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= 0015.0085.p (351 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... 578 e-166 gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 132 4e-32 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 127 2e-30 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 116 2e-27 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 57 2e-09 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 578 bits (1490), Expect = e-166, Method: Compositional matrix adjust. Identities = 314/349 (89%), Positives = 335/349 (95%), Gaps = 1/349 (0%) Query: 3 MTTPATPSTPSISPSRRIWLRFRADRTGYWSLVIFSILFIVSLGAELVSNDKPLVASYQG 62 M+T +P+ PSISP RRIWLRF ADR GYWSL +FS+LF++SLGAEL+SND+PL+A YQG Sbjct: 1 MSTTTSPA-PSISPGRRIWLRFCADRAGYWSLWLFSLLFVLSLGAELISNDRPLMARYQG 59 Query: 63 KLMFPMLKDYSDKHFGGDFDSPADYLDPFIEQQFRKDGNWVIYPLNRYGYNTLNYFAKEP 122 KL+FP+++DYSDK FGGDFDSPADYLDPFI+ Q RKDGNWV+YP NRYGYNTLNYFAK+P Sbjct: 60 KLIFPIVQDYSDKSFGGDFDSPADYLDPFIQAQLRKDGNWVLYPPNRYGYNTLNYFAKQP 119 Query: 123 NPAAPSSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVILGVAAGAVQGYFAGRT 182 NPAAPSSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGV+LGVAAGAVQGYFAGRT Sbjct: 120 NPAAPSSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRT 179 Query: 183 DLITQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNL 242 DL TQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNL Sbjct: 180 DLFTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNL 239 Query: 243 EYVQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPS 302 EY+QAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPS Sbjct: 240 EYIQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPS 299 Query: 303 LGELLAQGKNNLDAWWIAVATFVVLTVTLLLLTNIGNGLRNALDVRRKA 351 LGELLAQGKNNLDAWWIA++TFVVLTVTLLLLTNIGN LRNALDVRRKA Sbjct: 300 LGELLAQGKNNLDAWWIALSTFVVLTVTLLLLTNIGNALRNALDVRRKA 348 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 132 bits (332), Expect = 4e-32, Method: Compositional matrix adjust. Identities = 72/242 (29%), Positives = 134/242 (55%), Gaps = 9/242 (3%) Query: 106 PLNRYGYNTLNYFAKEPNPAAPSSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGV 165 P N + Y+ LN + P+ +W G D GRD+F+R++ G R+S+ G IG Sbjct: 71 PENFFDYDALN--------SPPTWVHWFGVDSLGRDIFSRIVMGTRISLAAGFFSVAIGA 122 Query: 166 ILGVAAGAVQGYFAGRTDLITQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGW 225 ++G G + GY+ G D IT R+ ++ + P + L I +I + +++ +S+F Sbjct: 123 VIGTVFGLLAGYYEGWWDRITMRICDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSI 182 Query: 226 MSLSDYVRADFLRNRNLEYVQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILA 285 + + VR + L+ +NL Y++A R++G D I+W+H+ P +++ +V + R+ +I+ Sbjct: 183 PAFARLVRGNTLQLKNLTYIEATRSIGASDMTIMWKHIFPGTISAIVVYFTMRIGTSIIT 242 Query: 286 LTSLDFLGLGVPPSTPSLGELLAQGKNNL-DAWWIAVATFVVLTVTLLLLTNIGNGLRNA 344 L FLGLG TP G +L + + ++ + +A+ + + +T+L +G+GLR+A Sbjct: 243 AAGLSFLGLGAQSPTPEWGLMLNEARADMVTSPHVALVPSIAIFLTVLAFNLLGDGLRDA 302 Query: 345 LD 346 LD Sbjct: 303 LD 304 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 127 bits (318), Expect = 2e-30, Method: Compositional matrix adjust. Identities = 86/227 (37%), Positives = 130/227 (57%), Gaps = 3/227 (1%) Query: 125 AAPSSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVILGVAAGAVQGYFAGRTDL 184 A S E+ LGTD GRD F+RL+YG RVS+ G+A I ++G G + GYF GRTD Sbjct: 78 AQGSWEHILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDA 137 Query: 185 ITQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLEY 244 + L+ +MP + + + +S+ SL +++VLL L W + R+ + R+ E+ Sbjct: 138 VISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEF 197 Query: 245 VQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLG 304 + AA+A+G I+ R +LPN M ++ + M+ AIL +L FLGLGV P TPS G Sbjct: 198 IAAAKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWG 257 Query: 305 ELLAQGKNNL-DAWWIAVATFVVLTVTLLLLTNIGNGLR--NALDVR 348 ++A+GK + W+ V V L + +L + +G+GLR NA D R Sbjct: 258 LMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAPDGR 304 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 116 bits (291), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 74/251 (29%), Positives = 125/251 (49%), Gaps = 6/251 (2%) Query: 104 IYPLNRYGYNTLNYFAKEPNPA----APSSENWLGTDDRGRDVFARLLYGFRVSVLFGMA 159 I P N Y L+ +P A + WLGTD +GRD+ + +LYG R+SV G+ Sbjct: 67 ITPQNPYDLMQLDVLDARLHPGTLNGAGTYTYWLGTDGQGRDLVSAILYGLRISVGIGVG 126 Query: 160 LTFIGVILGVAAGAVQGYFAGRTDLITQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVL 219 I ++G G + Y G+ D + R ++ S P + + ++ + + ++ Sbjct: 127 SALIAGVIGTLIGLLAAYAGGKLDTLLMRFADLVLSFPSILVAMLILAYVGKGIFNVMAT 186 Query: 220 LSLFGWMSLSDYVRADFLRNRNLEYVQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRM 279 L + W + R L R EYV+AAR + L I+ RH+LPN + ++ ++ Sbjct: 187 LVVLEWAYYARTARGQALVERRKEYVEAARGLNLSSWRIMVRHILPNCLPPLIVIGTLQV 246 Query: 280 SAAILALTSLDFLGLGVPPSTPSLGELLAQGKNNL--DAWWIAVATFVVLTVTLLLLTNI 337 + AI +L FLGLGVP + PSLG L++ G + +WI+ + L V ++ + + Sbjct: 247 ARAITLEATLSFLGLGVPITEPSLGLLISNGYQYMLSGEYWISFYPGITLLVVIVAINLV 306 Query: 338 GNGLRNALDVR 348 G+ LR+ L+ R Sbjct: 307 GDRLRDILNPR 317 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 59/195 (30%), Positives = 93/195 (47%), Gaps = 2/195 (1%) Query: 128 SSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVILGVAAGAVQGYFAGRTDLITQ 187 S + LG+D GRD+ +R+L+G R ++ +A T + G A + G D + Sbjct: 71 SHKFLLGSDYLGRDMLSRILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVIS 130 Query: 188 RLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRN-RNLEYVQ 246 R L+ S+P ++ + F S+ LLLVL + +M + + N + +EYVQ Sbjct: 131 RALDALISIPSKMFALMMVATFGSSM-LLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQ 189 Query: 247 AARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLGEL 306 AARA G I+ +LPN + V+ R +L L+ L FL LGV P G L Sbjct: 190 AARARGEGVWYIMTVEMLPNMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSL 249 Query: 307 LAQGKNNLDAWWIAV 321 + + + L +AV Sbjct: 250 VRENISGLGEGALAV 264 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 0.141 0.435 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: 1,023,909 Number of extensions: 42163 Number of successful extensions: 208 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 203 Number of HSP's successfully gapped: 6 Length of query: 351 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 265 Effective length of database: 1,212,660 Effective search space: 321354900 Effective search space used: 321354900 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)