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= 0002.0126.p (305 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... 589 e-170 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 192 4e-50 gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 182 2e-47 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 116 3e-27 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 115 6e-27 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 589 bits (1519), Expect = e-170, Method: Compositional matrix adjust. Identities = 304/305 (99%), Positives = 304/305 (99%) Query: 1 MSATTTTMPPTPLLQGALPPLPAWRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPH 60 MSATTTTMPPTPLLQGALPPLPAWRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPH Sbjct: 1 MSATTTTMPPTPLLQGALPPLPAWRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPH 60 Query: 61 DPFDQDVTARLIPPVWQAQGSWEHILGTDKLGRDYLSRLIYGARVSLTIGLAAALISGLI 120 DPFDQDVTARLIPPVWQAQGSWEHILGTDKLGRDY SRLIYGARVSLTIGLAAALISGLI Sbjct: 61 DPFDQDVTARLIPPVWQAQGSWEHILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLI 120 Query: 121 GTTLGVLAGYFGGRTDAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDR 180 GTTLGVLAGYFGGRTDAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDR Sbjct: 121 GTTLGVLAGYFGGRTDAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDR 180 Query: 181 FAVVTRSATQQLRDAEFIAAAKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEA 240 FAVVTRSATQQLRDAEFIAAAKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEA Sbjct: 181 FAVVTRSATQQLRDAEFIAAAKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEA 240 Query: 241 TLSFLGLGVQPPTPSWGLMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNA 300 TLSFLGLGVQPPTPSWGLMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNA Sbjct: 241 TLSFLGLGVQPPTPSWGLMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNA 300 Query: 301 PDGRN 305 PDGRN Sbjct: 301 PDGRN 305 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 192 bits (487), Expect = 4e-50, Method: Compositional matrix adjust. Identities = 113/283 (39%), Positives = 174/283 (61%), Gaps = 5/283 (1%) Query: 24 WRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPHDPFD----QDVTARLIPPVWQAQ 79 WRR +R + R M+G ++ ++++ AI AP + P +P+D + ARL P Sbjct: 34 WRRVMRHFVASRSAMLGLVIVLLLIVGAIAAPWITPQNPYDLMQLDVLDARLHPGTLNGA 93 Query: 80 GSWEHILGTDKLGRDYLSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVI 139 G++ + LGTD GRD +S ++YG R+S+ IG+ +ALI+G+IGT +G+LA Y GG+ D ++ Sbjct: 94 GTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSALIAGVIGTLIGLLAAYAGGKLDTLL 153 Query: 140 SYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIA 199 L+ P +LVA+ + + VG + V+ L +L W +A R R E++ Sbjct: 154 MRFADLVLSFPSILVAMLILAYVGKGIFNVMATLVVLEWAYYARTARGQALVERRKEYVE 213 Query: 200 AAKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLM 259 AA+ + S+ I++R ILPN + LIV+ TL++A AI LEATLSFLGLGV PS GL+ Sbjct: 214 AARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVARAITLEATLSFLGLGVPITEPSLGLL 273 Query: 260 VAEGKTYMFF-KPWVIVIPGVALALLVLAINLVGDGLRDVNAP 301 ++ G YM + W+ PG+ L ++++AINLVGD LRD+ P Sbjct: 274 ISNGYQYMLSGEYWISFYPGITLLVVIVAINLVGDRLRDILNP 316 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 182 bits (463), Expect = 2e-47, Method: Compositional matrix adjust. Identities = 104/281 (37%), Positives = 152/281 (54%), Gaps = 11/281 (3%) Query: 24 WRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPHDP---FDQDVTARLIPPVWQAQG 80 WR R+ + + +V AI AP + P DP FD D PP Sbjct: 33 WREFWRKFKKQHLAVYAGVFILFLVAVAILAPWIVPFDPENFFDYDALNS--PP------ 84 Query: 81 SWEHILGTDKLGRDYLSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVIS 140 +W H G D LGRD SR++ G R+SL G + I +IGT G+LAGY+ G D + Sbjct: 85 TWVHWFGVDSLGRDIFSRIVMGTRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWDRITM 144 Query: 141 YLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAA 200 + A P +L+A+ + +++GG + VI+ + + FA + R T QL++ +I A Sbjct: 145 RICDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEA 204 Query: 201 AKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLMV 260 ++IGAS I+ + I P + A++V T+ + +I+ A LSFLGLG Q PTP WGLM+ Sbjct: 205 TRSIGASDMTIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLML 264 Query: 261 AEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAP 301 E + M P V ++P +A+ L VLA NL+GDGLRD P Sbjct: 265 NEARADMVTSPHVALVPSIAIFLTVLAFNLLGDGLRDALDP 305 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 116 bits (290), Expect = 3e-27, Method: Compositional matrix adjust. Identities = 84/265 (31%), Positives = 145/265 (54%), Gaps = 12/265 (4%) Query: 39 IGAAVLAVIVLAAIFAPLLAPHDP---FDQDVTARLIPPVWQAQGSWEHILGTDKLGRDY 95 IG A++ +L AI P ++P+D D DV + + S + +LG+D LGRD Sbjct: 35 IGMAIVGFWILMAILGPSISPYDATAIVDTDVFSGM---------SHKFLLGSDYLGRDM 85 Query: 96 LSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVISYLITTRLAMPVVLVA 155 LSR+++G R ++ + LAA +++ GT + + A + GG DAVIS + +++P + A Sbjct: 86 LSRILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVISRALDALISIPSKMFA 145 Query: 156 LAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAKAIGASTPYILLRE 215 L M + G S+ ++++ + + RS ++ E++ AA+A G YI+ E Sbjct: 146 LMMVATFGSSMLLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGVWYIMTVE 205 Query: 216 ILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAEGKTYMFFKPWVIV 275 +LPN++ ++ L + +LL + LSFL LGVQPP WG +V E + + ++ Sbjct: 206 MLPNMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSLVRENISGLGEGALAVI 265 Query: 276 IPGVALALLVLAINLVGDGLRDVNA 300 +P +A+A L + +NL+ D LR A Sbjct: 266 MPALAIASLTIGVNLLIDNLRSKRA 290 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 115 bits (287), Expect = 6e-27, Method: Compositional matrix adjust. Identities = 71/183 (38%), Positives = 106/183 (57%) Query: 83 EHILGTDKLGRDYLSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVISYL 142 E+ LGTD GRD +RL+YG RVS+ G+A I ++G G + GYF GRTD L Sbjct: 127 ENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDLFTQRL 186 Query: 143 ITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAK 202 + +MP + + + +S+ SL +++VLL L W + R+ + R+ E+I AA+ Sbjct: 187 LEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLEYIQAAR 246 Query: 203 AIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAE 262 A+G I+ R +LPN M ++ + M+ AIL +L FLGLGV P TPS G ++A+ Sbjct: 247 AMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLGELLAQ 306 Query: 263 GKT 265 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 0.423 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: 627,442 Number of extensions: 22015 Number of successful extensions: 163 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 164 Number of HSP's successfully gapped: 6 Length of query: 305 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 220 Effective length of database: 1,217,395 Effective search space: 267826900 Effective search space used: 267826900 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)