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= 0020.0030.p (256 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... 360 e-101 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 127 9e-31 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 127 1e-30 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 89 5e-19 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 82 3e-17 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 360 bits (925), Expect = e-101, Method: Compositional matrix adjust. Identities = 187/286 (65%), Positives = 213/286 (74%), Gaps = 45/286 (15%) Query: 16 ASKPIRTPWSEFWRKFKKQPLALAAGAFVLFLSSVAVGA--------------------- 54 + + IRTPW EFWRKFKKQ LA+ AG F+LFL +VA+ A Sbjct: 25 SGQKIRTPWREFWRKFKKQHLAVYAGVFILFLVAVAILAPWIVPFDPENFFDYDALNSPP 84 Query: 55 -------------------IAGT-----GXFSSVAVGAIAGTFLGLVAGYYEGWADRVIM 90 + GT F SVA+GA+ GT GL+AGYYEGW DR+ M Sbjct: 85 TWVHWFGVDSLGRDIFSRIVMGTRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWDRITM 144 Query: 91 RICDVLFAFPGILLAIAIVAILGNGMTNVIIAVAIFSIPAFARLVRGNTLSLKQLTYIEA 150 RICDVLFAFPGILLAI IVAILG GM NVII+V++FSIPAFARLVRGNTL LK LTYIEA Sbjct: 145 RICDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEA 204 Query: 151 VRSIGANDMTIILRHIFPGTISSVVVYFTMRIGTSIITAASLSFLGLGAQPPTPEWGAML 210 RSIGA+DMTI+ +HIFPGTIS++VVYFTMRIGTSIITAA LSFLGLGAQ PTPEWG ML Sbjct: 205 TRSIGASDMTIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLML 264 Query: 211 NEARADMMTAPHIAIFPSLAIFLTVLAFNLLGDGLRDALDPKLDQK 256 NEARADM+T+PH+A+ PS+AIFLTVLAFNLLGDGLRDALDPK+DQ+ Sbjct: 265 NEARADMVTSPHVALVPSIAIFLTVLAFNLLGDGLRDALDPKIDQR 310 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 127 bits (319), Expect = 9e-31, Method: Compositional matrix adjust. Identities = 71/187 (37%), Positives = 111/187 (59%) Query: 66 VGAIAGTFLGLVAGYYEGWADRVIMRICDVLFAFPGILLAIAIVAILGNGMTNVIIAVAI 125 + + GT LG++AGY+ G D VI + A P +L+A+A+ +++G + VI+ + + Sbjct: 116 ISGLIGTTLGVLAGYFGGRTDAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGL 175 Query: 126 FSIPAFARLVRGNTLSLKQLTYIEAVRSIGANDMTIILRHIFPGTISSVVVYFTMRIGTS 185 FA + R T L+ +I A ++IGA+ I+LR I P + +++V T+ + + Sbjct: 176 LLWDRFAVVTRSATQQLRDAEFIAAAKAIGASTPYILLREILPNIMGALIVVVTLEMAHA 235 Query: 186 IITAASLSFLGLGAQPPTPEWGAMLNEARADMMTAPHIAIFPSLAIFLTVLAFNLLGDGL 245 I+ A+LSFLGLG QPPTP WG M+ E + M P + + P +A+ L VLA NL+GDGL Sbjct: 236 ILLEATLSFLGLGVQPPTPSWGLMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGL 295 Query: 246 RDALDPK 252 RD P Sbjct: 296 RDVNAPD 302 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 127 bits (318), Expect = 1e-30, Method: Compositional matrix adjust. Identities = 67/200 (33%), Positives = 117/200 (58%), Gaps = 2/200 (1%) Query: 57 GTGXFSSVAVGAIAGTFLGLVAGYYEGWADRVIMRICDVLFAFPGILLAIAIVAILGNGM 116 G G S++ G I GT +GL+A Y G D ++MR D++ +FP IL+A+ I+A +G G+ Sbjct: 122 GIGVGSALIAGVI-GTLIGLLAAYAGGKLDTLLMRFADLVLSFPSILVAMLILAYVGKGI 180 Query: 117 TNVIIAVAIFSIPAFARLVRGNTLSLKQLTYIEAVRSIGANDMTIILRHIFPGTISSVVV 176 NV+ + + +AR RG L ++ Y+EA R + + I++RHI P + ++V Sbjct: 181 FNVMATLVVLEWAYYARTARGQALVERRKEYVEAARGLNLSSWRIMVRHILPNCLPPLIV 240 Query: 177 YFTMRIGTSIITAASLSFLGLGAQPPTPEWGAMLNEARADMMTAPH-IAIFPSLAIFLTV 235 T+++ +I A+LSFLGLG P G +++ M++ + I+ +P + + + + Sbjct: 241 IGTLQVARAITLEATLSFLGLGVPITEPSLGLLISNGYQYMLSGEYWISFYPGITLLVVI 300 Query: 236 LAFNLLGDGLRDALDPKLDQ 255 +A NL+GD LRD L+P+ + Sbjct: 301 VAINLVGDRLRDILNPRWQK 320 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 88.6 bits (218), Expect = 5e-19, Method: Compositional matrix adjust. Identities = 56/185 (30%), Positives = 101/185 (54%), Gaps = 1/185 (0%) Query: 66 VGAIAGTFLGLVAGYYEGWADRVIMRICDVLFAFPGILLAIAIVAILGNGMTNVIIAVAI 125 +G + G G V GY+ G D R+ ++ + P + L I +I + +++ +++ Sbjct: 160 IGVVLGVAAGAVQGYFAGRTDLFTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSL 219 Query: 126 FSIPAFARLVRGNTLSLKQLTYIEAVRSIGANDMTIILRHIFPGTISSVVVYFTMRIGTS 185 F + + VR + L + L YI+A R++G D II RH+ P ++++VV + R+ + Sbjct: 220 FGWMSLSDYVRADFLRNRNLEYIQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAA 279 Query: 186 IITAASLSFLGLGAQPPTPEWGAMLNEARADMMTAPHIAIFPSLAIFLTVLAFNLLGDGL 245 I+ SL FLGLG P TP G +L + + + + A IA+ + + +T+L +G+ L Sbjct: 280 ILALTSLDFLGLGVPPSTPSLGELLAQGKNN-LDAWWIALSTFVVLTVTLLLLTNIGNAL 338 Query: 246 RDALD 250 R+ALD Sbjct: 339 RNALD 343 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 82.4 bits (202), Expect = 3e-17, Method: Compositional matrix adjust. Identities = 61/202 (30%), Positives = 101/202 (50%), Gaps = 1/202 (0%) Query: 46 FLSSVAVGAIAGTG-XFSSVAVGAIAGTFLGLVAGYYEGWADRVIMRICDVLFAFPGILL 104 LS + G A G ++ + + GT + L A + GW D VI R D L + P + Sbjct: 85 MLSRILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVISRALDALISIPSKMF 144 Query: 105 AIAIVAILGNGMTNVIIAVAIFSIPAFARLVRGNTLSLKQLTYIEAVRSIGANDMTIILR 164 A+ +VA G+ M +++ AI +P R+ R ++++ + Y++A R+ G I+ Sbjct: 145 ALMMVATFGSSMLLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGVWYIMTV 204 Query: 165 HIFPGTISSVVVYFTMRIGTSIITAASLSFLGLGAQPPTPEWGAMLNEARADMMTAPHIA 224 + P I V+ F +R ++ + LSFL LG QPP +WG+++ E + + Sbjct: 205 EMLPNMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSLVRENISGLGEGALAV 264 Query: 225 IFPSLAIFLTVLAFNLLGDGLR 246 I P+LAI + NLL D LR Sbjct: 265 IMPALAIASLTIGVNLLIDNLR 286 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 0.139 0.410 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: 714,308 Number of extensions: 26354 Number of successful extensions: 187 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 188 Number of HSP's successfully gapped: 7 Length of query: 256 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 173 Effective length of database: 1,226,865 Effective search space: 212247645 Effective search space used: 212247645 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: 129 (54.3 bits)