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= 0034.0040.p (309 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 494 e-141 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 192 3e-50 gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 178 5e-46 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 114 1e-26 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 111 7e-26 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 494 bits (1271), Expect = e-141, Method: Compositional matrix adjust. Identities = 256/293 (87%), Positives = 279/293 (95%) Query: 17 FVQATLKPVPLWRRKLNRMLGHRGLVLGAAILAVIVLAALFAPLLAPHDPFEQNVSQRLI 76 +Q L P+P WRRKL R+LGHRGL++GAA+LAVIVLAA+FAPLLAPHDPF+Q+V+ RLI Sbjct: 13 LLQGALPPLPAWRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPHDPFDQDVTARLI 72 Query: 77 PPIWNALGSWDHVLGTDKLGRDYLSRLIYGARVSLIIGCAAALISGVIGTTLGVLAGYFG 136 PP+W A GSW+H+LGTDKLGRDY SRLIYGARVSL IG AAALISG+IGTTLGVLAGYFG Sbjct: 73 PPVWQAQGSWEHILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFG 132 Query: 137 GRVDALISYVITTRLSMPVVLVALAMASLVGGSLKVVIILLGLLLWDRFAVVTRSATQQL 196 GR DA+ISY+ITTRL+MPVVLVALAMASLVGGSLKVVI+LLGLLLWDRFAVVTRSATQQL Sbjct: 133 GRTDAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQL 192 Query: 197 RDAEFIAAAKAIGASTPYILVREILPNIMSALIVVITLEMAHAILLEATLSFLGLGVQPP 256 RDAEFIAAAKAIGASTPYIL+REILPNIM ALIVV+TLEMAHAILLEATLSFLGLGVQPP Sbjct: 193 RDAEFIAAAKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPP 252 Query: 257 TPSWGLMVSEGKSYMFFKPWVIVIPGVALAILVLAINLVGDGLRDVNAPDGRN 309 TPSWGLMV+EGK+YMFFKPWVIVIPGVALA+LVLAINLVGDGLRDVNAPDGRN Sbjct: 253 TPSWGLMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAPDGRN 305 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 192 bits (488), Expect = 3e-50, Method: Compositional matrix adjust. Identities = 119/292 (40%), Positives = 177/292 (60%), Gaps = 6/292 (2%) Query: 19 QATLKPVPLWRRKLNRMLGHRGLVLGAAILAVIVLAALFAPLLAPHDPFE----QNVSQR 74 QA + P WRR + + R +LG I+ ++++ A+ AP + P +P++ + R Sbjct: 26 QAPRRESP-WRRVMRHFVASRSAMLGLVIVLLLIVGAIAAPWITPQNPYDLMQLDVLDAR 84 Query: 75 LIPPIWNALGSWDHVLGTDKLGRDYLSRLIYGARVSLIIGCAAALISGVIGTTLGVLAGY 134 L P N G++ + LGTD GRD +S ++YG R+S+ IG +ALI+GVIGT +G+LA Y Sbjct: 85 LHPGTLNGAGTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSALIAGVIGTLIGLLAAY 144 Query: 135 FGGRVDALISYVITTRLSMPVVLVALAMASLVGGSLKVVIILLGLLLWDRFAVVTRSATQ 194 GG++D L+ LS P +LVA+ + + VG + V+ L +L W +A R Sbjct: 145 AGGKLDTLLMRFADLVLSFPSILVAMLILAYVGKGIFNVMATLVVLEWAYYARTARGQAL 204 Query: 195 QLRDAEFIAAAKAIGASTPYILVREILPNIMSALIVVITLEMAHAILLEATLSFLGLGVQ 254 R E++ AA+ + S+ I+VR ILPN + LIV+ TL++A AI LEATLSFLGLGV Sbjct: 205 VERRKEYVEAARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVARAITLEATLSFLGLGVP 264 Query: 255 PPTPSWGLMVSEGKSYMFF-KPWVIVIPGVALAILVLAINLVGDGLRDVNAP 305 PS GL++S G YM + W+ PG+ L ++++AINLVGD LRD+ P Sbjct: 265 ITEPSLGLLISNGYQYMLSGEYWISFYPGITLLVVIVAINLVGDRLRDILNP 316 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 178 bits (452), Expect = 5e-46, Method: Compositional matrix adjust. Identities = 102/281 (36%), Positives = 154/281 (54%), Gaps = 11/281 (3%) Query: 28 WRRKLNRMLGHRGLVLGAAILAVIVLAALFAPLLAPHDP---FEQNVSQRLIPPIWNALG 84 WR + V + +V A+ AP + P DP F+ + PP Sbjct: 33 WREFWRKFKKQHLAVYAGVFILFLVAVAILAPWIVPFDPENFFDYDALNS--PP------ 84 Query: 85 SWDHVLGTDKLGRDYLSRLIYGARVSLIIGCAAALISGVIGTTLGVLAGYFGGRVDALIS 144 +W H G D LGRD SR++ G R+SL G + I VIGT G+LAGY+ G D + Sbjct: 85 TWVHWFGVDSLGRDIFSRIVMGTRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWDRITM 144 Query: 145 YVITTRLSMPVVLVALAMASLVGGSLKVVIILLGLLLWDRFAVVTRSATQQLRDAEFIAA 204 + + P +L+A+ + +++GG + VII + + FA + R T QL++ +I A Sbjct: 145 RICDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEA 204 Query: 205 AKAIGASTPYILVREILPNIMSALIVVITLEMAHAILLEATLSFLGLGVQPPTPSWGLMV 264 ++IGAS I+ + I P +SA++V T+ + +I+ A LSFLGLG Q PTP WGLM+ Sbjct: 205 TRSIGASDMTIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLML 264 Query: 265 SEGKSYMFFKPWVIVIPGVALAILVLAINLVGDGLRDVNAP 305 +E ++ M P V ++P +A+ + VLA NL+GDGLRD P Sbjct: 265 NEARADMVTSPHVALVPSIAIFLTVLAFNLLGDGLRDALDP 305 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 114 bits (284), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 68/183 (37%), Positives = 107/183 (58%) Query: 87 DHVLGTDKLGRDYLSRLIYGARVSLIIGCAAALISGVIGTTLGVLAGYFGGRVDALISYV 146 ++ LGTD GRD +RL+YG RVS++ G A I V+G G + GYF GR D + Sbjct: 127 ENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDLFTQRL 186 Query: 147 ITTRLSMPVVLVALAMASLVGGSLKVVIILLGLLLWDRFAVVTRSATQQLRDAEFIAAAK 206 + SMP + + + +S+ SL ++++LL L W + R+ + R+ E+I AA+ Sbjct: 187 LEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLEYIQAAR 246 Query: 207 AIGASTPYILVREILPNIMSALIVVITLEMAHAILLEATLSFLGLGVQPPTPSWGLMVSE 266 A+G I+ R +LPN M+ ++ + M+ AIL +L FLGLGV P TPS G ++++ Sbjct: 247 AMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLGELLAQ 306 Query: 267 GKS 269 GK+ Sbjct: 307 GKN 309 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 111 bits (278), Expect = 7e-26, Method: Compositional matrix adjust. Identities = 80/262 (30%), Positives = 144/262 (54%), Gaps = 6/262 (2%) Query: 43 LGAAILAVIVLAALFAPLLAPHDPFEQNVSQRLIPPIWNALGSWDHVLGTDKLGRDYLSR 102 +G AI+ +L A+ P ++P+D + + +++ + S +LG+D LGRD LSR Sbjct: 35 IGMAIVGFWILMAILGPSISPYD-----ATAIVDTDVFSGM-SHKFLLGSDYLGRDMLSR 88 Query: 103 LIYGARVSLIIGCAAALISGVIGTTLGVLAGYFGGRVDALISYVITTRLSMPVVLVALAM 162 +++G R ++ + AA +++ GT + + A + GG DA+IS + +S+P + AL M Sbjct: 89 ILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVISRALDALISIPSKMFALMM 148 Query: 163 ASLVGGSLKVVIILLGLLLWDRFAVVTRSATQQLRDAEFIAAAKAIGASTPYILVREILP 222 + G S+ ++++ + + RS ++ E++ AA+A G YI+ E+LP Sbjct: 149 VATFGSSMLLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGVWYIMTVEMLP 208 Query: 223 NIMSALIVVITLEMAHAILLEATLSFLGLGVQPPTPSWGLMVSEGKSYMFFKPWVIVIPG 282 N++ ++ L + +LL + LSFL LGVQPP WG +V E S + +++P Sbjct: 209 NMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSLVRENISGLGEGALAVIMPA 268 Query: 283 VALAILVLAINLVGDGLRDVNA 304 +A+A L + +NL+ D LR A Sbjct: 269 LAIASLTIGVNLLIDNLRSKRA 290 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 0.140 0.418 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: 669,239 Number of extensions: 20947 Number of successful extensions: 139 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 136 Number of HSP's successfully gapped: 6 Length of query: 309 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 224 Effective length of database: 1,217,395 Effective search space: 272696480 Effective search space used: 272696480 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: 130 (54.7 bits)