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= 0001.3373.p (355 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 537 e-154 gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 137 1e-33 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 125 5e-30 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 122 4e-29 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 62 8e-11 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 537 bits (1384), Expect = e-154, Method: Compositional matrix adjust. Identities = 288/345 (83%), Positives = 318/345 (92%) Query: 11 TTSSTPSISPGRRIWLRFRANRTGYWSLLIFSVLFVLSLGAELFSNDKPLVASYQGHIIF 70 TTS PSISPGRRIWLRF A+R GYWSL +FS+LFVLSLGAEL SND+PL+A YQG +IF Sbjct: 4 TTSPAPSISPGRRIWLRFCADRAGYWSLWLFSLLFVLSLGAELISNDRPLMARYQGKLIF 63 Query: 71 PMFKDYSDKSFGGDFDTPADYLDPFIQDQFKKNGNWALYPLNRYNHETLNYFAKSPNPAP 130 P+ +DYSDKSFGGDFD+PADYLDPFIQ Q +K+GNW LYP NRY + TLNYFAK PNPA Sbjct: 64 PIVQDYSDKSFGGDFDSPADYLDPFIQAQLRKDGNWVLYPPNRYGYNTLNYFAKQPNPAA 123 Query: 131 PSADNWLGTDDRGRDVFARLLYGFRLSVLFGLALTAIGVVLGVLAGAIQGYFAGRTDLVI 190 PS++NWLGTDDRGRDVFARLLYGFR+SVLFG+ALT IGVVLGV AGA+QGYFAGRTDL Sbjct: 124 PSSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDLFT 183 Query: 191 QRLLEIWGSMPELYLLIIFFSIFQPSLLVLLVLMAAFGWMDLADYLRAEFLRNRNLDYVQ 250 QRLLEIWGSMPELYLLIIF SIFQPSL +LLVL++ FGWM L+DY+RA+FLRNRNL+Y+Q Sbjct: 184 QRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLEYIQ 243 Query: 251 AARAMGLSNRQIIWRHVLPNSMTTVVTFLPFRMSASILALTSLDFLGLGVPPSTPSLGEL 310 AARAMGL +R IIWRHVLPNSMTTVVTFLPFRMSA+ILALTSLDFLGLGVPPSTPSLGEL Sbjct: 244 AARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLGEL 303 Query: 311 LSQGKNNLDAWWIALSTFLVLTVTLLLLTNIGDALRNALDVRRKA 355 L+QGKNNLDAWWIALSTF+VLTVTLLLLTNIG+ALRNALDVRRKA Sbjct: 304 LAQGKNNLDAWWIALSTFVVLTVTLLLLTNIGNALRNALDVRRKA 348 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 137 bits (346), Expect = 1e-33, Method: Compositional matrix adjust. Identities = 73/242 (30%), Positives = 136/242 (56%), Gaps = 9/242 (3%) Query: 110 PLNRYNHETLNYFAKSPNPAPPSADNWLGTDDRGRDVFARLLYGFRLSVLFGLALTAIGV 169 P N ++++ LN +PP+ +W G D GRD+F+R++ G R+S+ G AIG Sbjct: 71 PENFFDYDALN--------SPPTWVHWFGVDSLGRDIFSRIVMGTRISLAAGFFSVAIGA 122 Query: 170 VLGVLAGAIQGYFAGRTDLVIQRLLEIWGSMPELYLLIIFFSIFQPSLLVLLVLMAAFGW 229 V+G + G + GY+ G D + R+ ++ + P + L I +I ++ +++ ++ F Sbjct: 123 VIGTVFGLLAGYYEGWWDRITMRICDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSI 182 Query: 230 MDLADYLRAEFLRNRNLDYVQAARAMGLSNRQIIWRHVLPNSMTTVVTFLPFRMSASILA 289 A +R L+ +NL Y++A R++G S+ I+W+H+ P +++ +V + R+ SI+ Sbjct: 183 PAFARLVRGNTLQLKNLTYIEATRSIGASDMTIMWKHIFPGTISAIVVYFTMRIGTSIIT 242 Query: 290 LTSLDFLGLGVPPSTPSLGELLSQGKNNL-DAWWIALSTFLVLTVTLLLLTNIGDALRNA 348 L FLGLG TP G +L++ + ++ + +AL + + +T+L +GD LR+A Sbjct: 243 AAGLSFLGLGAQSPTPEWGLMLNEARADMVTSPHVALVPSIAIFLTVLAFNLLGDGLRDA 302 Query: 349 LD 350 LD Sbjct: 303 LD 304 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 125 bits (314), Expect = 5e-30, Method: Compositional matrix adjust. Identities = 75/249 (30%), Positives = 129/249 (51%), Gaps = 6/249 (2%) Query: 110 PLNRYNHETLNYFAKSPNPAPPSADN----WLGTDDRGRDVFARLLYGFRLSVLFGLALT 165 P N Y+ L+ +P + WLGTD +GRD+ + +LYG R+SV G+ Sbjct: 69 PQNPYDLMQLDVLDARLHPGTLNGAGTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSA 128 Query: 166 AIGVVLGVLAGAIQGYFAGRTDLVIQRLLEIWGSMPELYLLIIFFSIFQPSLLVLLVLMA 225 I V+G L G + Y G+ D ++ R ++ S P + + ++ + + ++ + Sbjct: 129 LIAGVIGTLIGLLAAYAGGKLDTLLMRFADLVLSFPSILVAMLILAYVGKGIFNVMATLV 188 Query: 226 AFGWMDLADYLRAEFLRNRNLDYVQAARAMGLSNRQIIWRHVLPNSMTTVVTFLPFRMSA 285 W A R + L R +YV+AAR + LS+ +I+ RH+LPN + ++ +++ Sbjct: 189 VLEWAYYARTARGQALVERRKEYVEAARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVAR 248 Query: 286 SILALTSLDFLGLGVPPSTPSLGELLSQGKNNL--DAWWIALSTFLVLTVTLLLLTNIGD 343 +I +L FLGLGVP + PSLG L+S G + +WI+ + L V ++ + +GD Sbjct: 249 AITLEATLSFLGLGVPITEPSLGLLISNGYQYMLSGEYWISFYPGITLLVVIVAINLVGD 308 Query: 344 ALRNALDVR 352 LR+ L+ R Sbjct: 309 RLRDILNPR 317 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 122 bits (307), Expect = 4e-29, Method: Compositional matrix adjust. Identities = 81/222 (36%), Positives = 127/222 (57%), Gaps = 3/222 (1%) Query: 134 DNWLGTDDRGRDVFARLLYGFRLSVLFGLALTAIGVVLGVLAGAIQGYFAGRTDLVIQRL 193 ++ LGTD GRD F+RL+YG R+S+ GLA I ++G G + GYF GRTD VI L Sbjct: 83 EHILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVISYL 142 Query: 194 LEIWGSMPELYLLIIFFSIFQPSLLVLLVLMAAFGWMDLADYLRAEFLRNRNLDYVQAAR 253 + +MP + + + S+ SL V++VL+ W A R+ + R+ +++ AA+ Sbjct: 143 ITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAK 202 Query: 254 AMGLSNRQIIWRHVLPNSMTTVVTFLPFRMSASILALTSLDFLGLGVPPSTPSLGELLSQ 313 A+G S I+ R +LPN M ++ + M+ +IL +L FLGLGV P TPS G ++++ Sbjct: 203 AIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAE 262 Query: 314 GKNNL-DAWWIALSTFLVLTVTLLLLTNIGDALR--NALDVR 352 GK + W+ + + L + +L + +GD LR NA D R Sbjct: 263 GKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAPDGR 304 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 62.0 bits (149), Expect = 8e-11, Method: Compositional matrix adjust. Identities = 48/147 (32%), Positives = 72/147 (48%), Gaps = 2/147 (1%) Query: 137 LGTDDRGRDVFARLLYGFRLSVLFGLALTAIGVVLGVLAGAIQGYFAGRTDLVIQRLLEI 196 LG+D GRD+ +R+L+G R ++ LA T + G + G D VI R L+ Sbjct: 76 LGSDYLGRDMLSRILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVISRALDA 135 Query: 197 WGSMPELYLLIIFFSIFQPSLLVLLVLMAAFGWMDLADYLRAEFLRN-RNLDYVQAARAM 255 S+P ++ + F S+L LLVL AA +M A + N + ++YVQAARA Sbjct: 136 LISIPSKMFALMMVATFGSSML-LLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARAR 194 Query: 256 GLSNRQIIWRHVLPNSMTTVVTFLPFR 282 G I+ +LPN + V+ R Sbjct: 195 GEGVWYIMTVEMLPNMIRPVLADFGLR 221 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 0.325 0.140 0.432 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: 1,010,201 Number of extensions: 42294 Number of successful extensions: 230 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 225 Number of HSP's successfully gapped: 6 Length of query: 355 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 269 Effective length of database: 1,212,660 Effective search space: 326205540 Effective search space used: 326205540 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 131 (55.1 bits)