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= 0001.0812.p (335 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310352|ref|YP_003774444.1| sugar ABC transporter permease ... 640 0.0 gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galacto... 103 3e-23 gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease ... 93 4e-20 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 92 9e-20 gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease ... 91 9e-20 >gi|300310352|ref|YP_003774444.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 337 Score = 640 bits (1651), Expect = 0.0, Method: Compositional matrix adjust. Identities = 324/335 (96%), Positives = 333/335 (99%) Query: 1 MKLKISDPQLLFLLLINLAILLVATVFSHGEFLDIYNFQSMASQLPELGLLAIGVALAMI 60 MKLKISDPQLLFLL+IN+AILLVATVFSHG+FLDIYNFQSMASQLPELGLLAIGVALAMI Sbjct: 3 MKLKISDPQLLFLLVINVAILLVATVFSHGDFLDIYNFQSMASQLPELGLLAIGVALAMI 62 Query: 61 SGNGGIDLSGIGLANLAGVVAAATMPLLVAAPDAAPWTYTLGFVAVALVTGLLGGALNGW 120 SGNGGIDLSGIGLANLAGVVAAA MPLLVAAPDAAPWTYTLGF+AVALVTGLLGGALNGW Sbjct: 63 SGNGGIDLSGIGLANLAGVVAAAAMPLLVAAPDAAPWTYTLGFIAVALVTGLLGGALNGW 122 Query: 121 LIARGNLTPILCTLGTQMIFTGLAVVLTNGSSLRINVVDPISAIGNESVLGVPIPFIIFV 180 LI+RGNLTPILCTLGTQMIFTGLAVVLTNGSSLRI+VVDPISAIGNESVLGVPIPFIIFV Sbjct: 123 LISRGNLTPILCTLGTQMIFTGLAVVLTNGSSLRISVVDPISAIGNESVLGVPIPFIIFV 182 Query: 181 ALLLLVGWLMRYSLFGIKLYLLGTNARAARYAGISQNRLRFATYTLSGVLASVAGIIIAA 240 ALLLLVGWLMRYSLFGIKLYLLGTNARAARYAGISQNRLRFATY +SGVLASVAGIIIAA Sbjct: 183 ALLLLVGWLMRYSLFGIKLYLLGTNARAARYAGISQNRLRFATYVISGVLASVAGIIIAA 242 Query: 241 RTASVKADYGNSYLLIAILIAVMAGIRPQGGYGRMVCLFFSALALQLLSSTFNLLEISNF 300 RTASVKADYGNSYLLIAILIAVMAG+RPQGGYGRMVCLFFSALALQLLSSTFNLLEISNF Sbjct: 243 RTASVKADYGNSYLLIAILIAVMAGVRPQGGYGRMVCLFFSALALQLLSSTFNLLEISNF 302 Query: 301 FRDCAWGLLLLCFLASARISWRDFFPNSKAQLRKS 335 FRDCAWGLLLLCFLASAR+SWRDFFPNSKAQLRKS Sbjct: 303 FRDCAWGLLLLCFLASARVSWRDFFPNSKAQLRKS 337 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 103 bits (256), Expect = 3e-23, Method: Compositional matrix adjust. Identities = 89/292 (30%), Positives = 151/292 (51%), Gaps = 12/292 (4%) Query: 31 EFLDIYNFQSMASQLPELGLLAIGVALAMISGNGGIDLSGIGLANLAGVVAAATMPLLVA 90 F + N+ ++ Q+ +G+LA+G++ +++G GIDLS LAG ++A L+V Sbjct: 49 NFFTLSNWFNVLRQVSIVGILAVGMSFVILTG--GIDLSVGAAMALAGTISAG---LIVN 103 Query: 91 APDAAPWTYTLGFVAVALVTGLLGGALNGWLIARGNLTPILCTLGTQMIFTGLAVVLTNG 150 + AP G V +A GLL GAL W G + I+ TL T + G+ ++ + G Sbjct: 104 SGLPAPLALLCG-VGLATCIGLLNGALVAW----GRMPAIIVTLATMGVARGVGLIYSGG 158 Query: 151 SSLRINVVDPISAIGNESVLGVPIPFIIFVALLLLVGWLMRYSLFGIKLYLLGTNARAAR 210 + + IS G + VP+P I+ + + L L++ + FG +Y +G N AAR Sbjct: 159 YPIS-GLPGWISWFGVGRIGMVPVPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAAR 217 Query: 211 YAGISQNRLRFATYTLSGVLASVAGIIIAARTASVKADYGNSYLLIAILIAVMAGIRPQG 270 +G+ R++ A Y +SG + +A II+ R S + + G + L AI V+ G G Sbjct: 218 LSGVKTTRIKLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAG 277 Query: 271 GYGRMVCLFFSALALQLLSSTFNLLEISNFFRDCAWGLLLLCFLASARISWR 322 G G +V A+ L +L++ NL+ I+ + +D G+++L + AR WR Sbjct: 278 GRGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILLAIYIAR-EWR 328 >gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 342 Score = 92.8 bits (229), Expect = 4e-20, Method: Compositional matrix adjust. Identities = 79/290 (27%), Positives = 138/290 (47%), Gaps = 13/290 (4%) Query: 31 EFLDIYNFQSMASQLPELGLLAIGVALAMISGNGGIDLSGIGLANLAGVVAAATMPLLVA 90 F D YN E ++A+ +AL +I ID+S ++ ++A A++ + +A Sbjct: 56 HFFDPYNLADSTFNFSEKAMIALPMALLIICRE--IDIS------VSAIIALASVAMGLA 107 Query: 91 APDAAPWTYTLGFVAVALVTGLLGGALNGWLIARGNLTPILCTLGTQMIFTGLAVVLTNG 150 P LG + VA+ TG G LNG L+ R L I+ T+G+ +F GLA V+ G Sbjct: 108 NQAGVP---PLGLLLVAIATGTACGLLNGALVTRLGLPSIVVTIGSMSLFRGLASVVL-G 163 Query: 151 SSLRINVVDPISAIGNESVLGV-PIPFIIFVALLLLVGWLMRYSLFGIKLYLLGTNARAA 209 + + G V P PF++++ ++ L+ + +G +LY +G N AA Sbjct: 164 DQAFTQYPEVLGDWGQGYFFDVLPRPFVVWLLAAVVFAVLLHVTRWGRRLYAIGNNPVAA 223 Query: 210 RYAGISQNRLRFATYTLSGVLASVAGIIIAARTASVKADYGNSYLLIAILIAVMAGIRPQ 269 R++G++ +R R A + L+G +A +A + R S + + + L I + ++ G+ Sbjct: 224 RFSGVAVDRYRLALFVLTGAMAGLAAFFLTGRIGSTRPNIAMGWELEIITVVILGGVSIA 283 Query: 270 GGYGRMVCLFFSALALQLLSSTFNLLEISNFFRDCAWGLLLLCFLASARI 319 GG G + + S L + +L+ L I G LLL +A R+ Sbjct: 284 GGTGSIGGVMLSVLVMGMLTYGLALANIPGIIMTIVVGALLLATIAIPRL 333 >gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 91.7 bits (226), Expect = 9e-20, Method: Compositional matrix adjust. Identities = 65/214 (30%), Positives = 115/214 (53%), Gaps = 2/214 (0%) Query: 110 TGLLGGALNGWLIARGNLTPILCTLGTQMIFTGLAVVLTNGSSLRINVVDPISAIGNESV 169 +GL+ G +NG ++A N+ + TLGT F G A +L +G+++ N + IGN Sbjct: 126 SGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGNGDF 185 Query: 170 LGVPIPFIIFVALLLLVGWLMRYSLFGIKLYLLGTNARAARYAGISQNRLRFATYTLSGV 229 L VP + VA++LL ++R ++ G+ +Y +G N +AAR GI + Y++SG+ Sbjct: 186 LHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGL 245 Query: 230 LASVAGIIIAARTASVKADYGNSYLLIAILIAVMAGIRPQGGYGRMVCLFFSALALQLLS 289 + +AG + A+R ++G+ Y L AI V+ G GG G + AL + +++ Sbjct: 246 FSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMN 305 Query: 290 STFNLLEISNFFRDCAWGLLLLCFLASARISWRD 323 + +L +S+F++ A G +++ LA WR Sbjct: 306 NGLTILGLSSFWQYVAKGAVIV--LAVILDKWRQ 337 >gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 352 Score = 91.3 bits (225), Expect = 9e-20, Method: Compositional matrix adjust. Identities = 70/217 (32%), Positives = 113/217 (52%), Gaps = 13/217 (5%) Query: 103 FVAVALVTGLLGGALNGWLIARGNLTPILCTLGTQMIFTGLAVVLTNGS--SLRINVVD- 159 F+ +A++ GL+ G LNGWLI L PI+ TLG+ ++ G+ VL+ G+ S R D Sbjct: 111 FILMAVLIGLMLGLLNGWLIGYLELPPIVVTLGSMSVYRGMVFVLSGGAWVSSRNMPADF 170 Query: 160 ---PISAIGNESVLGVPIPFIIFVALLLLVGW-LMRYSLFGIKLYLLGTNARAARYAGIS 215 P++ +G + L + AL ++ W L R++ FG LY +G + AA Y GI+ Sbjct: 171 IAFPLARLGGLTHL------VWLGALAVVAIWFLARHTRFGRDLYAIGNDPAAAAYVGIA 224 Query: 216 QNRLRFATYTLSGVLASVAGIIIAARTASVKADYGNSYLLIAILIAVMAGIRPQGGYGRM 275 TY LSG +A +AG + AR A + + L I V+ G+ GG G++ Sbjct: 225 SRGRLLWTYGLSGAMAGLAGYLWVARYAVAYTEIAYGFELTVIAACVIGGVSIAGGVGQV 284 Query: 276 VCLFFSALALQLLSSTFNLLEISNFFRDCAWGLLLLC 312 AL L ++++ ++ IS F++ GL++LC Sbjct: 285 SGAVLGALFLSVINNALPIMRISPFWQSALTGLVILC 321 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 0.328 0.142 0.420 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: 841,693 Number of extensions: 30504 Number of successful extensions: 238 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 230 Number of HSP's successfully gapped: 14 Length of query: 335 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 249 Effective length of database: 1,212,660 Effective search space: 301952340 Effective search space used: 301952340 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: 131 (55.1 bits)