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= 0003.0052.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|300313081|ref|YP_003777173.1| transcription regulator protein... 334 3e-93 gi|300311850|ref|YP_003775942.1| AraC family transcription regul... 166 2e-42 gi|300313912|ref|YP_003778004.1| AraC family transcription regul... 156 1e-39 gi|300312798|ref|YP_003776890.1| AraC family transcription regul... 141 4e-35 gi|300311694|ref|YP_003775786.1| AraC family transcription regul... 90 2e-19 >gi|300313081|ref|YP_003777173.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 330 Score = 334 bits (857), Expect = 3e-93, Method: Compositional matrix adjust. Identities = 171/196 (87%), Positives = 185/196 (94%) Query: 1 MPARDIAFLIFADCSMLDFTGPLSAFDAANRVSGRALYRITLYSEPGGLIRSSAGAMIQT 60 MP R+ AFLIFADCSMLDFTGPLSAFDAANR++G+ LYR+TLYSEPGG+IRSSAGA+I T Sbjct: 1 MPLRETAFLIFADCSMLDFTGPLSAFDAANRLAGKTLYRLTLYSEPGGMIRSSAGALIHT 60 Query: 61 ERIGRASFDTLVVAGGGAPREGLVSDALRRYILRAASRSRRIAGVCTGAFVLAAAGLLDG 120 ERIGR SFDTL+VAGGGAPREGLVS ALRR++LRAA+RSRRIAG+CTGAFVLAA GLLDG Sbjct: 61 ERIGRTSFDTLIVAGGGAPREGLVSPALRRHVLRAAARSRRIAGICTGAFVLAATGLLDG 120 Query: 121 KRATTHWRMAAKLQQMHPQVKVDSDRIYSCDGKVWTSAGISAGIDLALALIEEDHGAELA 180 KRATTHWRMAAKLQQMHP VKVDSDRIYS DG VWTSAGISAGIDLALALIE+DHG ELA Sbjct: 121 KRATTHWRMAAKLQQMHPAVKVDSDRIYSRDGAVWTSAGISAGIDLALALIEDDHGVELA 180 Query: 181 KSVARELVVYHRRPGG 196 +SVARELVVYHRRPGG Sbjct: 181 RSVARELVVYHRRPGG 196 >gi|300311850|ref|YP_003775942.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 343 Score = 166 bits (419), Expect = 2e-42, Method: Compositional matrix adjust. Identities = 89/203 (43%), Positives = 132/203 (65%), Gaps = 8/203 (3%) Query: 2 PARDIAFLIFADCSMLDFTGPLSAFDAANRVSGRALYRITLYSEPGGLIRSSAG------ 55 P R + FL +A ++LD +GP+ NR+ GR +YR+ + S GG I +SAG Sbjct: 6 PPRRVVFLAYAGMNLLDLSGPMQVLATTNRLQGREVYRLHVVSAQGGTILTSAGLPVGTQ 65 Query: 56 AMIQTERIGRASFD--TLVVAGGGAPREGLVSDALRRYILRAASRSRRIAGVCTGAFVLA 113 ++ + +R+ +A+ D TL+ GG + + + AL +I + A + RI VCTGAF LA Sbjct: 66 SLQEMDRLLQATPDLHTLISPGGSSGDQFPLDAALVAWIRQHAQAAVRICSVCTGAFHLA 125 Query: 114 AAGLLDGKRATTHWRMAAKLQQMHPQVKVDSDRIYSCDGKVWTSAGISAGIDLALALIEE 173 AG+LDG R TTHW A +LQ+ +P ++VD+D IY G++WTSAG++AGIDLALAL+E+ Sbjct: 126 EAGVLDGLRVTTHWDWAQELQRRYPALQVDADPIYIRQGRIWTSAGVTAGIDLALALVEQ 185 Query: 174 DHGAELAKSVARELVVYHRRPGG 196 D G A + AR+LV++ +RPGG Sbjct: 186 DLGHASAIATARQLVMFIKRPGG 208 >gi|300313912|ref|YP_003778004.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 313 Score = 156 bits (394), Expect = 1e-39, Method: Compositional matrix adjust. Identities = 85/174 (48%), Positives = 115/174 (66%), Gaps = 1/174 (0%) Query: 24 SAFDAANRVSGRALYRITLYSEPGGLIRSSAGAMIQTERIGRA-SFDTLVVAGGGAPREG 82 + F+ AN+V+G YR+ YS GG + SS G + T + S DT VV G G P E Sbjct: 21 AVFEYANKVAGHEFYRLHNYSVGGGELASSLGMRVTTAKAAATASIDTWVVCGVGNPLES 80 Query: 83 LVSDALRRYILRAASRSRRIAGVCTGAFVLAAAGLLDGKRATTHWRMAAKLQQMHPQVKV 142 S ++ RAA ++RRIAG+CTG FVLA AGLL +RATTHW A +Q+ P ++V Sbjct: 81 PASAEECAFLQRAAKKARRIAGICTGGFVLAEAGLLARRRATTHWAFARAMQERFPDIQV 140 Query: 143 DSDRIYSCDGKVWTSAGISAGIDLALALIEEDHGAELAKSVARELVVYHRRPGG 196 + DRIY DG +WTSAG++AG+DLALA++ +D G E A+SVAR+LV++ R GG Sbjct: 141 EDDRIYIVDGPLWTSAGMTAGLDLALAMVGKDLGEEAARSVARKLVMHQHRAGG 194 >gi|300312798|ref|YP_003776890.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 335 Score = 141 bits (356), Expect = 4e-35, Method: Compositional matrix adjust. Identities = 86/202 (42%), Positives = 119/202 (58%), Gaps = 10/202 (4%) Query: 1 MPARDIAFLIFADCSMLDFTGPLSAFDAANRVSGRALYRITLYSEPGGLIR-----SSAG 55 + AR + F+ F LD GP+ F A ++ + Y + + S G L+R S AG Sbjct: 15 LAARTVVFIAFDGAEPLDLMGPIGVFSRAEELAPGS-YALRVASVDGALLRTRSPLSLAG 73 Query: 56 AMIQTERIGRASFDTLVVAGG--GAPREGLVSDALRRYILRAASRSRRIAGVCTGAFVLA 113 + + GR DT++VAGG A + AL ++ R ++RRI +CTGAFVL Sbjct: 74 IVPLSSIEGR--LDTVLVAGGHEQAIHQAATEVALVEWLNRRGRQARRIGSICTGAFVLG 131 Query: 114 AAGLLDGKRATTHWRMAAKLQQMHPQVKVDSDRIYSCDGKVWTSAGISAGIDLALALIEE 173 AAGLLDG+ TTHW LQQ P+ KVD D IY DG + TSAG++ GIDLALAL+ + Sbjct: 132 AAGLLDGRYVTTHWAAVDLLQQYFPKAKVDPDAIYRIDGPICTSAGVTTGIDLALALVRD 191 Query: 174 DHGAELAKSVARELVVYHRRPG 195 D G E+A ++AR+LV++ RPG Sbjct: 192 DLGQEIASAIARDLVLFLHRPG 213 >gi|300311694|ref|YP_003775786.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 375 Score = 89.7 bits (221), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 54/155 (34%), Positives = 81/155 (52%), Gaps = 3/155 (1%) Query: 38 YRITLYSEPGGLIRSSAGAMIQTERIGRA---SFDTLVVAGGGAPREGLVSDALRRYILR 94 Y +L S GG+I +S+ I T + +FD++++A G L ++ Sbjct: 73 YHFSLLSVRGGMITTSSSVQIGTLSLQHHDIRAFDSIIIADGRGNFADCNDPQLLNWLAT 132 Query: 95 AASRSRRIAGVCTGAFVLAAAGLLDGKRATTHWRMAAKLQQMHPQVKVDSDRIYSCDGKV 154 AA + RIA +CTG VLA AGLLD K+ HW + +LQ+ P + V+ D V Sbjct: 133 AALHAPRIAALCTGVLVLAEAGLLDRKKVAAHWALRDRLQREFPDIHVEPGDTLVQDQNV 192 Query: 155 WTSAGISAGIDLALALIEEDHGAELAKSVARELVV 189 +TSA G ++ALALIE+D G+ A + + L V Sbjct: 193 FTSADSGTGAEVALALIEDDLGSSFAHRIEQSLTV 227 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 0.323 0.138 0.408 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: 583,414 Number of extensions: 21284 Number of successful extensions: 84 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 82 Number of HSP's successfully gapped: 6 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: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 128 (53.9 bits)