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= 0001.0053.p (333 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 ... 647 0.0 gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galacto... 198 5e-52 gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease ... 191 8e-50 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 190 1e-49 gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease ... 132 5e-32 >gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 347 Score = 647 bits (1669), Expect = 0.0, Method: Compositional matrix adjust. Identities = 327/333 (98%), Positives = 331/333 (99%) Query: 1 MANTASPSGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNG 60 MANTAS GLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNG Sbjct: 15 MANTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNG 74 Query: 61 VLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWVSG 120 VLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGW+SG Sbjct: 75 VLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISG 134 Query: 121 MVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPI 180 MVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPI Sbjct: 135 MVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPI 194 Query: 181 PNAVLILFIVAIGASVILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICG 240 PNAVLILF+VAIGAS+ILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICG Sbjct: 195 PNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICG 254 Query: 241 IAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGL 300 IAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGL Sbjct: 255 IAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGL 314 Query: 301 RIMSVAQEWQTVVTGIIIILAVYLDILRRRRRA 333 RIMSVAQEWQTVVTG+IIILAVYLDILRRRRRA Sbjct: 315 RIMSVAQEWQTVVTGVIIILAVYLDILRRRRRA 347 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 198 bits (503), Expect = 5e-52, Method: Compositional matrix adjust. Identities = 124/329 (37%), Positives = 197/329 (59%), Gaps = 14/329 (4%) Query: 3 NTASPSGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVL 62 +TA+ + R+ + +P A L A L+++ L AS NF + N ++L+ ++ G+L Sbjct: 14 HTAASARWRSLIHSPLA----LPLAGLVVVSLLMGLASDNFFTLSNWFNVLRQVSIVGIL 69 Query: 63 AIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWVSGMV 122 A+ ++VI+T GIDLSVG M ++ ++ N G+P PL + + G ++G + Sbjct: 70 AVGMSFVILTGGIDLSVGAAMALAGTISAGLIVNSGLPAPLALLCGVGLATCIGLLNGAL 129 Query: 123 IAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPN 182 +A ++P I TL M + +G+ L+ SG PI + G+ + IG +P+P Sbjct: 130 VAWGRMPAIIVTLATMGVARGVGLIYSGGYPI--SGLPGWISWFGVGRIG----MVPVP- 182 Query: 183 AVLILFIVAIGASVILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIA 242 V+++ IV A ++L +T FGR+ +A+G NE A RLSGVK K+AVY SG G+A Sbjct: 183 -VILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGLA 241 Query: 243 GLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRI 302 +I+ RL S QP G G+ELDAIAAVV+GGT+++GG G ++GT+IGA ++ +L NGL + Sbjct: 242 AIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLNL 301 Query: 303 MSVAQEWQTVVTGIIIILAVYLDILRRRR 331 M + Q ++ G+II+LA+Y I R R Sbjct: 302 MGINPYLQDIIRGVIILLAIY--IAREWR 328 >gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 191 bits (484), Expect = 8e-50, Method: Compositional matrix adjust. Identities = 122/332 (36%), Positives = 189/332 (56%), Gaps = 17/332 (5%) Query: 3 NTASPSGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVL 62 ++++P+ R + + L A+LL M + F+F S NF+ +++ V+ Sbjct: 4 SSSTPAASRQAAYLAGFKNYLGLMAALLAMCVMFAFLSENFLSAATFITLSNDIPPLVVM 63 Query: 63 AIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPL----PLGIAAAIFFGALSGWV 118 ++ T+++I GIDLSVG++M A M + + WG PL PLG+ A AL G + Sbjct: 64 SVGMTFILIIGGIDLSVGSVMALAASMLSMAMVRWGWPLYAAAPLGVVVA----ALCGTL 119 Query: 119 SGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSL 178 +GMV ++P FI +LG++ + +GL+ ++ +R Y I+ L G + P+ Sbjct: 120 TGMVSVHWRIPSFIVSLGVLEIARGLAYQVTNSRTEYIGSA--VDVISSPILFG-MSPAF 176 Query: 179 PIPNAVLILFIVAIGASVILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAI 238 A++I+ A ++L +TV GRY +G+NEEA+RLSGV + K+ + GA+ Sbjct: 177 LSAIAIVII------AQLVLTRTVLGRYWIGIGTNEEAVRLSGVNPNPSKILAFALMGAL 230 Query: 239 CGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVN 298 GIA L SRL +A P G G EL IAAVVIGGTSL GG G+I+ T IG I+SVL Sbjct: 231 AGIAALFQVSRLEAADPNGGVGMELQVIAAVVIGGTSLMGGRGSIVSTFIGVLIISVLEA 290 Query: 299 GLRIMSVAQEWQTVVTGIIIILAVYLDILRRR 330 GL + V++ + ++TG +I++AV LD RRR Sbjct: 291 GLAQVGVSEPMKRIITGAVIVVAVILDTYRRR 322 >gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 190 bits (483), Expect = 1e-49, Method: Compositional matrix adjust. Identities = 121/300 (40%), Positives = 176/300 (58%), Gaps = 21/300 (7%) Query: 40 SPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGM 99 + NF +N ++IL+ A+N VLA T+VI+T+GIDLSVG+++ AV+ GM Sbjct: 57 TSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVL--------GM 108 Query: 100 PLPLGIAAA------IFFGALSGWVSGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRP 153 + LG A IF G + G V+G ++A L + F+ TLG M +G + +++ Sbjct: 109 QVSLGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTT 168 Query: 154 IYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFIVAIGASVILNKTVFGRYTFALGSN 213 + ND F I GD L +P + + V + + VIL KTV G + +A+G N Sbjct: 169 VLNNDIPSFEWIGN----GDF---LHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGN 221 Query: 214 EEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGG 273 +A RL+G++V + VY+ SG G+AG + ASRL A G GYELDAIAAVV+GG Sbjct: 222 LQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGG 281 Query: 274 TSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGIIIILAVYLDILRRRRRA 333 TSL GG G+I GT++GA I+ V+ NGL I+ ++ WQ V G +I+LAV LD R++ A Sbjct: 282 TSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQKDAA 341 >gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 352 Score = 132 bits (331), Expect = 5e-32, Method: Compositional matrix adjust. Identities = 90/300 (30%), Positives = 165/300 (55%), Gaps = 19/300 (6%) Query: 40 SPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNW-G 98 +P F+ ++ ++L +A+ +LA+A VI+T GIDLSV + + +M+ ++ ++ Sbjct: 46 APVFLSAQSMDNLLTDSAITIMLALAQMLVILTRGIDLSVASNLALSGMMSALLAMHFPA 105 Query: 99 MPLPLGIAAAIFFGALSGWVSGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFND 158 +P+ + I A+ G + G ++G +I L++PP + TLG M + +G+ V+SG Sbjct: 106 LPVGVFILMAVLIGLMLGLLNGWLIGYLELPPIVVTLGSMSVYRGMVFVLSGG------- 158 Query: 159 TEGFSAIAQDSLIGDLIPSLPIPNAVLILFIVAIGASVIL------NKTVFGRYTFALGS 212 + ++ ++ D I + P+ + +V +GA ++ T FGR +A+G+ Sbjct: 159 ----AWVSSRNMPADFI-AFPLARLGGLTHLVWLGALAVVAIWFLARHTRFGRDLYAIGN 213 Query: 213 NEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIG 272 + A G+ + Y SGA+ G+AG + +R A + G+EL IAA VIG Sbjct: 214 DPAAAAYVGIASRGRLLWTYGLSGAMAGLAGYLWVARYAVAYTEIAYGFELTVIAACVIG 273 Query: 273 GTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGIIIILAVYLDILRRRRR 332 G S++GG G + G ++GA +SV+ N L IM ++ WQ+ +TG++I+ AV L+ ++ R Sbjct: 274 GVSIAGGVGQVSGAVLGALFLSVINNALPIMRISPFWQSALTGLVILCAVVLNARGKQGR 333 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 0.407 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: 792,845 Number of extensions: 27009 Number of successful extensions: 209 Number of sequences better than 1.0e-08: 20 Number of HSP's gapped: 203 Number of HSP's successfully gapped: 22 Length of query: 333 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 247 Effective length of database: 1,212,660 Effective search space: 299527020 Effective search space used: 299527020 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)