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= 0124.0005.p (213 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312421|ref|YP_003776513.1| propionate catabolism operon re... 253 6e-69 gi|300313916|ref|YP_003778008.1| two component response regulato... 111 5e-26 gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 107 7e-25 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 106 1e-24 gi|300314016|ref|YP_003778108.1| two component transcription reg... 105 2e-24 >gi|300312421|ref|YP_003776513.1| propionate catabolism operon regulatory protein [Herbaspirillum seropedicae SmR1] Length = 544 Score = 253 bits (647), Expect = 6e-69, Method: Compositional matrix adjust. Identities = 127/149 (85%), Positives = 136/149 (91%) Query: 1 LPLQTRLLRVLEEREVVRVGGTRPIPVNVRIISATHCDLDARVREGRFRADLFYRLSVLR 60 LPLQTRLLRVLEEREVVRVGGTRPIPV VRIISATHCDL ARVREGRFRADL+YRLSVL Sbjct: 336 LPLQTRLLRVLEEREVVRVGGTRPIPVQVRIISATHCDLQARVREGRFRADLYYRLSVLC 395 Query: 61 MTLPPLRERPDDLAPLAEWCLKNALAAMDIRPHANLHAEILRCAPLLARYRWPGNVRELR 120 + LPPLRER DD+A LAEW LK+ALAA+D+RPHANL AEI+RCAPLL RY WPGNVRELR Sbjct: 396 LQLPPLRERRDDIAALAEWHLKHALAALDVRPHANLGAEIVRCAPLLCRYDWPGNVRELR 455 Query: 121 NMMERLALFLAAEPLQALTPNLIARIAPH 149 N+MERLALFLAAEPLQALTP LI R+AP Sbjct: 456 NLMERLALFLAAEPLQALTPALIQRVAPE 484 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 111 bits (277), Expect = 5e-26, Method: Compositional matrix adjust. Identities = 63/131 (48%), Positives = 83/131 (63%), Gaps = 11/131 (8%) Query: 1 LPLQTRLLRVLEEREVVRVGGTRPIPVNVRIISATHCDLDARVREGRFRADLFYRLSVLR 60 L Q ++LRVL+ERE+ VGG + + V+VR+I+ATH DL + +GRFR DL+YRL VL Sbjct: 242 LATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLT 301 Query: 61 MTLPPLRERPDDLAPLAEWCLK--NALAAMDIRPHANLHAEILRCAPLLARYRWPGNVRE 118 + +P LRERP D+ +AE L+ A I P A A LL ++ WPGNVRE Sbjct: 302 IMVPALRERPGDILTIAEHFLRQLGGDAPKRISPAA---------ARLLLQHAWPGNVRE 352 Query: 119 LRNMMERLALF 129 LRN MER A+ Sbjct: 353 LRNTMERAAVM 363 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 107 bits (267), Expect = 7e-25, Method: Compositional matrix adjust. Identities = 61/136 (44%), Positives = 82/136 (60%), Gaps = 4/136 (2%) Query: 1 LPLQTRLLRVLEEREVVRVGGTRPIPVNVRIISATHCDLDARVREGRFRADLFYRLSVLR 60 L Q +LLRVL+E E RVG RP+ V+VR+++AT+ DL VREGRFR DLF+RL+V Sbjct: 370 LVAQGKLLRVLQEGEFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQDLFFRLNVFP 429 Query: 61 MTLPPLRERPDDLAPLAEWCLKNALAAMDIRPHANLHAEILRCAPLLARYRWPGNVRELR 120 + LPPLRER DD+ PL + + L R + R L Y +PGN+REL+ Sbjct: 430 IHLPPLRERRDDI-PL---LMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSFPGNIRELQ 485 Query: 121 NMMERLALFLAAEPLQ 136 N++ER + PL Sbjct: 486 NLIERGVILAQGHPLD 501 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 106 bits (265), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 58/133 (43%), Positives = 83/133 (62%), Gaps = 14/133 (10%) Query: 3 LQTRLLRVLEEREVVRVGGTRPIPVNVRIISATHCDLDARVREGRFRADLFYRLSVLRMT 62 Q +LLRVL+ERE RVGG+R I V+VR+++AT+ DL+ V +G FRADL+YR++V+ + Sbjct: 311 FQAKLLRVLQEREFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIF 370 Query: 63 LPPLRERPDDLAPLAEWCL-----KNALAAMDIRPHANLHAEILRCAPLLARYRWPGNVR 117 +PPLRER +D+ L E L +N A + + P A ++ WPGNVR Sbjct: 371 IPPLRERREDIPYLVEHFLEKFRVENQRAMVAMSPQA---------MKVMMNCYWPGNVR 421 Query: 118 ELRNMMERLALFL 130 EL N +ER A + Sbjct: 422 ELENCVERTATMM 434 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 105 bits (263), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 63/128 (49%), Positives = 83/128 (64%), Gaps = 8/128 (6%) Query: 1 LPLQTRLLRVLEEREVVRVGGTRPIPVNVRIISATHCDLDARVREGRFRADLFYRLSVLR 60 LPLQ +LLRVL+E+ V +VG + V+VRIISATH DL+A +REG+FR DL+YRL+V+ Sbjct: 250 LPLQVKLLRVLQEKTVRQVGANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVT 309 Query: 61 MTLPPLRERPDDLAPLAEWCLKNALAAMDIR--PHANLHAEILRCAPLLARYRWPGNVRE 118 + LP L ER +D+A LA LK A R A EIL A WPGNVR+ Sbjct: 310 LHLPALEERREDIALLANHFLKTIAAKYPKRLTGFAPDALEILSLA------HWPGNVRQ 363 Query: 119 LRNMMERL 126 L N++E++ Sbjct: 364 LYNVVEQV 371 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 0.328 0.139 0.447 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: 660,449 Number of extensions: 27214 Number of successful extensions: 138 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 128 Number of HSP's successfully gapped: 12 Length of query: 213 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 132 Effective length of database: 1,236,335 Effective search space: 163196220 Effective search space used: 163196220 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 128 (53.9 bits)