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= 0001.0013.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 ... 634 0.0 gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galacto... 100 3e-22 gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease ... 90 2e-19 gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease ... 89 5e-19 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 87 2e-18 >gi|300310352|ref|YP_003774444.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 337 Score = 634 bits (1636), Expect = 0.0, Method: Compositional matrix adjust. Identities = 324/335 (96%), Positives = 330/335 (98%) Query: 1 MKLKISDPQLLFLLVINLAILLVATVFSRGDFLDLYNFQSMASQLPELGLLAIGVALAMI 60 MKLKISDPQLLFLLVIN+AILLVATVFS GDFLD+YNFQSMASQLPELGLLAIGVALAMI Sbjct: 3 MKLKISDPQLLFLLVINVAILLVATVFSHGDFLDIYNFQSMASQLPELGLLAIGVALAMI 62 Query: 61 SGNGGIDLSGIGLANLAGVVAAATMPLLVAAPDAAPWTYTLSFIAVALVTGLVGGALNGW 120 SGNGGIDLSGIGLANLAGVVAAA MPLLVAAPDAAPWTYTL FIAVALVTGL+GGALNGW Sbjct: 63 SGNGGIDLSGIGLANLAGVVAAAAMPLLVAAPDAAPWTYTLGFIAVALVTGLLGGALNGW 122 Query: 121 LISRGNLTPILCTLGTQMIFTGLAVVLTNGSSLRISVVDPISAIGNESVLGVPIPFIIFV 180 LISRGNLTPILCTLGTQMIFTGLAVVLTNGSSLRISVVDPISAIGNESVLGVPIPFIIFV Sbjct: 123 LISRGNLTPILCTLGTQMIFTGLAVVLTNGSSLRISVVDPISAIGNESVLGVPIPFIIFV 182 Query: 181 ALLLGVGWLMRYSLFGIKLYLLGTNARAARYAGISQNRLRFATYTLSGVLASVAGVIIAA 240 ALLL VGWLMRYSLFGIKLYLLGTNARAARYAGISQNRLRFATY +SGVLASVAG+IIAA Sbjct: 183 ALLLLVGWLMRYSLFGIKLYLLGTNARAARYAGISQNRLRFATYVISGVLASVAGIIIAA 242 Query: 241 RTASVKADYGNSYLLIAILIAVMAGIRPQGGYGRMVCLFFSALALQLLSSTFNLLEISNF 300 RTASVKADYGNSYLLIAILIAVMAG+RPQGGYGRMVCLFFSALALQLLSSTFNLLEISNF Sbjct: 243 RTASVKADYGNSYLLIAILIAVMAGVRPQGGYGRMVCLFFSALALQLLSSTFNLLEISNF 302 Query: 301 FRDCAWGLLLLCFLASARVSWRDFFPNSKAQLRKS 335 FRDCAWGLLLLCFLASARVSWRDFFPNSKAQLRKS Sbjct: 303 FRDCAWGLLLLCFLASARVSWRDFFPNSKAQLRKS 337 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 99.8 bits (247), Expect = 3e-22, Method: Compositional matrix adjust. Identities = 87/293 (29%), Positives = 154/293 (52%), Gaps = 14/293 (4%) Query: 31 DFLDLYNFQSMASQLPELGLLAIGVALAMISGNGGIDLSGIGLANLAGVVAAATMPLLVA 90 +F L N+ ++ Q+ +G+LA+G++ +++G GIDLS LAG ++A L+V Sbjct: 49 NFFTLSNWFNVLRQVSIVGILAVGMSFVILTG--GIDLSVGAAMALAGTISAG---LIVN 103 Query: 91 APDAAPWTYTLSFIAVALVTGLVGGALNGWLISRGNLTPILCTLGTQMIFTGLAVVLTNG 150 + AP L + +A GL+ GAL W G + I+ TL T + G+ ++ + G Sbjct: 104 SGLPAPLAL-LCGVGLATCIGLLNGALVAW----GRMPAIIVTLATMGVARGVGLIYSGG 158 Query: 151 SSLRISVVDPISAIGNESVLGVPIPFIIFVALLLGVGWLM-RYSLFGIKLYLLGTNARAA 209 + + IS G + VP+P I+ + ++ + WL+ + + FG +Y +G N AA Sbjct: 159 YPIS-GLPGWISWFGVGRIGMVPVPVILML-IVYALAWLLLQRTAFGRHVYAIGGNEMAA 216 Query: 210 RYAGISQNRLRFATYTLSGVLASVAGVIIAARTASVKADYGNSYLLIAILIAVMAGIRPQ 269 R +G+ R++ A Y +SG + +A +I+ R S + + G + L AI V+ G Sbjct: 217 RLSGVKTTRIKLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIA 276 Query: 270 GGYGRMVCLFFSALALQLLSSTFNLLEISNFFRDCAWGLLLLCFLASARVSWR 322 GG G +V A+ L +L++ NL+ I+ + +D G+++L + AR WR Sbjct: 277 GGRGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILLAIYIAR-EWR 328 >gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 352 Score = 90.1 bits (222), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 68/218 (31%), Positives = 114/218 (52%), Gaps = 15/218 (6%) Query: 103 FIAVALVTGLVGGALNGWLISRGNLTPILCTLGTQMIFTGLAVVLTNGS--SLRISVVD- 159 FI +A++ GL+ G LNGWLI L PI+ TLG+ ++ G+ VL+ G+ S R D Sbjct: 111 FILMAVLIGLMLGLLNGWLIGYLELPPIVVTLGSMSVYRGMVFVLSGGAWVSSRNMPADF 170 Query: 160 ---PISAIGNESVLGVPIPFIIFVALL--LGVGWLMRYSLFGIKLYLLGTNARAARYAGI 214 P++ +G + ++++ L + + +L R++ FG LY +G + AA Y GI Sbjct: 171 IAFPLARLGG-------LTHLVWLGALAVVAIWFLARHTRFGRDLYAIGNDPAAAAYVGI 223 Query: 215 SQNRLRFATYTLSGVLASVAGVIIAARTASVKADYGNSYLLIAILIAVMAGIRPQGGYGR 274 + TY LSG +A +AG + AR A + + L I V+ G+ GG G+ Sbjct: 224 ASRGRLLWTYGLSGAMAGLAGYLWVARYAVAYTEIAYGFELTVIAACVIGGVSIAGGVGQ 283 Query: 275 MVCLFFSALALQLLSSTFNLLEISNFFRDCAWGLLLLC 312 + AL L ++++ ++ IS F++ GL++LC Sbjct: 284 VSGAVLGALFLSVINNALPIMRISPFWQSALTGLVILC 321 >gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 342 Score = 89.0 bits (219), Expect = 5e-19, Method: Compositional matrix adjust. Identities = 78/290 (26%), Positives = 137/290 (47%), Gaps = 13/290 (4%) Query: 31 DFLDLYNFQSMASQLPELGLLAIGVALAMISGNGGIDLSGIGLANLAGVVAAATMPLLVA 90 F D YN E ++A+ +AL +I ID+S ++ ++A A++ + +A Sbjct: 56 HFFDPYNLADSTFNFSEKAMIALPMALLIICRE--IDIS------VSAIIALASVAMGLA 107 Query: 91 APDAAPWTYTLSFIAVALVTGLVGGALNGWLISRGNLTPILCTLGTQMIFTGLAVVLTNG 150 P L + VA+ TG G LNG L++R L I+ T+G+ +F GLA V+ G Sbjct: 108 NQAGVP---PLGLLLVAIATGTACGLLNGALVTRLGLPSIVVTIGSMSLFRGLASVVL-G 163 Query: 151 SSLRISVVDPISAIGNESVLGV-PIPFIIFVALLLGVGWLMRYSLFGIKLYLLGTNARAA 209 + + G V P PF++++ + L+ + +G +LY +G N AA Sbjct: 164 DQAFTQYPEVLGDWGQGYFFDVLPRPFVVWLLAAVVFAVLLHVTRWGRRLYAIGNNPVAA 223 Query: 210 RYAGISQNRLRFATYTLSGVLASVAGVIIAARTASVKADYGNSYLLIAILIAVMAGIRPQ 269 R++G++ +R R A + L+G +A +A + R S + + + L I + ++ G+ Sbjct: 224 RFSGVAVDRYRLALFVLTGAMAGLAAFFLTGRIGSTRPNIAMGWELEIITVVILGGVSIA 283 Query: 270 GGYGRMVCLFFSALALQLLSSTFNLLEISNFFRDCAWGLLLLCFLASARV 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 = 87.0 bits (214), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 87/305 (28%), Positives = 154/305 (50%), Gaps = 22/305 (7%) Query: 25 TVFSRGDFLDLYNFQSMASQLPELGLLAIGVALA----MISGNGGIDLSGIGLANLAGVV 80 T++ GD NF S + + L +AI + LA + GIDLS + V+ Sbjct: 49 TLYLSGD--GTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLS------VGSVL 100 Query: 81 AAATMPLLVAAPDAAP-WTYTLSFIAVALVTGLVGGALNGWLISRGNLTPILCTLGTQMI 139 A + + + + AAP W I + + +GLV G +NG +++ N+ + TLGT Sbjct: 101 AVSAVLGMQVSLGAAPGWA-----IPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTA 155 Query: 140 FTGLAVVLTNGSSLRISVVDPISAIGNESVLGVPIPFIIFVALLLGVGW-LMRYSLFGIK 198 F G A +L +G+++ + + IGN L VP + VA++L + W ++R ++ G+ Sbjct: 156 FRGAAYLLADGTTVLNNDIPSFEWIGNGDFLHVPWLIWVAVAVVL-LSWVILRKTVLGMH 214 Query: 199 LYLLGTNARAARYAGISQNRLRFATYTLSGVLASVAGVIIAARTASVKADYGNSYLLIAI 258 +Y +G N +AAR GI + Y++SG+ + +AG + A+R ++G+ Y L AI Sbjct: 215 IYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAI 274 Query: 259 LIAVMAGIRPQGGYGRMVCLFFSALALQLLSSTFNLLEISNFFRDCAWGLLLLCFLASAR 318 V+ G GG G + AL + ++++ +L +S+F++ A G +++ LA Sbjct: 275 AAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIV--LAVIL 332 Query: 319 VSWRD 323 WR Sbjct: 333 DKWRQ 337 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 0.327 0.141 0.416 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: 917,953 Number of extensions: 36020 Number of successful extensions: 294 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 281 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)