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= 0029.0042.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|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 243 1e-65 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 182 4e-47 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 150 2e-37 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 107 2e-24 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 102 3e-23 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 243 bits (621), Expect = 1e-65, Method: Compositional matrix adjust. Identities = 122/271 (45%), Positives = 171/271 (63%), Gaps = 1/271 (0%) Query: 33 RRFAGNRLAVLGAAIILLLVLIAIFAPLLATHDPIFDQDYGNLLSGPDTTHWMGTDDLGR 92 R+F LAV IL LV +AI AP + DP DY L S P HW G D LGR Sbjct: 38 RKFKKQHLAVYAGVFILFLVAVAILAPWIVPFDPENFFDYDALNSPPTWVHWFGVDSLGR 97 Query: 93 DIFSRMLYGARISLQAALIAVGLAFCVGVPVGIASGYFRGFWDEWVVMRIVDALQAFPPL 152 DIFSR++ G RISL A +V + +G G+ +GY+ G+WD + MRI D L AFP + Sbjct: 98 DIFSRIVMGTRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWDR-ITMRICDVLFAFPGI 156 Query: 153 ILALALAAALGGGFYNAMAAVGIGFAPAFIRLARGQAMSIRNLDYVMAARSVGAGHLRIM 212 +LA+ + A LGGG N + +V + PAF RL RG + ++NL Y+ A RS+GA + IM Sbjct: 157 LLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEATRSIGASDMTIM 216 Query: 213 WRYVLPNAMAPLIIQATFAMGSAIIAEAGLSYLGLGARAEDPSWGSMLHIAQGYLNTNPT 272 W+++ P ++ +++ T +G++II AGLS+LGLGA++ P WG ML+ A+ + T+P Sbjct: 217 WKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLMLNEARADMVTSPH 276 Query: 273 LALWPGVAIFAVVLGFNLLGDGIREVFDPKL 303 +AL P +AIF VL FNLLGDG+R+ DPK+ Sbjct: 277 VALVPSIAIFLTVLAFNLLGDGLRDALDPKI 307 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 182 bits (461), Expect = 4e-47, Method: Compositional matrix adjust. Identities = 111/276 (40%), Positives = 165/276 (59%), Gaps = 8/276 (2%) Query: 32 LRRFAGNRLAVLGAAIILLLVLIAIFAPLLATHDPIFDQDYGNLLSGP------DTTHWM 85 LRR G+R ++GAA++ ++VL AIFAPLLA HDP FDQD L P H + Sbjct: 28 LRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPHDP-FDQDVTARLIPPVWQAQGSWEHIL 86 Query: 86 GTDDLGRDIFSRMLYGARISLQAALIAVGLAFCVGVPVGIASGYFRGFWDEWVVMRIVDA 145 GTD LGRD FSR++YGAR+SL L A ++ +G +G+ +GYF G D V+ ++ Sbjct: 87 GTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDA-VISYLITT 145 Query: 146 LQAFPPLILALALAAALGGGFYNAMAAVGIGFAPAFIRLARGQAMSIRNLDYVMAARSVG 205 A P +++ALA+A+ +GG + +G+ F + R +R+ +++ AA+++G Sbjct: 146 RLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAKAIG 205 Query: 206 AGHLRIMWRYVLPNAMAPLIIQATFAMGSAIIAEAGLSYLGLGARAEDPSWGSMLHIAQG 265 A I+ R +LPN M LI+ T M AI+ EA LS+LGLG + PSWG M+ + Sbjct: 206 ASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAEGKT 265 Query: 266 YLNTNPTLALWPGVAIFAVVLGFNLLGDGIREVFDP 301 Y+ P + + PGVA+ +VL NL+GDG+R+V P Sbjct: 266 YMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAP 301 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 150 bits (378), Expect = 2e-37, Method: Compositional matrix adjust. Identities = 105/293 (35%), Positives = 169/293 (57%), Gaps = 17/293 (5%) Query: 24 PRRQR--FTGLRRFAGNRLAVLGAAIILLLVLIAIFAPLLATHDP-------IFD-QDYG 73 PRR+ +R F +R A+LG I+LLL++ AI AP + +P + D + + Sbjct: 28 PRRESPWRRVMRHFVASRSAMLGLVIVLLLIVGAIAAPWITPQNPYDLMQLDVLDARLHP 87 Query: 74 NLLSGPDT-THWMGTDDLGRDIFSRMLYGARISLQAALIAVGLAFCVGVPVGIASGYFRG 132 L+G T T+W+GTD GRD+ S +LYG RIS+ + + +A +G +G+ + Y G Sbjct: 88 GTLNGAGTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSALIAGVIGTLIGLLAAYAGG 147 Query: 133 FWDEWVVMRIVDALQAFPPLILALALAAALGGGFYNAMAAVGIGFAPAFIRLARGQAMSI 192 D ++MR D + +FP +++A+ + A +G G +N MA + + + R ARGQA+ Sbjct: 148 KLDT-LLMRFADLVLSFPSILVAMLILAYVGKGIFNVMATLVVLEWAYYARTARGQALVE 206 Query: 193 RNLDYVMAARSVGAGHLRIMWRYVLPNAMAPLIIQATFAMGSAIIAEAGLSYLGLGARAE 252 R +YV AAR + RIM R++LPN + PLI+ T + AI EA LS+LGLG Sbjct: 207 RRKEYVEAARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVARAITLEATLSFLGLGVPIT 266 Query: 253 DPSWGSMLHIAQGY---LNTNPTLALWPGVAIFAVVLGFNLLGDGIREVFDPK 302 +PS G L I+ GY L+ ++ +PG+ + V++ NL+GD +R++ +P+ Sbjct: 267 EPSLG--LLISNGYQYMLSGEYWISFYPGITLLVVIVAINLVGDRLRDILNPR 317 >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 = 83/262 (31%), Positives = 136/262 (51%), Gaps = 6/262 (2%) Query: 38 NRLAVLGAAIILLLVLIAIFAPLLATHDP--IFDQDYGNLLSGPDTTHWMGTDDLGRDIF 95 + +A +G AI+ +L+AI P ++ +D I D D + SG +G+D LGRD+ Sbjct: 30 STMAWIGMAIVGFWILMAILGPSISPYDATAIVDTD---VFSGMSHKFLLGSDYLGRDML 86 Query: 96 SRMLYGARISLQAALIAVGLAFCVGVPVGIASGYFRGFWDEWVVMRIVDALQAFPPLILA 155 SR+L+G R ++ AL A LA G + + + F G W + V+ R +DAL + P + A Sbjct: 87 SRILFGTRATIGLALAATVLASATGTAIALFAA-FSGGWRDAVISRALDALISIPSKMFA 145 Query: 156 LALAAALGGGFYNAMAAVGIGFAPAFIRLARGQAMSIRNLDYVMAARSVGAGHLRIMWRY 215 L + A G + I + P R+AR A++++ ++YV AAR+ G G IM Sbjct: 146 LMMVATFGSSMLLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGVWYIMTVE 205 Query: 216 VLPNAMAPLIIQATFAMGSAIIAEAGLSYLGLGARAEDPSWGSMLHIAQGYLNTNPTLAL 275 +LPN + P++ ++ +GLS+L LG + D WGS++ L + Sbjct: 206 MLPNMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSLVRENISGLGEGALAVI 265 Query: 276 WPGVAIFAVVLGFNLLGDGIRE 297 P +AI ++ +G NLL D +R Sbjct: 266 MPALAIASLTIGVNLLIDNLRS 287 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 102 bits (255), Expect = 3e-23, Method: Compositional matrix adjust. Identities = 66/206 (32%), Positives = 106/206 (51%), Gaps = 6/206 (2%) Query: 77 SGPDTTHWMGTDDLGRDIFSRMLYGARISLQAALIAVGLAFCVGVPVGIASGYFRGFWDE 136 + P + +W+GTDD GRD+F+R+LYG R+S+ + + +GV G GYF G D Sbjct: 122 AAPSSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDL 181 Query: 137 WVVMRIVDALQAFPPLILALALAAALGGGFYNAMAAVGIGFAPAFIRLARGQAMSIRNLD 196 R+++ + P L L + ++ + + + + R + RNL+ Sbjct: 182 -FTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLE 240 Query: 197 YVMAARSVGAGHLRIMWRYVLPNAMAPLIIQATFAMGSAIIAEAGLSYLGLGARAEDPSW 256 Y+ AAR++G I+WR+VLPN+M ++ F M +AI+A L +LGLG PS Sbjct: 241 YIQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSL 300 Query: 257 GSMLHIAQGYLNTNPTLALWPGVAIF 282 G +L AQG N + A W ++ F Sbjct: 301 GELL--AQGKNNLD---AWWIALSTF 321 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 0.328 0.142 0.437 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: 915,688 Number of extensions: 36116 Number of successful extensions: 251 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 244 Number of HSP's successfully gapped: 7 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 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 130 (54.7 bits)