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= 0001.0102.p (369 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311924|ref|YP_003776016.1| transcription repressor for pur... 766 0.0 gi|300309932|ref|YP_003774024.1| transcription regulator protein... 129 5e-31 gi|300311611|ref|YP_003775703.1| transcription regulator DNA-bin... 127 1e-30 gi|300311238|ref|YP_003775330.1| LacI family transcription regul... 116 3e-27 gi|300309618|ref|YP_003773710.1| LacI family transcription regul... 100 3e-22 >gi|300311924|ref|YP_003776016.1| transcription repressor for pur regulon regulator protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 766 bits (1978), Expect = 0.0, Method: Compositional matrix adjust. Identities = 369/369 (100%), Positives = 369/369 (100%) Query: 1 MSRLTIKDVAKAAGVSFQTVSLVLNHPEKVAPRTRELVQAAIDALNFIPNVAARSLRNIS 60 MSRLTIKDVAKAAGVSFQTVSLVLNHPEKVAPRTRELVQAAIDALNFIPNVAARSLRNIS Sbjct: 1 MSRLTIKDVAKAAGVSFQTVSLVLNHPEKVAPRTRELVQAAIDALNFIPNVAARSLRNIS 60 Query: 61 TRTLACVMFNGSSYDERSERTQDTHYHNVVQTLTRAADRAGYTLLQRNLMREDEASLVYV 120 TRTLACVMFNGSSYDERSERTQDTHYHNVVQTLTRAADRAGYTLLQRNLMREDEASLVYV Sbjct: 61 TRTLACVMFNGSSYDERSERTQDTHYHNVVQTLTRAADRAGYTLLQRNLMREDEASLVYV 120 Query: 121 RDLFLAGRIDGMIAMVNRAGNPVVSELHRLGYPCVVYGMADPACHHVVQSDRQAGLAVVE 180 RDLFLAGRIDGMIAMVNRAGNPVVSELHRLGYPCVVYGMADPACHHVVQSDRQAGLAVVE Sbjct: 121 RDLFLAGRIDGMIAMVNRAGNPVVSELHRLGYPCVVYGMADPACHHVVQSDRQAGLAVVE 180 Query: 181 HLYRSGCRRIALVTGPQKDHQPGKSREQGVPTSSEARYFGYLDGLEKCGLTPRPEWVVTG 240 HLYRSGCRRIALVTGPQKDHQPGKSREQGVPTSSEARYFGYLDGLEKCGLTPRPEWVVTG Sbjct: 181 HLYRSGCRRIALVTGPQKDHQPGKSREQGVPTSSEARYFGYLDGLEKCGLTPRPEWVVTG 240 Query: 241 DWSLESGYRAAAQLCHQAERPDAIFLGNDRMALGALKALYDLGVKVPHEISVVGFDNMRY 300 DWSLESGYRAAAQLCHQAERPDAIFLGNDRMALGALKALYDLGVKVPHEISVVGFDNMRY Sbjct: 241 DWSLESGYRAAAQLCHQAERPDAIFLGNDRMALGALKALYDLGVKVPHEISVVGFDNMRY 300 Query: 301 DDFSIPSLTSVDAPMLEMCEFAVKLLLERIEQRQEQRSQSADPAAAQAALVQKMFSTHLV 360 DDFSIPSLTSVDAPMLEMCEFAVKLLLERIEQRQEQRSQSADPAAAQAALVQKMFSTHLV Sbjct: 301 DDFSIPSLTSVDAPMLEMCEFAVKLLLERIEQRQEQRSQSADPAAAQAALVQKMFSTHLV 360 Query: 361 IRDSTRPVM 369 IRDSTRPVM Sbjct: 361 IRDSTRPVM 369 >gi|300309932|ref|YP_003774024.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 358 Score = 129 bits (323), Expect = 5e-31, Method: Compositional matrix adjust. Identities = 108/340 (31%), Positives = 166/340 (48%), Gaps = 35/340 (10%) Query: 3 RLTIKDVAKAAGVSFQTVSLVLNHPEKVAPRTRELVQAAIDALNFIPNVAARSLRNISTR 62 R +IK VA AGVS TVS +LN P V+ T E + +I L F PN R+LR ++R Sbjct: 2 RPSIKQVAHLAGVSIATVSRLLNKPGSVSAETAEKIHRSIAELGFRPNFTGRNLRAGNSR 61 Query: 63 TLACVMFNGSSYDERSERTQDTHYHNVVQTLTRAADRAGYTLL--QRNLMREDEASLVYV 120 T+ V+ S +T + +Q + AA Y+++ + E+E + V Sbjct: 62 TVGVVVPTLS----------NTVFAQCLQGIELAARALDYSVMFTTTEYLPEEETAAV-- 109 Query: 121 RDLFLAGRIDGMIAMV-NRAGNPVVSELHRLGYPCVV-YG------MADPACHHVVQSDR 172 +L L R+DGMI V + + N + L R P V+ Y A PA V +R Sbjct: 110 -ELLLGHRVDGMILTVADASANATLDLLERERIPFVLAYNQLGTDQTAAPARASVSVDNR 168 Query: 173 QAGLAVVEHLYRSGCRRIALVTGPQKDHQPGKSREQGVPTSSEARYFGYLDGLEKCGLTP 232 A V HL G RRI +++G + + ++ + RY+GYLD + GL P Sbjct: 169 AAACDAVAHLIGLGHRRIQMLSG--RFNASDRAMQ---------RYYGYLDAMRAAGLAP 217 Query: 233 RPEWVVTGDWSLESGYRAAAQLCHQAERPDAIFLGNDRMALGALKALYDLGVKVPHEISV 292 V +L + + +RP A+F ND +A+ A++ L LG+KVP++ISV Sbjct: 218 MAVIEVE-RHTLTAAADYQQMMADPRQRPTALFCSNDLLAMSAMRDLRALGMKVPNDISV 276 Query: 293 VGFDNMRYDDFSIPSLTSVDAPMLEMCEFAVKLLLERIEQ 332 +GFD + P L SV P ++ E A+++L+E IE+ Sbjct: 277 MGFDGIPVGALMEPVLASVVQPSEQIGEVALRVLVEAIER 316 >gi|300311611|ref|YP_003775703.1| transcription regulator DNA-binding repressor protein [Herbaspirillum seropedicae SmR1] Length = 337 Score = 127 bits (320), Expect = 1e-30, Method: Compositional matrix adjust. Identities = 109/335 (32%), Positives = 167/335 (49%), Gaps = 38/335 (11%) Query: 5 TIKDVAKAAGVSFQTVSLVLNHPEKVAPRTRELVQAAIDALNFIPNVAARSLRNISTRTL 64 TIKDVA+ AGVS+ TVS VLN V+ RE V AA+ L+++P+ ARSLR+ T ++ Sbjct: 3 TIKDVARLAGVSYTTVSHVLNQTRPVSSDARERVLAAVKELDYVPSALARSLRSKVTGSI 62 Query: 65 ACVMFNGSS--YDERSERTQDTHYHNVVQTLTRAADRAGYTLLQRNLMREDEASLVYVRD 122 ++ N ++ + E + +D Y AGY+++ N + + Y++ Sbjct: 63 GLIIPNNTNPYFSELARGIEDHCYG------------AGYSVILCNSDDDPDKQRDYLQ- 109 Query: 123 LFLAGRIDGMI-AMVNRAG-NPVVSELHRLGYPCVVYGMADPACH-HVVQSDRQAGLAVV 179 + DG+I A +N+A NP +L P V+ A +V +D G ++ Sbjct: 110 VLQTKHCDGLIIATLNQADLNPA----GKLDIPTVLLDRAPKELDIDLVSTDNAVGGSLA 165 Query: 180 -EHLYRSGCRRIALVTGPQKDHQPGKSREQGVPTSSEARYFGYLDGLEKCGLTPRPEWVV 238 HL R+A + GP G+ S E R G+ LE+ GL ++ Sbjct: 166 ARHLLDLRRCRVACIAGPD-----------GLELSDE-RVRGFRQTLEQGGLALADSDLL 213 Query: 239 TGDWSLESGYRAAAQLCH---QAERPDAIFLGNDRMALGALKALYDLGVKVPHEISVVGF 295 D+S GY+AA +L +RPDAIF ND MA+G L+A +L ++VP E+SVVGF Sbjct: 214 HADFSGIGGYQAAMRLLQGRPADQRPDAIFCCNDMMAIGVLRAAGELQIEVPGELSVVGF 273 Query: 296 DNMRYDDFSIPSLTSVDAPMLEMCEFAVKLLLERI 330 D++ F P LT+V ++ + LLERI Sbjct: 274 DDIELAQFVHPPLTTVAQNTRKLGNLTAQFLLERI 308 >gi|300311238|ref|YP_003775330.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 340 Score = 116 bits (290), Expect = 3e-27, Method: Compositional matrix adjust. Identities = 102/333 (30%), Positives = 157/333 (47%), Gaps = 33/333 (9%) Query: 4 LTIKDVAKAAGVSFQTVSLVLNHPEKVAPRTRELVQAAIDALNFIPNVAARSLRNISTRT 63 +T +DVA+AAGVS TVS V+N PEKV+P TRE V+A I ++ +IPN+ A L + TR Sbjct: 15 VTKEDVARAAGVSHITVSRVINSPEKVSPATRERVEAFIASMGYIPNLLAGGLASRRTRI 74 Query: 64 LACVMFNGSSYDERSERTQDTHYHNVVQTLTRAADRAGYTLL--QRNLMREDEASLVYVR 121 +A ++ + + ++ L+ GY LL Q N E E LV Sbjct: 75 VAAIV----------PTISHSIFAETLRGLSEQLCMQGYQLLLGQTNYSEEAETGLV--- 121 Query: 122 DLFLAGRIDGMIAMVNRAGNPVVSE-LHRLGYPCV-VYGMADPACHHVVQSDRQ-AGLAV 178 ++F+ R+DG++ + +P+ + L G P V + + D + D AG A+ Sbjct: 122 EVFIGRRVDGLV-LTGVQHSPMTRQRLKAAGIPVVETWDLTDTPIDMLAGFDNHAAGRAM 180 Query: 179 VEHLYRSGCRRIALVTGPQKDHQPGKSREQGVPTSSEARYFGYLDGLEKCGLTPRPEWVV 238 ++LY+ G RR+A V G D G AR G + L G V+ Sbjct: 181 GDYLYQKGYRRMAFVGG---DDPRGM-----------ARVAGLRESLRHHGAAEPVHLVM 226 Query: 239 TGDWSLESGYRAAAQLCHQAERPDAIFLGNDRMALGALKALYDLGVKVPHEISVVGFDNM 298 L++G A +L Q DA F ND +A GA G+ VP I++ GF N+ Sbjct: 227 PMGAFLQAGREAIGRLLTQHPEVDAAFFSNDVIAAGAALECARRGIAVPGRIALAGFANL 286 Query: 299 RYDDFSIPSLTSVDAPMLEMCEFAVKLLLERIE 331 +P+LT+V ++ A ++LL R + Sbjct: 287 EIATEVLPALTTVQISAHQIGLTAAEMLLTRFD 319 >gi|300309618|ref|YP_003773710.1| LacI family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 99.8 bits (247), Expect = 3e-22, Method: Compositional matrix adjust. Identities = 96/339 (28%), Positives = 156/339 (46%), Gaps = 39/339 (11%) Query: 5 TIKDVAKAAGVSFQTVSLVLNHPEKVAPRTRELVQAAIDALNFIPNVAARSLRNISTRTL 64 T+ +VA+ AGV+ TVS VL KV +TR+ V A+ L + P++ AR+L TL Sbjct: 3 TLSEVARLAGVTSATVSNVLRQRGKVGEQTRQRVLDAVAQLGYRPHLTARALAEGRAPTL 62 Query: 65 ACVMFNGSSYDERSERTQDTHYHNVVQTLTRAADRAGYTLLQRNLMREDEASLVYVRDLF 124 A V+ + + Y RAA G L+ N + + Y+ + Sbjct: 63 ALVVSS----------IANPFYPEFALAAERAARDHGRFLIVCNTNDDPDIGRAYLDQI- 111 Query: 125 LAGRIDGMIAMVNRAGNPVVSELHRL---GYPCVVYGM----ADPACHHVVQSDRQAGLA 177 AG + + ++N N + EL + G P V+ A P + +AG Sbjct: 112 -AGTLSDGVLIMN--ANLPMDELRKTEQRGAPVVLCMWEKPDAPPELPCIAVDFFEAGAI 168 Query: 178 VVEHLYRSGCRRIALVTGPQKDHQPGKSREQGVPTSSEARYFGYLDGLEKCG---LTPRP 234 HL G + A + G S++ G+ RY G+ ++ G T R Sbjct: 169 AARHLLGLGHQCFAALVG---------SKKSGI---HAERYRGFASACKEAGHPHPTQRT 216 Query: 235 EWVVTGDWSLESGYRAAAQLCHQAERPDAIFLGNDRMALGALKALYDLGVKVPHEISVVG 294 ++ + ++ESGYRA +L + + AIF ND ALGA+ A+ D+G+ VP ++SV G Sbjct: 217 RYI---NDTVESGYRATMELLREHPQVTAIFASNDLPALGAMNAIADMGMNVPRDVSVTG 273 Query: 295 FDNMRYDDFSIPSLTSVDAPMLEMCEFAVKLLLERIEQR 333 ++++ S P+LT+V P +++LLL IE+R Sbjct: 274 ITDIQWARVSRPALTTVAVPTEAAARMSIELLLALIERR 312 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 0.321 0.134 0.391 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: 1,034,215 Number of extensions: 40633 Number of successful extensions: 138 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 129 Number of HSP's successfully gapped: 7 Length of query: 369 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 282 Effective length of database: 1,207,925 Effective search space: 340634850 Effective search space used: 340634850 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)