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= 0006.0007.p (348 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... 691 0.0 gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 129 4e-31 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 120 2e-28 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 117 1e-27 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 57 3e-09 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 691 bits (1783), Expect = 0.0, Method: Compositional matrix adjust. Identities = 347/348 (99%), Positives = 347/348 (99%) Query: 1 MSTTTSPAPSISPGRRIWLRFCADRAGYWSLWLFSLLFVLSLGAELISNDRPLMARYQGK 60 MSTTTSPAPSISPGRRIWLRFCADRAGYWSLWLFSLLFVLSLGAELISNDRPLMARYQGK Sbjct: 1 MSTTTSPAPSISPGRRIWLRFCADRAGYWSLWLFSLLFVLSLGAELISNDRPLMARYQGK 60 Query: 61 LIFPIVQDYSDKSFGGDFDSPADYLDPFIQAQLRKDGNWVLYPPNRYGYNTLNYFAKQPN 120 LIFPIVQDYSDKSFGGDFDSPADYLDPFIQAQLRKDGNWVLYPPNRYGYNTLNYFAKQPN Sbjct: 61 LIFPIVQDYSDKSFGGDFDSPADYLDPFIQAQLRKDGNWVLYPPNRYGYNTLNYFAKQPN 120 Query: 121 PAAPSSENWLGTDDRGRDVLARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTD 180 PAAPSSENWLGTDDRGRDV ARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTD Sbjct: 121 PAAPSSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTD 180 Query: 181 LFTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLE 240 LFTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLE Sbjct: 181 LFTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLE 240 Query: 241 YIQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSL 300 YIQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSL Sbjct: 241 YIQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSL 300 Query: 301 GELLAQGKNNLDAWWIALSTFVVLTVTLLLLTNIGNALRNALDVRRKA 348 GELLAQGKNNLDAWWIALSTFVVLTVTLLLLTNIGNALRNALDVRRKA Sbjct: 301 GELLAQGKNNLDAWWIALSTFVVLTVTLLLLTNIGNALRNALDVRRKA 348 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 129 bits (324), Expect = 4e-31, Method: Compositional matrix adjust. Identities = 72/242 (29%), Positives = 131/242 (54%), Gaps = 9/242 (3%) Query: 103 PPNRYGYNTLNYFAKQPNPAAPSSENWLGTDDRGRDVLARLLYGFRVSVLFGMALTFIGV 162 P N + Y+ LN + P+ +W G D GRD+ +R++ G R+S+ G IG Sbjct: 71 PENFFDYDALN--------SPPTWVHWFGVDSLGRDIFSRIVMGTRISLAAGFFSVAIGA 122 Query: 163 VLGVAAGAVQGYFAGRTDLFTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGW 222 V+G G + GY+ G D T R+ ++ + P + L I +I + +++ +S+F Sbjct: 123 VIGTVFGLLAGYYEGWWDRITMRICDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSI 182 Query: 223 MSLSDYVRADFLRNRNLEYIQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILA 282 + + VR + L+ +NL YI+A R++G D I+W+H+ P +++ +V + R+ +I+ Sbjct: 183 PAFARLVRGNTLQLKNLTYIEATRSIGASDMTIMWKHIFPGTISAIVVYFTMRIGTSIIT 242 Query: 283 LTSLDFLGLGVPPSTPSLGELLAQGKNNL-DAWWIALSTFVVLTVTLLLLTNIGNALRNA 341 L FLGLG TP G +L + + ++ + +AL + + +T+L +G+ LR+A Sbjct: 243 AAGLSFLGLGAQSPTPEWGLMLNEARADMVTSPHVALVPSIAIFLTVLAFNLLGDGLRDA 302 Query: 342 LD 343 LD Sbjct: 303 LD 304 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 120 bits (300), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 82/222 (36%), Positives = 125/222 (56%), Gaps = 3/222 (1%) Query: 127 ENWLGTDDRGRDVLARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDLFTQRL 186 E+ LGTD GRD +RL+YG RVS+ G+A I ++G G + GYF GRTD L Sbjct: 83 EHILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVISYL 142 Query: 187 LEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLEYIQAAR 246 + +MP + + + +S+ SL +++VLL L W + R+ + R+ E+I AA+ Sbjct: 143 ITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAK 202 Query: 247 AMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLGELLAQ 306 A+G I+ R +LPN M ++ + M+ AIL +L FLGLGV P TPS G ++A+ Sbjct: 203 AIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAE 262 Query: 307 GKNNL-DAWWIALSTFVVLTVTLLLLTNIGNALR--NALDVR 345 GK + W+ + V L + +L + +G+ LR NA D R Sbjct: 263 GKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAPDGR 304 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 117 bits (294), Expect = 1e-27, Method: Compositional matrix adjust. Identities = 73/249 (29%), Positives = 125/249 (50%), Gaps = 6/249 (2%) Query: 103 PPNRYGYNTLNYFAKQPNPA----APSSENWLGTDDRGRDVLARLLYGFRVSVLFGMALT 158 P N Y L+ + +P A + WLGTD +GRD+++ +LYG R+SV G+ Sbjct: 69 PQNPYDLMQLDVLDARLHPGTLNGAGTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSA 128 Query: 159 FIGVVLGVAAGAVQGYFAGRTDLFTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLS 218 I V+G G + Y G+ D R ++ S P + + ++ + + ++ L Sbjct: 129 LIAGVIGTLIGLLAAYAGGKLDTLLMRFADLVLSFPSILVAMLILAYVGKGIFNVMATLV 188 Query: 219 LFGWMSLSDYVRADFLRNRNLEYIQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSA 278 + W + R L R EY++AAR + L I+ RH+LPN + ++ +++ Sbjct: 189 VLEWAYYARTARGQALVERRKEYVEAARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVAR 248 Query: 279 AILALTSLDFLGLGVPPSTPSLGELLAQGKNNL--DAWWIALSTFVVLTVTLLLLTNIGN 336 AI +L FLGLGVP + PSLG L++ G + +WI+ + L V ++ + +G+ Sbjct: 249 AITLEATLSFLGLGVPITEPSLGLLISNGYQYMLSGEYWISFYPGITLLVVIVAINLVGD 308 Query: 337 ALRNALDVR 345 LR+ L+ R Sbjct: 309 RLRDILNPR 317 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 56.6 bits (135), Expect = 3e-09, Method: Compositional matrix adjust. Identities = 45/152 (29%), Positives = 73/152 (48%), Gaps = 2/152 (1%) Query: 125 SSENWLGTDDRGRDVLARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDLFTQ 184 S + LG+D GRD+L+R+L+G R ++ +A T + G A + G D Sbjct: 71 SHKFLLGSDYLGRDMLSRILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVIS 130 Query: 185 RLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRN-RNLEYIQ 243 R L+ S+P ++ + F S+ LLLVL + +M + + N + +EY+Q Sbjct: 131 RALDALISIPSKMFALMMVATFGSSM-LLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQ 189 Query: 244 AARAMGLPDRLIIWRHVLPNSMTTVVTFLPFR 275 AARA G I+ +LPN + V+ R Sbjct: 190 AARARGEGVWYIMTVEMLPNMIRPVLADFGLR 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 0.141 0.441 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: 924,425 Number of extensions: 34689 Number of successful extensions: 148 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 145 Number of HSP's successfully gapped: 6 Length of query: 348 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 262 Effective length of database: 1,212,660 Effective search space: 317716920 Effective search space used: 317716920 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)