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= 0002.0211.p (250 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease ... 418 e-118 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 162 3e-41 gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease ... 157 1e-39 gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galacto... 147 1e-36 gi|300313778|ref|YP_003777870.1| D-xylose ABC transporter permea... 124 9e-30 >gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 347 Score = 418 bits (1074), Expect = e-118, Method: Compositional matrix adjust. Identities = 222/250 (88%), Positives = 235/250 (94%) Query: 1 MTFCSVMAGVFLTYWGLPIYFGIFAAIFFGALCGWTSGMLIAKLKVPPFIATLGMMMLLK 60 MTFC+VMAGV LT WG+P+ GI AAIFFGAL GW SGM+IAKLKVPPFIATLGMMMLLK Sbjct: 97 MTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLK 156 Query: 61 GLSLVISGTKPIYFNDTPSFPQISQESLIGDLIPALPIPNAVLILFLVAIAAGVILNKTV 120 GLSLVISGT+PIYFNDT F I+Q+SLIGDLIP+LPIPNAVLILFLVAI A +ILNKTV Sbjct: 157 GLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTV 216 Query: 121 FGRYTFALGSNEEALRLSGVKVDFWKVTVYTVSGAICGIAGLLIASRLNSAQPALGQGYE 180 FGRYTFALGSNEEALRLSGVKVDFWKV VYT SGAICGIAGL+IASRLNSAQPALGQGYE Sbjct: 217 FGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYE 276 Query: 181 LDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLINGLRIMSVAQEWQTVVTGVIIILAV 240 LDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVL+NGLRIMSVAQEWQTVVTGVIIILAV Sbjct: 277 LDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAV 336 Query: 241 YMDILRRRRQ 250 Y+DILRRRR+ Sbjct: 337 YLDILRRRRR 346 >gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 162 bits (409), Expect = 3e-41, Method: Compositional matrix adjust. Identities = 94/234 (40%), Positives = 140/234 (59%), Gaps = 13/234 (5%) Query: 15 WGLPIYFGIFAAIFFGALCGWTSGMLIAKLKVPPFIATLGMMMLLKGLSLVISGTKPIYF 74 W +P++ IF G + G +G ++A L + F+ TLG M +G + +++ + Sbjct: 118 WAIPMF------IFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLN 171 Query: 75 NDTPSFPQISQESLIGDLIPALPIPNAVLILFLVAIAAGVILNKTVFGRYTFALGSNEEA 134 ND PSF I GD L +P + + V + + VIL KTV G + +A+G N +A Sbjct: 172 NDIPSFEWIGN----GDF---LHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQA 224 Query: 135 LRLSGVKVDFWKVTVYTVSGAICGIAGLLIASRLNSAQPALGQGYELDAIAAVVIGGTSL 194 RL+G++V + VY++SG G+AG + ASRL A G GYELDAIAAVV+GGTSL Sbjct: 225 ARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSL 284 Query: 195 SGGTGTILGTIIGAFIMSVLINGLRIMSVAQEWQTVVTGVIIILAVYMDILRRR 248 GG G+I GT++GA I+ V+ NGL I+ ++ WQ V G +I+LAV +D R++ Sbjct: 285 MGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQK 338 >gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 157 bits (396), Expect = 1e-39, Method: Compositional matrix adjust. Identities = 99/254 (38%), Positives = 145/254 (57%), Gaps = 17/254 (6%) Query: 1 MTFCSVMAGVFLTYWGLPIYFGIFAAIFFGALCGWTSGMLIAKLKVPPFIATLGMMMLLK 60 M + M + + WG P+Y + ALCG +GM+ ++P FI +LG++ + + Sbjct: 84 MALAASMLSMAMVRWGWPLYAAAPLGVVVAALCGTLTGMVSVHWRIPSFIVSLGVLEIAR 143 Query: 61 GLSLVISGTKPIYFNDTPSFPQISQESLIGDLIPALPIPNAVLILFLVAIA----AGVIL 116 GL+ ++ ++ Y + IS L G + PA FL AIA A ++L Sbjct: 144 GLAYQVTNSRTEYIGS--AVDVISSPILFG-MSPA----------FLSAIAIVIIAQLVL 190 Query: 117 NKTVFGRYTFALGSNEEALRLSGVKVDFWKVTVYTVSGAICGIAGLLIASRLNSAQPALG 176 +TV GRY +G+NEEA+RLSGV + K+ + + GA+ GIA L SRL +A P G Sbjct: 191 TRTVLGRYWIGIGTNEEAVRLSGVNPNPSKILAFALMGALAGIAALFQVSRLEAADPNGG 250 Query: 177 QGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLINGLRIMSVAQEWQTVVTGVII 236 G EL IAAVVIGGTSL GG G+I+ T IG I+SVL GL + V++ + ++TG +I Sbjct: 251 VGMELQVIAAVVIGGTSLMGGRGSIVSTFIGVLIISVLEAGLAQVGVSEPMKRIITGAVI 310 Query: 237 ILAVYMDILRRRRQ 250 ++AV +D RRR Q Sbjct: 311 VVAVILDTYRRRGQ 324 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 147 bits (370), Expect = 1e-36, Method: Compositional matrix adjust. Identities = 89/227 (39%), Positives = 137/227 (60%), Gaps = 8/227 (3%) Query: 16 GLPIYFGIFAAIFFGALCGWTSGMLIAKLKVPPFIATLGMMMLLKGLSLVISGTKPIYFN 75 GLP + + G +G L+A ++P I TL M + +G+ L+ SG PI + Sbjct: 105 GLPAPLALLCGVGLATCIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPI--S 162 Query: 76 DTPSFPQISQESLIGDLIPALPIPNAVLILFLVAIAAGVILNKTVFGRYTFALGSNEEAL 135 P + IG +P+P V+++ +V A ++L +T FGR+ +A+G NE A Sbjct: 163 GLPGWISWFGVGRIG----MVPVP--VILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAA 216 Query: 136 RLSGVKVDFWKVTVYTVSGAICGIAGLLIASRLNSAQPALGQGYELDAIAAVVIGGTSLS 195 RLSGVK K+ VY +SG G+A +++ RL S QP G G+ELDAIAAVV+GGT+++ Sbjct: 217 RLSGVKTTRIKLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIA 276 Query: 196 GGTGTILGTIIGAFIMSVLINGLRIMSVAQEWQTVVTGVIIILAVYM 242 GG G ++GT+IGA ++ +L NGL +M + Q ++ GVII+LA+Y+ Sbjct: 277 GGRGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILLAIYI 323 >gi|300313778|ref|YP_003777870.1| D-xylose ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 385 Score = 124 bits (310), Expect = 9e-30, Method: Compositional matrix adjust. Identities = 63/130 (48%), Positives = 90/130 (69%) Query: 118 KTVFGRYTFALGSNEEALRLSGVKVDFWKVTVYTVSGAICGIAGLLIASRLNSAQPALGQ 177 +TVFGR +++GSN EA RLSGV V K+ V+ + G +C +AGL+ +RL + P+ G Sbjct: 253 QTVFGRRIYSVGSNMEATRLSGVNVQAVKLWVFGIMGVMCALAGLVNTARLAAGSPSAGN 312 Query: 178 GYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLINGLRIMSVAQEWQTVVTGVIII 237 ELDAIAA IGGTS+ GG+GTI G +IGA +M+ L NG+ ++ V WQ +V G I++ Sbjct: 313 MGELDAIAACFIGGTSMRGGSGTIYGALIGALVMASLDNGMSMLDVGTYWQMIVKGSILV 372 Query: 238 LAVYMDILRR 247 LAV++D+ R Sbjct: 373 LAVWVDVSTR 382 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 0.143 0.428 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: 562,273 Number of extensions: 16599 Number of successful extensions: 148 Number of sequences better than 1.0e-08: 25 Number of HSP's gapped: 150 Number of HSP's successfully gapped: 25 Length of query: 250 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 167 Effective length of database: 1,226,865 Effective search space: 204886455 Effective search space used: 204886455 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: 129 (54.3 bits)