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= 0007.0062.p (693 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... 330 2e-91 gi|300312843|ref|YP_003776935.1| response regulator containing a... 265 1e-71 gi|300310865|ref|YP_003774957.1| response regulator containing a... 202 1e-52 gi|300313022|ref|YP_003777114.1| two component sensor histidine ... 120 5e-28 gi|300313918|ref|YP_003778010.1| transmembrane protein [Herbaspi... 106 7e-24 >gi|300311586|ref|YP_003775678.1| ATP-dependent DNA ligase [Herbaspirillum seropedicae SmR1] Length = 856 Score = 330 bits (847), Expect = 2e-91, Method: Compositional matrix adjust. Identities = 181/287 (63%), Positives = 201/287 (70%), Gaps = 23/287 (8%) Query: 384 RAKRDFKITPEPPPEPVARRSG---KTLSYFIQRHHARALHYDFRLEVNGVLKSWAVPKG 440 RAKRDF ITPEP R+G ++L +FIQRHHAR LHYDFRLE++GVLKSWAVPKG Sbjct: 10 RAKRDFTITPEPSGHASRSRAGAQSQSLQFFIQRHHARRLHYDFRLELDGVLKSWAVPKG 69 Query: 441 PSLDPHDKRLAVHVEDHPYDYGSFEGRIPAHQYGAGEVVLWDRGEWLPIGDPVAGLKKGH 500 PSLDPHDKRLAV VEDHP+DYGSFEG IPAHQYGAG VVLWDRG+W P GD AGL KGH Sbjct: 70 PSLDPHDKRLAVRVEDHPFDYGSFEGDIPAHQYGAGHVVLWDRGQWRPHGDARAGLAKGH 129 Query: 501 LEFELRGAKLSGRWNLVRMGKPADKDKDKDDKTKENWLLIKEKDDAAREGKQADITALRP 560 L FEL G KL GRW LVRMGKPA KENWLLIK+ D AA G+QA IT LRP Sbjct: 130 LSFELEGEKLHGRWALVRMGKPA-------ADGKENWLLIKDDDAAAASGEQAAITELRP 182 Query: 561 ESVAGTATKKTGIAPGNAAEKPVETTSKKRKPAGRAATSMPMPDKVDAQLAMLVKEAPDG 620 ESV G+ A S K P ++ PMP ++ AQLA LV AP G Sbjct: 183 ESVKDL---------GDQAPLAKARASAKAAP----DSTGPMPAQMQAQLATLVDRAPAG 229 Query: 621 DAWLSEMKFDGYRGLCRIEGGKARIFTREHLDWSKRWPQLTQALAAL 667 + WL E+KFDGYRGLCRI+ G+A I+TRE LDWS RWP L QALA L Sbjct: 230 EQWLCELKFDGYRGLCRIDHGQAAIYTREGLDWSHRWPILVQALARL 276 >gi|300312843|ref|YP_003776935.1| response regulator containing a CheY-like receiver and a GGDEF domains protein [Herbaspirillum seropedicae SmR1] Length = 525 Score = 265 bits (677), Expect = 1e-71, Method: Compositional matrix adjust. Identities = 136/355 (38%), Positives = 215/355 (60%), Gaps = 1/355 (0%) Query: 34 ASVFVGLVCLSILILHISFAWNVRVKDLDDAQISTANLSRALAEHAQATLISADSVLFGM 93 A +FV L+C +I H+ + R L++ + + N+++ALA HA L + D +L M Sbjct: 20 ARLFVVLICAAIAGGHLWQSMTARGVQLENNRSYSGNVAKALARHAYDVLQATDGLLLDM 79 Query: 94 VQRLEVEGMDRDSLARLYPLLASYVKELPQIQGLFVYDQSGKWMVNSMDDSPWMLNNADR 153 R++ G+ L L P+L E+PQ+ GL+V+D+ GK ++ S NN+DR Sbjct: 80 SDRIDSVGIAHARLVDLMPMLRRLSSEMPQLDGLYVFDEHGKRLLTSSAPPLAPANNSDR 139 Query: 154 EYFIYHMTHEDRNPHVGEPVKSRSSGDWIIPLSRRINHPDGSFAGVVLASVEVEYFLKFY 213 +YFI+H H+D PHVG+ + SRS+G WIIP+SRR+NHPDGSFAGV+LA++++ +F + Y Sbjct: 140 DYFIWHRDHDDVGPHVGKALLSRSTGRWIIPMSRRLNHPDGSFAGVLLATLDINHFNQLY 199 Query: 214 RSFDIGKHGEILLATQPGILLAKWPASGEIIGKNISNSNIVSDHASRNRNG-IAIITGAD 272 R+ +IGK G I L + G LL + P I ++ S + + + G + +++ D Sbjct: 200 RTVEIGKGGSIALLLRDGTLLTRMPFDPGYINRDFSQGRLFLEGLPHSPFGYLEVVSPLD 259 Query: 273 GVKRLHSYKRLEKYPLFVTAALSYDEVLASWRTETLMQSVGVLILVAMLAWMGKRLINQI 332 +R SY+ ++KYPL + L+ +E LA W+ +T + VL+L+A++ G RL+ QI Sbjct: 260 ARQRFLSYQAVDKYPLVLVVTLAREEALADWKQQTFVYGAAVLLLLAIIGVFGWRLVGQI 319 Query: 333 KLRAQAQQKLLSAREKLVEMNKTLQKMALEDGLTGVANRRQFDVTLANEFNRAKR 387 +LR +A+ + L A +L N L+ +A +DGLTG+ANRR D L EF RA+R Sbjct: 320 ELRLRAEDRALQAMGELQMANHRLEMLAHQDGLTGLANRRHLDTMLETEFKRAER 374 >gi|300310865|ref|YP_003774957.1| response regulator containing a CheY-like receiver domain and a GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 554 Score = 202 bits (513), Expect = 1e-52, Method: Compositional matrix adjust. Identities = 104/324 (32%), Positives = 184/324 (56%), Gaps = 1/324 (0%) Query: 53 AWNVRVKDLDDAQISTANLSRALAEHAQATLISADSVLFGMVQRLEVEGMDRDSLARLYP 112 AW R L ++ +N++ AL +HA+ ++ AD VL + + L+ E + R + Sbjct: 45 AWRAREVALSESTTDASNVALALIQHAEQSIKEADIVLETVQEHLDHEDRSASARIRTHD 104 Query: 113 LLASYVKELPQIQGLFVYDQSGKWMVNSMDDSPWMLNNADREYFIYHMTHEDRNPHVGEP 172 + V LPQ+ L V D+ G+ + +S + +YF YH P +G+P Sbjct: 105 FMIRSVASLPQLAQLTVVDEQGRTVASSQQRMVQTGSPVQDDYFQYHQHRRSDRPFIGQP 164 Query: 173 VKSRSSGDWIIPLSRRINHPDGSFAGVVLASVEVEYFLKFYRSFDIGKHGEILLATQPGI 232 ++S +G + +SRRINH DGSFAGV++A +++ YF ++Y F+IG HG IL G Sbjct: 165 MRSHVTGQRTLTVSRRINHVDGSFAGVIVAEIDLAYFQRYYEQFNIGPHGVILFGLTGGS 224 Query: 233 LLAKWPASGEIIGKNISNSNIVSDHASRNRNG-IAIITGADGVKRLHSYKRLEKYPLFVT 291 L+ + P ++ ++ + S + H + R G A+ + DGV+R+ +++ E YP+F Sbjct: 225 LILRRPLLADMTDRSPAMSEALRKHMEQARRGSFAMRSERDGVERISCFQQGEAYPIFTV 284 Query: 292 AALSYDEVLASWRTETLMQSVGVLILVAMLAWMGKRLINQIKLRAQAQQKLLSAREKLVE 351 AL+ D++L W ++ +GV++L+A++ + GKRL+ + R +A+ + ++AR++L Sbjct: 285 VALAKDDILEDWSRHVWVRGIGVVLLLAVICFGGKRLVVLVAGRERAEAQAIAARQELES 344 Query: 352 MNKTLQKMALEDGLTGVANRRQFD 375 + +TL+ + +DGLT V NRR FD Sbjct: 345 LYRTLEAQSQKDGLTDVFNRRYFD 368 >gi|300313022|ref|YP_003777114.1| two component sensor histidine kinase [Herbaspirillum seropedicae SmR1] Length = 556 Score = 120 bits (300), Expect = 5e-28, Method: Compositional matrix adjust. Identities = 95/333 (28%), Positives = 156/333 (46%), Gaps = 31/333 (9%) Query: 24 RSRRVNVRIFASVFVGLVCLSILILHISFAWNVRVKDLDDAQISTANLSRALAEHAQATL 83 R R+++R+ S+F L+ + + N R LDDA+ +LSR EHA T+ Sbjct: 12 RFARIDLRVALSLFSLLLICGLWLGAFKELQNSRNNYLDDARRDAQSLSRLFLEHAYRTI 71 Query: 84 ISADSVLFGMVQRLEVEG--------MDRDSLAR-LYPLLASYVKELPQIQGLFVYDQSG 134 +AD + R G +D +AR +Y L + + D G Sbjct: 72 EAADQAALYLRYRYAERGNALNLATEIDNGLVARNVYNLFS-------------IVDAQG 118 Query: 135 KWMVNSMDDSPWMLNNADREYFIYHMTHEDRNPHVGEPVKSRSSGDWIIPLSRRINHPDG 194 +++S +P +N ADRE+ HM + +PV R S W + ++RRIN PDG Sbjct: 119 DVVLSSKPFTP--VNLADREHVQVHMQGGQDQLFISKPVLGRVSKKWSLQITRRINRPDG 176 Query: 195 SFAGVVLASVEVEYFLKFYRSFDIGKHGEILLATQPGILLAKWPASGEIIGKNISNSNIV 254 F GVV+ S++ +YF + Y D+G HG I L G+ + + +G+ ++ + Sbjct: 177 GFGGVVVVSMDPQYFTRLYHQIDVGHHGVITLVGADGVARVRRTGDMDAMGEQVAGGKVY 236 Query: 255 SDHASRNRNGIAIITGADGVKRLHSYKRLEKYPLFVTAALSYDEVLASW---RTETLM-- 309 + ++ I ++ DG +RL+++++L YPLF + E LA + R TLM Sbjct: 237 AAMLAQGSGTIEAVSKIDGRERLYAFQKLRDYPLFAAVGIDLKERLAPYYRERERTLMLA 296 Query: 310 --QSVGVLILVAMLAWMGKRLINQIKLRAQAQQ 340 SV VL+ A+L W+ L+ + QA Q Sbjct: 297 ALLSVAVLVFNAVLLWLAGSLVRSRREALQANQ 329 >gi|300313918|ref|YP_003778010.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 515 Score = 106 bits (264), Expect = 7e-24, Method: Compositional matrix adjust. Identities = 95/396 (23%), Positives = 175/396 (44%), Gaps = 35/396 (8%) Query: 8 DIPP------AAPELGETPAVARSRRVNVRIFASVFVGLVCLSILILHISFAWNVRVKDL 61 D PP A E + + + + V I A + ++ +S L+ S+ R + Sbjct: 2 DRPPLLCVNYAPGEFAGSAKIKQLKNYLVVILAIAVLMVMAISASTLYQSY-QQTRQSAV 60 Query: 62 DDAQISTANLSRALAEHAQATLISADSVLFGMVQRLEVEGMDRDSLARLYPLLASYVKEL 121 +A T RA++ + + +S D++ + L ++ A+ Y L + Sbjct: 61 SNASNVTLVSQRAISRNLEMLSLSLDTLAYRFQHPLSARRLND---AQRYAYLFGSTTNV 117 Query: 122 PQIQGLFVYDQSGKWMVNSM----DDSPWMLNNADREYFIYHMTHEDRNPHVGEPVKSRS 177 I + V D G+ V+S + +P + ADR YFI H +V P+++ Sbjct: 118 SHIAVMAVLDADGRVQVSSRLGRGNGAP---HYADRAYFIAHRDSPTVGLYVSRPMQASL 174 Query: 178 SGDW-IIPLSRRINHPDGSFAGVVLASVEVEYFLKFYRSFDIGKHGEILLATQPGILLAK 236 + ++ LS+R+++ DGSFAGVV+ ++++ YF + + +G G I L + GI + Sbjct: 175 GNELQVVVLSKRLSNEDGSFAGVVVMALDLAYFRELFEGLALGDEGIISLYSDEGIAYMR 234 Query: 237 WPASGEIIGKNIS---NSNIVSDHASRNRNGIAIITGADGVKRLHSYKRLEKYPLFVTAA 293 P IIG++IS N + S DGV+RL++++R+ PL V Sbjct: 235 VPYRETIIGRDISQTGNFQRLRAMLSEEEGSFFAHATNDGVRRLYTFRRIPGSPLIVFVG 294 Query: 294 LSYDEVLASWRTETLMQSVGVLILVAMLAWMGKRLINQIKLRAQAQQKLLSAREKLVEMN 353 + + + +WR V + I + AW+ + +++ R A+++ Sbjct: 295 YAEEAIFKTWRKTFYAVLVSLAIFGLLTAWLLLHVRQELRRRVTAERQ------------ 342 Query: 354 KTLQKMALEDGLTGVANRRQFDVTLANEFNRAKRDF 389 L+ +A DGLT + NRR D L + R +R+ Sbjct: 343 --LEALARTDGLTDLLNRRALDEALQATWERCQRNL 376 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 0.318 0.134 0.402 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: 2,245,842 Number of extensions: 96232 Number of successful extensions: 325 Number of sequences better than 1.0e-08: 11 Number of HSP's gapped: 310 Number of HSP's successfully gapped: 11 Length of query: 693 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 601 Effective length of database: 1,184,250 Effective search space: 711734250 Effective search space used: 711734250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 134 (56.2 bits)