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= 0001.4598.p (301 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 215 3e-57 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 185 3e-48 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 166 2e-42 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 107 2e-24 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 82 5e-17 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 215 bits (548), Expect = 3e-57, Method: Compositional matrix adjust. Identities = 115/280 (41%), Positives = 165/280 (58%) Query: 21 RRSRGHWANVAARLVRNPGAMIAAAVLLLLIVAAIAAPWVMPGDPFAASMFSRLKPIGTV 80 ++ R W + + A+ A +L L+ AI APW++P DP + L T Sbjct: 27 QKIRTPWREFWRKFKKQHLAVYAGVFILFLVAVAILAPWIVPFDPENFFDYDALNSPPTW 86 Query: 81 GHLLGTDELGRDMFSRLLLGGRLSLFMGITPVLLAFVIGSALGIVAGYAGGFTNTIIMRS 140 H G D LGRD+FSR+++G R+SL G V + VIG+ G++AGY G+ + I MR Sbjct: 87 VHWFGVDSLGRDIFSRIVMGTRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWDRITMRI 146 Query: 141 IDILYAFPSVLLAIALSGALGAGIFNALTSLTIVFVPQIARIAESVTTQVRRSDYVDAAR 200 D+L+AFP +LLAI + LG G+ N + S+++ +P AR+ T Q++ Y++A R Sbjct: 147 CDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEATR 206 Query: 201 ASGASAFTIVRAHVLGNVLGPIFVYSTSLISVSMILASGLSFLGLGVKPPEPEWGLMLNT 260 + GAS TI+ H+ + I VY T I S+I A+GLSFLGLG + P PEWGLMLN Sbjct: 207 SIGASDMTIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLMLNE 266 Query: 261 LRTAIYTQPWVAALPGAFIFVTSISFNLLSDGLRSAMEVK 300 R + T P VA +P IF+T ++FNLL DGLR A++ K Sbjct: 267 ARADMVTSPHVALVPSIAIFLTVLAFNLLGDGLRDALDPK 306 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 185 bits (470), Expect = 3e-48, Method: Compositional matrix adjust. Identities = 107/274 (39%), Positives = 171/274 (62%), Gaps = 5/274 (1%) Query: 27 WANVAARLVRNPGAMIAAAVLLLLIVAAIAAPWVMPGDPFAASMFSRLKP-----IGTVG 81 W RL+ + G MI AAVL ++++AAI AP + P DPF + +RL P G+ Sbjct: 24 WRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPHDPFDQDVTARLIPPVWQAQGSWE 83 Query: 82 HLLGTDELGRDMFSRLLLGGRLSLFMGITPVLLAFVIGSALGIVAGYAGGFTNTIIMRSI 141 H+LGTD+LGRD FSRL+ G R+SL +G+ L++ +IG+ LG++AGY GG T+ +I I Sbjct: 84 HILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVISYLI 143 Query: 142 DILYAFPSVLLAIALSGALGAGIFNALTSLTIVFVPQIARIAESVTTQVRRSDYVDAARA 201 A P VL+A+A++ +G + + L ++ + A + S T Q+R ++++ AA+A Sbjct: 144 TTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAKA 203 Query: 202 SGASAFTIVRAHVLGNVLGPIFVYSTSLISVSMILASGLSFLGLGVKPPEPEWGLMLNTL 261 GAS I+ +L N++G + V T ++ +++L + LSFLGLGV+PP P WGLM+ Sbjct: 204 IGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAEG 263 Query: 262 RTAIYTQPWVAALPGAFIFVTSISFNLLSDGLRS 295 +T ++ +PWV +PG + + ++ NL+ DGLR Sbjct: 264 KTYMFFKPWVIVIPGVALALLVLAINLVGDGLRD 297 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 166 bits (420), Expect = 2e-42, Method: Compositional matrix adjust. Identities = 110/302 (36%), Positives = 171/302 (56%), Gaps = 15/302 (4%) Query: 7 VSSLKAAEAPATAMRRSRGHWANVAARLVRNPGAMIAAAVLLLLIVAAIAAPWVMPGDPF 66 V+ L A +AP R W V V + AM+ ++LLLIV AIAAPW+ P +P+ Sbjct: 19 VAELSAFQAP-----RRESPWRRVMRHFVASRSAMLGLVIVLLLIVGAIAAPWITPQNPY 73 Query: 67 AASMF----SRLKP-----IGTVGHLLGTDELGRDMFSRLLLGGRLSLFMGITPVLLAFV 117 +RL P GT + LGTD GRD+ S +L G R+S+ +G+ L+A V Sbjct: 74 DLMQLDVLDARLHPGTLNGAGTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSALIAGV 133 Query: 118 IGSALGIVAGYAGGFTNTIIMRSIDILYAFPSVLLAIALSGALGAGIFNALTSLTIVFVP 177 IG+ +G++A YAGG +T++MR D++ +FPS+L+A+ + +G GIFN + +L ++ Sbjct: 134 IGTLIGLLAAYAGGKLDTLLMRFADLVLSFPSILVAMLILAYVGKGIFNVMATLVVLEWA 193 Query: 178 QIARIAESVTTQVRRSDYVDAARASGASAFTIVRAHVLGNVLGPIFVYSTSLISVSMILA 237 AR A RR +YV+AAR S++ I+ H+L N L P+ V T ++ ++ L Sbjct: 194 YYARTARGQALVERRKEYVEAARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVARAITLE 253 Query: 238 SGLSFLGLGVKPPEPEWGLML-NTLRTAIYTQPWVAALPGAFIFVTSISFNLLSDGLRSA 296 + LSFLGLGV EP GL++ N + + + W++ PG + V ++ NL+ D LR Sbjct: 254 ATLSFLGLGVPITEPSLGLLISNGYQYMLSGEYWISFYPGITLLVVIVAINLVGDRLRDI 313 Query: 297 ME 298 + Sbjct: 314 LN 315 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 107 bits (266), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 82/272 (30%), Positives = 136/272 (50%), Gaps = 21/272 (7%) Query: 40 AMIAAAVLLLLIVAAIAAPWVMPGDPFA---ASMFSRLKPIGTVGHLLGTDELGRDMFSR 96 A I A++ I+ AI P + P D A +FS + LLG+D LGRDM SR Sbjct: 33 AWIGMAIVGFWILMAILGPSISPYDATAIVDTDVFSGMSH----KFLLGSDYLGRDMLSR 88 Query: 97 LLLGGRLSLFMGITPVLLAFVIGSALGIVAGYAGGFTNTIIMRSIDILYAFPSVLLAIAL 156 +L G R ++ + + +LA G+A+ + A ++GG+ + +I R++D L + PS + A+ + Sbjct: 89 ILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVISRALDALISIPSKMFALMM 148 Query: 157 SGALGAGIFNALTSLTIVFVPQIARIAESVTTQVRRSDYVDAARASGASAFTIVRAHVLG 216 G+ + + + I ++P RIA S+ V+ +YV AARA G + I+ +L Sbjct: 149 VATFGSSMLLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGVWYIMTVEMLP 208 Query: 217 NVLGPI-------FVYSTSLISVSMILASGLSFLGLGVKPPEPEWGLMLNTLRTAIYTQP 269 N++ P+ FVY L+S L+ GV+PP+ +WG ++ + + Sbjct: 209 NMIRPVLADFGLRFVYVVLLLSGLSFLSL-------GVQPPDADWGSLVRENISGLGEGA 261 Query: 270 WVAALPGAFIFVTSISFNLLSDGLRSAMEVKQ 301 +P I +I NLL D LRS K+ Sbjct: 262 LAVIMPALAIASLTIGVNLLIDNLRSKRAAKE 293 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 82.0 bits (201), Expect = 5e-17, Method: Compositional matrix adjust. Identities = 64/220 (29%), Positives = 109/220 (49%), Gaps = 1/220 (0%) Query: 82 HLLGTDELGRDMFSRLLLGGRLSLFMGITPVLLAFVIGSALGIVAGYAGGFTNTIIMRSI 141 + LGTD+ GRD+F+RLL G R+S+ G+ + V+G A G V GY G T+ R + Sbjct: 128 NWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDLFTQRLL 187 Query: 142 DILYAFPSVLLAIALSGALGAGIFNALTSLTIVFVPQIARIAESVTTQVRRSDYVDAARA 201 +I + P + L I S + L L++ ++ + + R +Y+ AARA Sbjct: 188 EIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLEYIQAARA 247 Query: 202 SGASAFTIVRAHVLGNVLGPIFVYSTSLISVSMILASGLSFLGLGVKPPEPEWGLMLNTL 261 G I+ HVL N + + + +S +++ + L FLGLGV P P G +L Sbjct: 248 MGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLGELLAQG 307 Query: 262 RTAIYTQPWVAALPGAFIFVTSISFNLLSDGLRSAMEVKQ 301 + + W+A + VT + + + LR+A++V++ Sbjct: 308 KNNLDAW-WIALSTFVVLTVTLLLLTNIGNALRNALDVRR 346 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 0.137 0.398 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: 787,038 Number of extensions: 27418 Number of successful extensions: 189 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 184 Number of HSP's successfully gapped: 6 Length of query: 301 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 216 Effective length of database: 1,217,395 Effective search space: 262957320 Effective search space used: 262957320 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: 130 (54.7 bits)