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= 0017.0025.p (353 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 536 e-154 gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 139 4e-34 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 128 8e-31 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 119 3e-28 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 61 1e-10 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 536 bits (1381), Expect = e-154, Method: Compositional matrix adjust. Identities = 287/348 (82%), Positives = 320/348 (91%) Query: 6 VTASSSPTPSISPGRRIWLRFRQNRNGYASLIIFLILFVISLGAELVSNDKPLVASYHGK 65 ++ ++SP PSISPGRRIWLRF +R GY SL +F +LFV+SLGAEL+SND+PL+A Y GK Sbjct: 1 MSTTTSPAPSISPGRRIWLRFCADRAGYWSLWLFSLLFVLSLGAELISNDRPLMARYQGK 60 Query: 66 ILFPIAHDYSEKTFGGDFESPADYLDPFIQEQFRKDGNWAIYPPNHYRFDTLNYFARQPN 125 ++FPI DYS+K+FGGDF+SPADYLDPFIQ Q RKDGNW +YPPN Y ++TLNYFA+QPN Sbjct: 61 LIFPIVQDYSDKSFGGDFDSPADYLDPFIQAQLRKDGNWVLYPPNRYGYNTLNYFAKQPN 120 Query: 126 PAPPSSENWLGTDDRGRDVFARLLYGFRISILFGLALTVTGVVLGLLAGAVQGYFAGRTD 185 PA PSSENWLGTDDRGRDVFARLLYGFR+S+LFG+ALT GVVLG+ AGAVQGYFAGRTD Sbjct: 121 PAAPSSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTD 180 Query: 186 LFMQRLLEIWGSMPELYLLIIFSSIFEPSIGLLLVLLSLFGWMGLSDYVRADFLRNRNLE 245 LF QRLLEIWGSMPELYLLIIFSSIF+PS+GLLLVLLSLFGWM LSDYVRADFLRNRNLE Sbjct: 181 LFTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLE 240 Query: 246 YVQAGRALGLSNMQIIWRHVLPNSLTPVVTFLPFRMSASILALTSLDFLGLGVPPSTPSL 305 Y+QA RA+GL + IIWRHVLPNS+T VVTFLPFRMSA+ILALTSLDFLGLGVPPSTPSL Sbjct: 241 YIQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSL 300 Query: 306 GELLAQGKNNLDAWWIALSTFIVLTVTLLLLTNIGDALRNALDVRRKA 353 GELLAQGKNNLDAWWIALSTF+VLTVTLLLLTNIG+ALRNALDVRRKA Sbjct: 301 GELLAQGKNNLDAWWIALSTFVVLTVTLLLLTNIGNALRNALDVRRKA 348 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 139 bits (350), Expect = 4e-34, Method: Compositional matrix adjust. Identities = 78/245 (31%), Positives = 134/245 (54%), Gaps = 1/245 (0%) Query: 105 AIYPPNHYRFDTLNYFARQPNPAPPSSENWLGTDDRGRDVFARLLYGFRISILFGLALTV 164 AI P FD N+F +PP+ +W G D GRD+F+R++ G RIS+ G Sbjct: 60 AILAPWIVPFDPENFFDYDALNSPPTWVHWFGVDSLGRDIFSRIVMGTRISLAAGFFSVA 119 Query: 165 TGVVLGLLAGAVQGYFAGRTDLFMQRLLEIWGSMPELYLLIIFSSIFEPSIGLLLVLLSL 224 G V+G + G + GY+ G D R+ ++ + P + L I +I + +++ +S+ Sbjct: 120 IGAVIGTVFGLLAGYYEGWWDRITMRICDVLFAFPGILLAIGIVAILGGGMINVIISVSV 179 Query: 225 FGWMGLSDYVRADFLRNRNLEYVQAGRALGLSNMQIIWRHVLPNSLTPVVTFLPFRMSAS 284 F + VR + L+ +NL Y++A R++G S+M I+W+H+ P +++ +V + R+ S Sbjct: 180 FSIPAFARLVRGNTLQLKNLTYIEATRSIGASDMTIMWKHIFPGTISAIVVYFTMRIGTS 239 Query: 285 ILALTSLDFLGLGVPPSTPSLGELLAQGKNNL-DAWWIALSTFIVLTVTLLLLTNIGDAL 343 I+ L FLGLG TP G +L + + ++ + +AL I + +T+L +GD L Sbjct: 240 IITAAGLSFLGLGAQSPTPEWGLMLNEARADMVTSPHVALVPSIAIFLTVLAFNLLGDGL 299 Query: 344 RNALD 348 R+ALD Sbjct: 300 RDALD 304 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 128 bits (321), Expect = 8e-31, Method: Compositional matrix adjust. Identities = 79/251 (31%), Positives = 129/251 (51%), Gaps = 6/251 (2%) Query: 106 IYPPNHYRFDTLNYFARQPNPAPPSSEN----WLGTDDRGRDVFARLLYGFRISILFGLA 161 I P N Y L+ + +P + WLGTD +GRD+ + +LYG RIS+ G+ Sbjct: 67 ITPQNPYDLMQLDVLDARLHPGTLNGAGTYTYWLGTDGQGRDLVSAILYGLRISVGIGVG 126 Query: 162 LTVTGVVLGLLAGAVQGYFAGRTDLFMQRLLEIWGSMPELYLLIIFSSIFEPSIGLLLVL 221 + V+G L G + Y G+ D + R ++ S P + + ++ + I ++ Sbjct: 127 SALIAGVIGTLIGLLAAYAGGKLDTLLMRFADLVLSFPSILVAMLILAYVGKGIFNVMAT 186 Query: 222 LSLFGWMGLSDYVRADFLRNRNLEYVQAGRALGLSNMQIIWRHVLPNSLTPVVTFLPFRM 281 L + W + R L R EYV+A R L LS+ +I+ RH+LPN L P++ ++ Sbjct: 187 LVVLEWAYYARTARGQALVERRKEYVEAARGLNLSSWRIMVRHILPNCLPPLIVIGTLQV 246 Query: 282 SASILALTSLDFLGLGVPPSTPSLGELLAQGKNNL--DAWWIALSTFIVLTVTLLLLTNI 339 + +I +L FLGLGVP + PSLG L++ G + +WI+ I L V ++ + + Sbjct: 247 ARAITLEATLSFLGLGVPITEPSLGLLISNGYQYMLSGEYWISFYPGITLLVVIVAINLV 306 Query: 340 GDALRNALDVR 350 GD LR+ L+ R Sbjct: 307 GDRLRDILNPR 317 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 119 bits (299), Expect = 3e-28, Method: Compositional matrix adjust. Identities = 89/255 (34%), Positives = 140/255 (54%), Gaps = 10/255 (3%) Query: 105 AIYPP---NHYRFDTLNYFARQPNP---APPSSENWLGTDDRGRDVFARLLYGFRISILF 158 AI+ P H FD + AR P A S E+ LGTD GRD F+RL+YG R+S+ Sbjct: 51 AIFAPLLAPHDPFDQ-DVTARLIPPVWQAQGSWEHILGTDKLGRDYFSRLIYGARVSLTI 109 Query: 159 GLALTVTGVVLGLLAGAVQGYFAGRTDLFMQRLLEIWGSMPELYLLIIFSSIFEPSIGLL 218 GLA + ++G G + GYF GRTD + L+ +MP + + + +S+ S+ ++ Sbjct: 110 GLAAALISGLIGTTLGVLAGYFGGRTDAVISYLITTRLAMPVVLVALAMASLVGGSLKVV 169 Query: 219 LVLLSLFGWMGLSDYVRADFLRNRNLEYVQAGRALGLSNMQIIWRHVLPNSLTPVVTFLP 278 +VLL L W + R+ + R+ E++ A +A+G S I+ R +LPN + ++ + Sbjct: 170 IVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAKAIGASTPYILLREILPNIMGALIVVVT 229 Query: 279 FRMSASILALTSLDFLGLGVPPSTPSLGELLAQGKNNL-DAWWIALSTFIVLTVTLLLLT 337 M+ +IL +L FLGLGV P TPS G ++A+GK + W+ + + L + +L + Sbjct: 230 LEMAHAILLEATLSFLGLGVQPPTPSWGLMVAEGKTYMFFKPWVIVIPGVALALLVLAIN 289 Query: 338 NIGDALR--NALDVR 350 +GD LR NA D R Sbjct: 290 LVGDGLRDVNAPDGR 304 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 61.2 bits (147), Expect = 1e-10, Method: Compositional matrix adjust. Identities = 47/147 (31%), Positives = 71/147 (48%), Gaps = 2/147 (1%) Query: 135 LGTDDRGRDVFARLLYGFRISILFGLALTVTGVVLGLLAGAVQGYFAGRTDLFMQRLLEI 194 LG+D GRD+ +R+L+G R +I LA TV G + G D + R L+ Sbjct: 76 LGSDYLGRDMLSRILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVISRALDA 135 Query: 195 WGSMPELYLLIIFSSIFEPSIGLLLVLLSLFGWM-GLSDYVRADFLRNRNLEYVQAGRAL 253 S+P ++ + F S+ LLLVL + +M G R+ + + +EYVQA RA Sbjct: 136 LISIPSKMFALMMVATFGSSM-LLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARAR 194 Query: 254 GLSNMQIIWRHVLPNSLTPVVTFLPFR 280 G I+ +LPN + PV+ R Sbjct: 195 GEGVWYIMTVEMLPNMIRPVLADFGLR 221 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 0.325 0.142 0.435 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: 933,505 Number of extensions: 34297 Number of successful extensions: 130 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 126 Number of HSP's successfully gapped: 6 Length of query: 353 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 267 Effective length of database: 1,212,660 Effective search space: 323780220 Effective search space used: 323780220 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: 131 (55.1 bits)