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= 0001.2438.p (321 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 331 5e-92 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 195 3e-51 gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 166 3e-42 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 122 4e-29 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 82 5e-17 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 331 bits (849), Expect = 5e-92, Method: Compositional matrix adjust. Identities = 163/287 (56%), Positives = 223/287 (77%) Query: 32 ESPWRVLARRFFKSRIGTAAALLLALMVVAAVASPLIAPQDPYDLAKVSILEAERSPGTL 91 ESPWR + R F SR +++ L++V A+A+P I PQ+PYDL ++ +L+A PGTL Sbjct: 31 ESPWRRVMRHFVASRSAMLGLVIVLLLIVGAIAAPWITPQNPYDLMQLDVLDARLHPGTL 90 Query: 92 STDHTMRYVLGTDGAGRDMLSAILYGLRISLGIGVASALVALVLGTSLGLISAYFGGKVD 151 + T Y LGTDG GRD++SAILYGLRIS+GIGV SAL+A V+GT +GL++AY GGK+D Sbjct: 91 NGAGTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSALIAGVIGTLIGLLAAYAGGKLD 150 Query: 152 ALLMRIVDVQLSVPTILVALVLLAVLGQGVDKTLMALVLVQWAIFARNVRGAALVERGKD 211 LLMR D+ LS P+ILVA+++LA +G+G+ + LV+++WA +AR RG ALVER K+ Sbjct: 151 TLLMRFADLVLSFPSILVAMLILAYVGKGIFNVMATLVVLEWAYYARTARGQALVERRKE 210 Query: 212 YIEAALGQGLPARRIMFRHVLPNCVAPLIVTTTNQMANAITLEATMSFLGIGLPQTKPSL 271 Y+EAA G L + RIM RH+LPNC+ PLIV T Q+A AITLEAT+SFLG+G+P T+PSL Sbjct: 211 YVEAARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVARAITLEATLSFLGLGVPITEPSL 270 Query: 272 GLLISNGFDYMLSNQYWISVFPGVALVLLVMAVSLVGDQLRLVLNPK 318 GLLISNG+ YMLS +YWIS +PG+ L+++++A++LVGD+LR +LNP+ Sbjct: 271 GLLISNGYQYMLSGEYWISFYPGITLLVVIVAINLVGDRLRDILNPR 317 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 195 bits (496), Expect = 3e-51, Method: Compositional matrix adjust. Identities = 115/283 (40%), Positives = 174/283 (61%), Gaps = 5/283 (1%) Query: 35 WRVLARRFFKSRIGTAAALLLALMVVAAVASPLIAPQDPYDLAKVSILEAERSPGTLSTD 94 WR RR R A +LA++V+AA+ +PL+AP DP+D + A P Sbjct: 24 WRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPHDPFD----QDVTARLIPPVWQAQ 79 Query: 95 HTMRYVLGTDGAGRDMLSAILYGLRISLGIGVASALVALVLGTSLGLISAYFGGKVDALL 154 + ++LGTD GRD S ++YG R+SL IG+A+AL++ ++GT+LG+++ YFGG+ DA++ Sbjct: 80 GSWEHILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVI 139 Query: 155 MRIVDVQLSVPTILVALVLLAVLGQGVDKTLMALVLVQWAIFARNVRGAALVERGKDYIE 214 ++ +L++P +LVAL + +++G + ++ L L+ W FA R A R ++I Sbjct: 140 SYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIA 199 Query: 215 AALGQGLPARRIMFRHVLPNCVAPLIVTTTNQMANAITLEATMSFLGIGLPQTKPSLGLL 274 AA G I+ R +LPN + LIV T +MA+AI LEAT+SFLG+G+ PS GL+ Sbjct: 200 AAKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLM 259 Query: 275 ISNGFDYMLSNQYWISVFPGVALVLLVMAVSLVGDQLRLVLNP 317 ++ G YM W+ V PGVAL LLV+A++LVGD LR V P Sbjct: 260 VAEGKTYMFFKP-WVIVIPGVALALLVLAINLVGDGLRDVNAP 301 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 166 bits (419), Expect = 3e-42, Method: Compositional matrix adjust. Identities = 96/289 (33%), Positives = 157/289 (54%), Gaps = 10/289 (3%) Query: 32 ESPWRVLARRFFKSRIGTAAALLLALMVVAAVASPLIAPQDPYDLAKVSILEAERSPGTL 91 +PWR R+F K + A + + +V A+ +P I P DP + +A SP Sbjct: 30 RTPWREFWRKFKKQHLAVYAGVFILFLVAVAILAPWIVPFDPENFFD---YDALNSP--- 83 Query: 92 STDHTMRYVLGTDGAGRDMLSAILYGLRISLGIGVASALVALVLGTSLGLISAYFGGKVD 151 T + G D GRD+ S I+ G RISL G S + V+GT GL++ Y+ G D Sbjct: 84 ---PTWVHWFGVDSLGRDIFSRIVMGTRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWD 140 Query: 152 ALLMRIVDVQLSVPTILVALVLLAVLGQGVDKTLMALVLVQWAIFARNVRGAALVERGKD 211 + MRI DV + P IL+A+ ++A+LG G+ ++++ + FAR VRG L + Sbjct: 141 RITMRICDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLT 200 Query: 212 YIEAALGQGLPARRIMFRHVLPNCVAPLIVTTTNQMANAITLEATMSFLGIGLPQTKPSL 271 YIEA G IM++H+ P ++ ++V T ++ +I A +SFLG+G P Sbjct: 201 YIEATRSIGASDMTIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEW 260 Query: 272 GLLISNGFDYMLSNQYWISVFPGVALVLLVMAVSLVGDQLRLVLNPKLD 320 GL+++ M+++ + +++ P +A+ L V+A +L+GD LR L+PK+D Sbjct: 261 GLMLNEARADMVTSPH-VALVPSIAIFLTVLAFNLLGDGLRDALDPKID 308 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 122 bits (306), Expect = 4e-29, Method: Compositional matrix adjust. Identities = 74/250 (29%), Positives = 139/250 (55%), Gaps = 6/250 (2%) Query: 67 LIAPQDPYDLAKVSILEAERSPGTLSTDHTMRYVLGTDGAGRDMLSAILYGLRISLGIGV 126 ++ P + Y ++ + +P S+++ LGTD GRD+ + +LYG R+S+ G+ Sbjct: 100 VLYPPNRYGYNTLNYFAKQPNPAAPSSENW----LGTDDRGRDVFARLLYGFRVSVLFGM 155 Query: 127 ASALVALVLGTSLGLISAYFGGKVDALLMRIVDVQLSVPTILVALVLLAVLGQGVDKTLM 186 A + +VLG + G + YF G+ D R++++ S+P + + ++ ++ + L+ Sbjct: 156 ALTFIGVVLGVAAGAVQGYFAGRTDLFTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLV 215 Query: 187 ALVLVQWAIFARNVRGAALVERGKDYIEAALGQGLPARRIMFRHVLPNCVAPLIVTTTNQ 246 L L W + VR L R +YI+AA GLP R I++RHVLPN + ++ + Sbjct: 216 LLSLFGWMSLSDYVRADFLRNRNLEYIQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFR 275 Query: 247 MANAITLEATMSFLGIGLPQTKPSLGLLISNGFDYMLSNQYWISVFPGVALVLLVMAVSL 306 M+ AI ++ FLG+G+P + PSLG L++ G + + + +WI++ V L + ++ ++ Sbjct: 276 MSAAILALTSLDFLGLGVPPSTPSLGELLAQGKNNL--DAWWIALSTFVVLTVTLLLLTN 333 Query: 307 VGDQLRLVLN 316 +G+ LR L+ Sbjct: 334 IGNALRNALD 343 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 82.4 bits (202), Expect = 5e-17, Method: Compositional matrix adjust. Identities = 53/191 (27%), Positives = 103/191 (53%), Gaps = 18/191 (9%) Query: 54 LLALMVVAAVASPLIAPQDPYDLAKVSILEAERSPGTLSTDHTMRYVLGTDGAGRDMLSA 113 ++ ++ A+ P I+P D + + + + +++LG+D GRDMLS Sbjct: 39 IVGFWILMAILGPSISPYDATAIVDTDVF----------SGMSHKFLLGSDYLGRDMLSR 88 Query: 114 ILYGLRISLGIGVASALVALVLGTSLGLISAYFGGKVDALLMRIVDVQLSVPTILVALVL 173 IL+G R ++G+ +A+ ++A GT++ L +A+ GG DA++ R +D +S+P+ + AL++ Sbjct: 89 ILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVISRALDALISIPSKMFALMM 148 Query: 174 LAVLGQGVDKTLMALVLVQWAIFA----RNVRGAALVERGKDYIEAALGQGLPARRIMFR 229 +A G +++ LVL + R R A+ + +Y++AA +G IM Sbjct: 149 VATFGS----SMLLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGVWYIMTV 204 Query: 230 HVLPNCVAPLI 240 +LPN + P++ Sbjct: 205 EMLPNMIRPVL 215 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 0.324 0.139 0.393 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: 911,714 Number of extensions: 35507 Number of successful extensions: 279 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 279 Number of HSP's successfully gapped: 6 Length of query: 321 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 236 Effective length of database: 1,217,395 Effective search space: 287305220 Effective search space used: 287305220 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 (21.5 bits) S2: 130 (54.7 bits)