPSTLAHTYLLPVINRIAR 140 G + R + + AL DDL + + +G++RI AP T +L P+ Sbjct: 61 AGALYLERCKQIVAALEEADDLLSSGSAKP----TGLLRINAPLTFGVLHLAPLWPMFLE 116 Query: 141 QHPDITLDLRLSE 153 +HP+I+LD+ LS+ Sbjct: 117 RHPEISLDITLSD 129 >gi|300311929|ref|YP_003776021.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 304 Score = 72.8 bits (177), Expect = 5e-14, Method: Compositional matrix adjust. Identities = 41/125 (32%), Positives = 71/125 (56%), Gaps = 5/125 (4%) Query: 30 LRIFCMAAESANFREAAVRLGISPQVVTRAVKELEAAFGEVLFHRNTRQVRITAFGERLM 89 + +FC AAE +F AA LG++P V+R++ LE+ G LF R TRQ+R+T GE Sbjct: 12 IELFCKAAELGSFTAAAEALGLTPASVSRSISRLESRLGVRLFARTTRQIRLTREGELYR 71 Query: 90 HRARLSINALDDL--FLDNNHRNDEILSGVVRITAPSTLAHTYLLPVINRIARQHPDITL 147 + + ++ + D L + + SG++RI+ + AH LLP++ R + +P I + Sbjct: 72 DQCQQALEQIADAERILTGQQK---VPSGLLRISVGTPYAHYRLLPLLPRFQQAYPQIEV 128 Query: 148 DLRLS 152 +L ++ Sbjct: 129 ELSIA 133 >gi|300311233|ref|YP_003775325.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 315 Score = 72.4 bits (176), Expect = 6e-14, Method: Compositional matrix adjust. Identities = 43/142 (30%), Positives = 72/142 (50%), Gaps = 6/142 (4%) Query: 27 IEQLRIFCMAAESANFREAAVRLGISPQVVTRAVKELEAAFGEVLFHRNTRQVRITAFGE 86 + ++ +F E+ +F EAA +LG +P ++RA+ LE A G L R TR++R++ G+ Sbjct: 10 LNEMAVFAKVVETGSFSEAARQLGATPSAISRAIARLEKALGTQLLQRTTRKLRLSESGQ 69 Query: 87 RLMHRARLSINALDDLFLDNNHRNDEILSGVVRITAPSTLAHTYLLPVINRIARQHPDIT 146 + R R +NA + + + E G VR++ P + H + P + HP + Sbjct: 70 DIHARCRDMLNAAQAVLAVSGAFDAEP-QGQVRVSVPKAVGHALVHPHVPDFLAAHPKVD 128 Query: 147 LDLRLSEXQHPDITLDLRDGEV 168 + LRL D +DL D EV Sbjct: 129 VLLRLE-----DRYMDLIDDEV 145 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 0.138 0.422 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: 1,212,519 Number of extensions: 48375 Number of successful extensions: 247 Number of sequences better than 1.0e-08: 33 Number of HSP's gapped: 237 Number of HSP's successfully gapped: 33 Length of query: 379 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 292 Effective length of database: 1,207,925 Effective search space: 352714100 Effective search space used: 352714100 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: 131 (55.1 bits)