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= 0001.1041.p (345 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310565|ref|YP_003774657.1| response regulator containing a... 589 e-170 gi|300313980|ref|YP_003778072.1| two component response regulato... 117 2e-27 gi|300314021|ref|YP_003778113.1| HD-GYP domain-containing protei... 114 9e-27 gi|300313282|ref|YP_003777374.1| HD-GYP domain-containing protei... 111 7e-26 gi|300311984|ref|YP_003776076.1| HD-GYP domain-containing protei... 107 1e-24 >gi|300310565|ref|YP_003774657.1| response regulator containing a CheY-like receiver domain and an HD-GYP domain [Herbaspirillum seropedicae SmR1] Length = 348 Score = 589 bits (1519), Expect = e-170, Method: Compositional matrix adjust. Identities = 281/345 (81%), Positives = 310/345 (89%) Query: 1 MKILIVDDDKTNLSLFTHMLGQLPDTDISTCPDALEALQWCGAHAPDLILLDYMMPGMDG 60 M ILIVDDDKTNLSLF+HMLGQ+P T I TC DA +AL WC HAPDLILLDYMMPGMDG Sbjct: 4 MNILIVDDDKTNLSLFSHMLGQVPQTRIDTCADARQALDWCQEHAPDLILLDYMMPGMDG 63 Query: 61 LDFLSRFRALPGQEMTPVIMITADMGLQVRHKALQMTANDFLSKPVNRVELLARVKNMLA 120 LDFLSRFRA+PGQEMTPVIMITADMGLQVRH ALQM+ANDFLSKPVNRVELLARVKNMLA Sbjct: 64 LDFLSRFRAMPGQEMTPVIMITADMGLQVRHTALQMSANDFLSKPVNRVELLARVKNMLA 123 Query: 121 MRKSQLAMSQKIEHLAEQVQEKSHQSNTLALNSVDLLTRAAGYRDPETGEHLVRMANYTR 180 MR+SQLAMSQKI+ L+EQV ++ S+TLAL+SVDLL RAAGYRDPETGEHL RMANY R Sbjct: 124 MRRSQLAMSQKIDTLSEQVDQQVRHSDTLALDSVDLLARAAGYRDPETGEHLTRMANYAR 183 Query: 181 IIASHLGLPKAEQDLLLAAAPMHDIGKMGIPDHILLKPGRLDEEELKIMRLHAQIGADIL 240 IIA+ +GL +Q+LLL AAPMHDIGKMGIPDHILLKPGRLDEEELK+MR+HA+IGADIL Sbjct: 184 IIAARMGLDSQQQELLLNAAPMHDIGKMGIPDHILLKPGRLDEEELKVMRMHARIGADIL 243 Query: 241 RDSPSVLLQTASQIAHSHHEKWDGSGYPNGLKGEDIPLYGRIVAVADVFDALTSSRPYKK 300 SPS LLQTASQIA +HHEKWDGSGYPNGLKGE IPLYGRIVAVADVFDALTSSRPYK Sbjct: 244 VASPSPLLQTASQIALTHHEKWDGSGYPNGLKGEQIPLYGRIVAVADVFDALTSSRPYKP 303 Query: 301 GWSLADAQRYLRDNAGSHFDPRCVDAFFAGWEEVVDIYNRNQDSK 345 GWSL A +YLR+ +G+HFDPRCV+AFFAGWEEV++I+NR Q+ K Sbjct: 304 GWSLERASQYLREQSGAHFDPRCVEAFFAGWEEVLEIFNRYQEGK 348 >gi|300313980|ref|YP_003778072.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 199 Score = 117 bits (292), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 66/182 (36%), Positives = 98/182 (53%), Gaps = 2/182 (1%) Query: 145 QSNTLALNSVDLLTRAAGYRDPETGEHLVRMANYTRIIASHLGLPKAEQDLLLAAAPMHD 204 +SN + +D + D T H + A +I HL L D L A+ +HD Sbjct: 5 ESNKIYQEVIDAMIAVHRLTDGYTPNHEDQTAELAVMIGRHLDLATERIDALHMASQVHD 64 Query: 205 IGKMGIPDHILLKPGRLDEEELKIMRLHAQIGADILRDSPSVLLQTASQIAHSHHEKWDG 264 IGK IP +L KPGR+ EE +++ H Q G +IL + S A +I H HHE DG Sbjct: 65 IGKARIPLALLTKPGRISVEEYDVLKTHVQFGYEIL-NKISFPFNLA-EIVHCHHEYLDG 122 Query: 265 SGYPNGLKGEDIPLYGRIVAVADVFDALTSSRPYKKGWSLADAQRYLRDNAGSHFDPRCV 324 SGYP G+ G++IPL RI+ VAD+ +++++ RPY+K ++ A ++ +G D V Sbjct: 123 SGYPRGISGDEIPLEARILTVADIVESMSADRPYRKSLGMSAALDEIQRQSGVRLDAVVV 182 Query: 325 DA 326 DA Sbjct: 183 DA 184 >gi|300314021|ref|YP_003778113.1| HD-GYP domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 401 Score = 114 bits (286), Expect = 9e-27, Method: Compositional matrix adjust. Identities = 61/147 (41%), Positives = 88/147 (59%), Gaps = 2/147 (1%) Query: 182 IASHLGLPKAEQDLLLAAAPMHDIGKMGIPDHILLKPGRLDEEELKIMRLHAQIGADILR 241 +A+ LG+ + A +HD+GKM +P IL KP +L EEE +R+H G IL+ Sbjct: 176 LANQLGMTPQQTKQAGMAGLLHDVGKMAVPLDILNKPAKLTEEEFASVRMHTVQGHGILQ 235 Query: 242 DSPSVLLQTASQIAHSHHEKWDGSGYPNGLKGEDIPLYGRIVAVADVFDALTSSRPYKKG 301 + + A ++ HHEK DGSGYP LK + I + ++ AV DV+DA+TS+RPYK G Sbjct: 236 QIEGIG-EVALDVSLHHHEKIDGSGYPFNLKADSISIMAKMGAVCDVYDAITSNRPYKAG 294 Query: 302 WSLADAQRYLRDNAGSHFDPRCVDAFF 328 W A + R++ +AG HFDP + AF Sbjct: 295 WDPARSIRHMAASAG-HFDPITMQAFV 320 >gi|300313282|ref|YP_003777374.1| HD-GYP domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 410 Score = 111 bits (278), Expect = 7e-26, Method: Compositional matrix adjust. Identities = 66/163 (40%), Positives = 88/163 (53%), Gaps = 2/163 (1%) Query: 165 DPETGEHLVRMANYTRIIASHLGLPKAEQDLLLAAAPMHDIGKMGIPDHILLKPGRLDEE 224 D T H V + + LGL +A + +HD+GK I D IL KPG+L E Sbjct: 153 DEYTYLHSVSVCALVIGLGRTLGLSEAACREAGLSGYLHDVGKAFIDDEILNKPGKLTAE 212 Query: 225 ELKIMRLHAQIGADILRDSPSVLLQTASQIAHSHHEKWDGSGYPNGLKGEDIPLYGRIVA 284 E +++ H ++G L +P + AS + HHE+ DG GYP+ L E I LY R+ A Sbjct: 213 EFALIKRHPELGYQYLIQTPD-MPAYASDVCRHHHERLDGRGYPDALPAESITLYARMTA 271 Query: 285 VADVFDALTSSRPYKKGWSLADAQRYLRDNAGSHFDPRCVDAF 327 V DV+DALTS RPYK GW A+A + G HFD R + AF Sbjct: 272 VCDVYDALTSERPYKHGWDPAEAISQMARWEG-HFDRRLLLAF 313 >gi|300311984|ref|YP_003776076.1| HD-GYP domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 406 Score = 107 bits (267), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 65/174 (37%), Positives = 93/174 (53%), Gaps = 6/174 (3%) Query: 165 DPETGEHLVRMANYTRIIASHLGLPKAEQDLLLAAAPMHDIGKMGIPDHILLKPGRLDEE 224 D T H V + +A LGL E+ A +HDIGKM +P IL KP +L EE Sbjct: 162 DNYTYMHSVAVCAMMISLADQLGLSAQERQQAGMAGLLHDIGKMTVPPSILNKPSKLTEE 221 Query: 225 ELKIMRLHAQIGADILRDSPSVLLQTASQIAHSHHEKWDGSGYPNGLKGEDIPLYGRIVA 284 E ++ H G +L++ P + ++ HHEK DG+GYP L G DI + R+ A Sbjct: 222 EFVSVQSHPLAGHRLLQELPGIG-DAPLDVSLHHHEKMDGTGYPYKLSGRDISMTARMGA 280 Query: 285 VADVFDALTSSRPYKKGWSLADAQRYLRDNAGSHFDPRCVDAFFAGWEEVVDIY 338 + DV+DA+TS RPYK GW + + +++ + G HFD + AF + V IY Sbjct: 281 ICDVYDAITSDRPYKSGWDPSRSIQHMAQSKG-HFDFDVLQAFV----KAVGIY 329 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 0.320 0.135 0.401 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: 1,093,987 Number of extensions: 46099 Number of successful extensions: 316 Number of sequences better than 1.0e-08: 36 Number of HSP's gapped: 322 Number of HSP's successfully gapped: 36 Length of query: 345 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 259 Effective length of database: 1,212,660 Effective search space: 314078940 Effective search space used: 314078940 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 (21.8 bits) S2: 131 (55.1 bits)