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= 0001.1701.p (314 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... 556 e-160 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 181 8e-47 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 180 1e-46 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 119 3e-28 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 109 4e-25 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 556 bits (1434), Expect = e-160, Method: Compositional matrix adjust. Identities = 282/314 (89%), Positives = 292/314 (92%), Gaps = 4/314 (1%) Query: 1 MSLSNSPLASSSETGAPLPPADPSAVIAAGQKIRTPWREFWRKFKKQRLAVYAGVFILLL 60 MSLSN+P++ + AV A+GQKIRTPWREFWRKFKKQ LAVYAGVFIL L Sbjct: 1 MSLSNAPISDTGAPLP----PPGPAVAASGQKIRTPWREFWRKFKKQHLAVYAGVFILFL 56 Query: 61 IVIAIIAPWIVPFDAENFFDYDALNSPPTWTHWFGVDSLGRDIFSRILMGARISLASGFF 120 + +AI+APWIVPFD ENFFDYDALNSPPTW HWFGVDSLGRDIFSRI+MG RISLA+GFF Sbjct: 57 VAVAILAPWIVPFDPENFFDYDALNSPPTWVHWFGVDSLGRDIFSRIVMGTRISLAAGFF 116 Query: 121 SVAIGAVIGTVFGLLAGYYEGWWDRITMRICDVLFAFPGILLAIGIVAILGGGMINVIIS 180 SVAIGAVIGTVFGLLAGYYEGWWDRITMRICDVLFAFPGILLAIGIVAILGGGMINVIIS Sbjct: 117 SVAIGAVIGTVFGLLAGYYEGWWDRITMRICDVLFAFPGILLAIGIVAILGGGMINVIIS 176 Query: 181 VSVFSIPAFARLVRGNTLQLKNLTYIEATRSIGASDATIMWKHIFPGTISAIVVYFTMRI 240 VSVFSIPAFARLVRGNTLQLKNLTYIEATRSIGASD TIMWKHIFPGTISAIVVYFTMRI Sbjct: 177 VSVFSIPAFARLVRGNTLQLKNLTYIEATRSIGASDMTIMWKHIFPGTISAIVVYFTMRI 236 Query: 241 GTSIITAAGLSFLGLGAQSPTPEWGLMLNEARADMVTSPHVALVPSIAIFLTVLAFNLLG 300 GTSIITAAGLSFLGLGAQSPTPEWGLMLNEARADMVTSPHVALVPSIAIFLTVLAFNLLG Sbjct: 237 GTSIITAAGLSFLGLGAQSPTPEWGLMLNEARADMVTSPHVALVPSIAIFLTVLAFNLLG 296 Query: 301 DGLRDALDPKIDQR 314 DGLRDALDPKIDQR Sbjct: 297 DGLRDALDPKIDQR 310 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 181 bits (458), Expect = 8e-47, Method: Compositional matrix adjust. Identities = 109/289 (37%), Positives = 159/289 (55%), Gaps = 10/289 (3%) Query: 32 KIRTPWREFWRKFKKQRLAVYAGVFILLLIVIAIIAPWIVPFDAENFFDYD--------- 82 + +PWR R F R A+ V +LLLIV AI APWI P + + D Sbjct: 29 RRESPWRRVMRHFVASRSAMLGLVIVLLLIVGAIAAPWITPQNPYDLMQLDVLDARLHPG 88 Query: 83 ALNSPPTWTHWFGVDSLGRDIFSRILMGARISLASGFFSVAIGAVIGTVFGLLAGYYEGW 142 LN T+T+W G D GRD+ S IL G RIS+ G S I VIGT+ GLLA Y G Sbjct: 89 TLNGAGTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSALIAGVIGTLIGLLAAYAGGK 148 Query: 143 WDRITMRICDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKN 202 D + MR D++ +FP IL+A+ I+A +G G+ NV+ ++ V +AR RG L + Sbjct: 149 LDTLLMRFADLVLSFPSILVAMLILAYVGKGIFNVMATLVVLEWAYYARTARGQALVERR 208 Query: 203 LTYIEATRSIGASDATIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTP 262 Y+EA R + S IM +HI P + ++V T+++ +I A LSFLGLG P Sbjct: 209 KEYVEAARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVARAITLEATLSFLGLGVPITEP 268 Query: 263 EWGLMLNEARADMVTSPH-VALVPSIAIFLTVLAFNLLGDGLRDALDPK 310 GL+++ M++ + ++ P I + + ++A NL+GD LRD L+P+ Sbjct: 269 SLGLLISNGYQYMLSGEYWISFYPGITLLVVIVAINLVGDRLRDILNPR 317 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 180 bits (456), Expect = 1e-46, Method: Compositional matrix adjust. Identities = 105/281 (37%), Positives = 156/281 (55%), Gaps = 11/281 (3%) Query: 37 WREFWRKFKKQRLAVYAGVFILLLIVIAIIAPWIVPFDAENFFDYDALNS--PP------ 88 WR R+ R + + ++++ AI AP + P D FD D PP Sbjct: 24 WRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPHDP---FDQDVTARLIPPVWQAQG 80 Query: 89 TWTHWFGVDSLGRDIFSRILMGARISLASGFFSVAIGAVIGTVFGLLAGYYEGWWDRITM 148 +W H G D LGRD FSR++ GAR+SL G + I +IGT G+LAGY+ G D + Sbjct: 81 SWEHILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVIS 140 Query: 149 RICDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEA 208 + A P +L+A+ + +++GG + VI+ + + FA + R T QL++ +I A Sbjct: 141 YLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAA 200 Query: 209 TRSIGASDATIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLML 268 ++IGAS I+ + I P + A++V T+ + +I+ A LSFLGLG Q PTP WGLM+ Sbjct: 201 AKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLMV 260 Query: 269 NEARADMVTSPHVALVPSIAIFLTVLAFNLLGDGLRDALDP 309 E + M P V ++P +A+ L VLA NL+GDGLRD P Sbjct: 261 AEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAP 301 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 119 bits (298), Expect = 3e-28, Method: Compositional matrix adjust. Identities = 71/236 (30%), Positives = 130/236 (55%), Gaps = 1/236 (0%) Query: 73 FDAENFFDYDALNSPPTWTHWFGVDSLGRDIFSRILMGARISLASGFFSVAIGAVIGTVF 132 ++ N+F + P+ +W G D GRD+F+R+L G R+S+ G IG V+G Sbjct: 109 YNTLNYFAKQPNPAAPSSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAA 168 Query: 133 GLLAGYYEGWWDRITMRICDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSIPAFARL 192 G + GY+ G D T R+ ++ + P + L I +I + +++ +S+F + + Sbjct: 169 GAVQGYFAGRTDLFTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDY 228 Query: 193 VRGNTLQLKNLTYIEATRSIGASDATIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSF 252 VR + L+ +NL YI+A R++G D I+W+H+ P +++ +V + R+ +I+ L F Sbjct: 229 VRADFLRNRNLEYIQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDF 288 Query: 253 LGLGAQSPTPEWGLMLNEARADMVTSPHVALVPSIAIFLTVLAFNLLGDGLRDALD 308 LGLG TP G +L + + ++ + +AL + + +T+L +G+ LR+ALD Sbjct: 289 LGLGVPPSTPSLGELLAQGKNNL-DAWWIALSTFVVLTVTLLLLTNIGNALRNALD 343 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 109 bits (272), Expect = 4e-25, Method: Compositional matrix adjust. Identities = 75/252 (29%), Positives = 126/252 (50%), Gaps = 5/252 (1%) Query: 61 IVIAIIAPWIVPFDAENFFDYDALNSPPTWTHWF--GVDSLGRDIFSRILMGARISLASG 118 I++AI+ P I P+DA D D + +H F G D LGRD+ SRIL G R ++ Sbjct: 44 ILMAILGPSISPYDATAIVDTDVFSG---MSHKFLLGSDYLGRDMLSRILFGTRATIGLA 100 Query: 119 FFSVAIGAVIGTVFGLLAGYYEGWWDRITMRICDVLFAFPGILLAIGIVAILGGGMINVI 178 + + + GT L A + GW D + R D L + P + A+ +VA G M+ ++ Sbjct: 101 LAATVLASATGTAIALFAAFSGGWRDAVISRALDALISIPSKMFALMMVATFGSSMLLLV 160 Query: 179 ISVSVFSIPAFARLVRGNTLQLKNLTYIEATRSIGASDATIMWKHIFPGTISAIVVYFTM 238 ++ ++ +P R+ R + ++ + Y++A R+ G IM + P I ++ F + Sbjct: 161 LTAAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGVWYIMTVEMLPNMIRPVLADFGL 220 Query: 239 RIGTSIITAAGLSFLGLGAQSPTPEWGLMLNEARADMVTSPHVALVPSIAIFLTVLAFNL 298 R ++ +GLSFL LG Q P +WG ++ E + + ++P++AI + NL Sbjct: 221 RFVYVVLLLSGLSFLSLGVQPPDADWGSLVRENISGLGEGALAVIMPALAIASLTIGVNL 280 Query: 299 LGDGLRDALDPK 310 L D LR K Sbjct: 281 LIDNLRSKRAAK 292 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 0.438 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: 809,676 Number of extensions: 28967 Number of successful extensions: 175 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 173 Number of HSP's successfully gapped: 6 Length of query: 314 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 229 Effective length of database: 1,217,395 Effective search space: 278783455 Effective search space used: 278783455 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)