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= 0015.0527.p (306 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 524 e-150 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 189 2e-49 gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 186 3e-48 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 112 5e-26 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 112 5e-26 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 524 bits (1349), Expect = e-150, Method: Compositional matrix adjust. Identities = 281/293 (95%), Positives = 286/293 (97%) Query: 14 VLSAALPPLPAWRRKLRRLLGHRGLVLGALFLAVIVLAAIFAPLLAPHDPFDQDVTARLI 73 +L ALPPLPAWRRKLRRLLGHRGL++GA LAVIVLAAIFAPLLAPHDPFDQDVTARLI Sbjct: 13 LLQGALPPLPAWRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPHDPFDQDVTARLI 72 Query: 74 PPVWQAQGSWEHILGTDKLGRDYLSRLIFGARVSLTIGIAAALISGLIGTTLGVLAGYFG 133 PPVWQAQGSWEHILGTDKLGRDY SRLI+GARVSLTIG+AAALISGLIGTTLGVLAGYFG Sbjct: 73 PPVWQAQGSWEHILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFG 132 Query: 134 GRTDAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQL 193 GRTDAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQL Sbjct: 133 GRTDAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQL 192 Query: 194 RDAEFIAAAKAIGASTPYILLREILPNIMGALIVVATLEMAHAILLEATLSFLGLGVQPP 253 RDAEFIAAAKAIGASTPYILLREILPNIMGALIVV TLEMAHAILLEATLSFLGLGVQPP Sbjct: 193 RDAEFIAAAKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPP 252 Query: 254 TPSWGLMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNATDGRN 306 TPSWGLMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNA DGRN Sbjct: 253 TPSWGLMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAPDGRN 305 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 189 bits (481), Expect = 2e-49, Method: Compositional matrix adjust. Identities = 111/280 (39%), Positives = 173/280 (61%), Gaps = 5/280 (1%) Query: 25 WRRKLRRLLGHRGLVLGALFLAVIVLAAIFAPLLAPHDPFD----QDVTARLIPPVWQAQ 80 WRR +R + R +LG + + ++++ AI AP + P +P+D + ARL P Sbjct: 34 WRRVMRHFVASRSAMLGLVIVLLLIVGAIAAPWITPQNPYDLMQLDVLDARLHPGTLNGA 93 Query: 81 GSWEHILGTDKLGRDYLSRLIFGARVSLTIGIAAALISGLIGTTLGVLAGYFGGRTDAVI 140 G++ + LGTD GRD +S +++G R+S+ IG+ +ALI+G+IGT +G+LA Y GG+ D ++ Sbjct: 94 GTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSALIAGVIGTLIGLLAAYAGGKLDTLL 153 Query: 141 SYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIA 200 L+ P +LVA+ + + VG + V+ L +L W +A R R E++ Sbjct: 154 MRFADLVLSFPSILVAMLILAYVGKGIFNVMATLVVLEWAYYARTARGQALVERRKEYVE 213 Query: 201 AAKAIGASTPYILLREILPNIMGALIVVATLEMAHAILLEATLSFLGLGVQPPTPSWGLM 260 AA+ + S+ I++R ILPN + LIV+ TL++A AI LEATLSFLGLGV PS GL+ Sbjct: 214 AARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVARAITLEATLSFLGLGVPITEPSLGLL 273 Query: 261 VAEGKTYMFF-KPWVIVIPGVALALLVLAINLVGDGLRDV 299 ++ G YM + W+ PG+ L ++++AINLVGD LRD+ Sbjct: 274 ISNGYQYMLSGEYWISFYPGITLLVVIVAINLVGDRLRDI 313 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 186 bits (471), Expect = 3e-48, Method: Compositional matrix adjust. Identities = 105/277 (37%), Positives = 153/277 (55%), Gaps = 11/277 (3%) Query: 25 WRRKLRRLLGHRGLVLGALFLAVIVLAAIFAPLLAPHDP---FDQDVTARLIPPVWQAQG 81 WR R+ V +F+ +V AI AP + P DP FD D PP Sbjct: 33 WREFWRKFKKQHLAVYAGVFILFLVAVAILAPWIVPFDPENFFDYDALNS--PP------ 84 Query: 82 SWEHILGTDKLGRDYLSRLIFGARVSLTIGIAAALISGLIGTTLGVLAGYFGGRTDAVIS 141 +W H G D LGRD SR++ G R+SL G + I +IGT G+LAGY+ G D + Sbjct: 85 TWVHWFGVDSLGRDIFSRIVMGTRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWDRITM 144 Query: 142 YLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAA 201 + A P +L+A+ + +++GG + VI+ + + FA + R T QL++ +I A Sbjct: 145 RICDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEA 204 Query: 202 AKAIGASTPYILLREILPNIMGALIVVATLEMAHAILLEATLSFLGLGVQPPTPSWGLMV 261 ++IGAS I+ + I P + A++V T+ + +I+ A LSFLGLG Q PTP WGLM+ Sbjct: 205 TRSIGASDMTIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLML 264 Query: 262 AEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRD 298 E + M P V ++P +A+ L VLA NL+GDGLRD Sbjct: 265 NEARADMVTSPHVALVPSIAIFLTVLAFNLLGDGLRD 301 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 112 bits (279), Expect = 5e-26, Method: Compositional matrix adjust. Identities = 81/256 (31%), Positives = 140/256 (54%), Gaps = 12/256 (4%) Query: 49 VLAAIFAPLLAPHDP---FDQDVTARLIPPVWQAQGSWEHILGTDKLGRDYLSRLIFGAR 105 +L AI P ++P+D D DV + + S + +LG+D LGRD LSR++FG R Sbjct: 44 ILMAILGPSISPYDATAIVDTDVFSGM---------SHKFLLGSDYLGRDMLSRILFGTR 94 Query: 106 VSLTIGIAAALISGLIGTTLGVLAGYFGGRTDAVISYLITTRLAMPVVLVALAMASLVGG 165 ++ + +AA +++ GT + + A + GG DAVIS + +++P + AL M + G Sbjct: 95 ATIGLALAATVLASATGTAIALFAAFSGGWRDAVISRALDALISIPSKMFALMMVATFGS 154 Query: 166 SLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAKAIGASTPYILLREILPNIMGAL 225 S+ ++++ + + RS ++ E++ AA+A G YI+ E+LPN++ + Sbjct: 155 SMLLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGVWYIMTVEMLPNMIRPV 214 Query: 226 IVVATLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAEGKTYMFFKPWVIVIPGVALALL 285 + L + +LL + LSFL LGVQPP WG +V E + + +++P +A+A L Sbjct: 215 LADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSLVRENISGLGEGALAVIMPALAIASL 274 Query: 286 VLAINLVGDGLRDVNA 301 + +NL+ D LR A Sbjct: 275 TIGVNLLIDNLRSKRA 290 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 112 bits (279), Expect = 5e-26, Method: Compositional matrix adjust. Identities = 70/183 (38%), Positives = 105/183 (57%) Query: 84 EHILGTDKLGRDYLSRLIFGARVSLTIGIAAALISGLIGTTLGVLAGYFGGRTDAVISYL 143 E+ LGTD GRD +RL++G RVS+ G+A I ++G G + GYF GRTD L Sbjct: 127 ENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDLFTQRL 186 Query: 144 ITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAK 203 + +MP + + + +S+ SL +++VLL L W + R+ + R+ E+I AA+ Sbjct: 187 LEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLEYIQAAR 246 Query: 204 AIGASTPYILLREILPNIMGALIVVATLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAE 263 A+G I+ R +LPN M ++ M+ AIL +L FLGLGV P TPS G ++A+ Sbjct: 247 AMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLGELLAQ 306 Query: 264 GKT 266 GK Sbjct: 307 GKN 309 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 0.326 0.141 0.418 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: 552,852 Number of extensions: 16155 Number of successful extensions: 111 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 111 Number of HSP's successfully gapped: 6 Length of query: 306 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 221 Effective length of database: 1,217,395 Effective search space: 269044295 Effective search space used: 269044295 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)