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= 0001.0070.p (328 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galacto... 572 e-164 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 197 1e-51 gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease ... 186 3e-48 gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease ... 154 1e-38 gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease ... 150 1e-37 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 572 bits (1473), Expect = e-164, Method: Compositional matrix adjust. Identities = 300/328 (91%), Positives = 314/328 (95%) Query: 1 MQHEANTLGSAPVRASSQARWRALIHSPLALPLVGLVVVSLLMGLASDNFFTVSNWLNVL 60 M H+AN L +A + ++ ARWR+LIHSPLALPL GLVVVSLLMGLASDNFFT+SNW NVL Sbjct: 1 MPHDANALPAASLHTAASARWRSLIHSPLALPLAGLVVVSLLMGLASDNFFTLSNWFNVL 60 Query: 61 RQVSIVGILAVGMTFVILTGGIDLSVGAAMALAGTLSAGLIVNSGLPAPVALLAGIALAV 120 RQVSIVGILAVGM+FVILTGGIDLSVGAAMALAGT+SAGLIVNSGLPAP+ALL G+ LA Sbjct: 61 RQVSIVGILAVGMSFVILTGGIDLSVGAAMALAGTISAGLIVNSGLPAPLALLCGVGLAT 120 Query: 121 GIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWISWFGVGRIGMIP 180 IGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWISWFGVGRIGM+P Sbjct: 121 CIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWISWFGVGRIGMVP 180 Query: 181 VPVILMLVVYALAWVLLQRTPFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGL 240 VPVILML+VYALAW+LLQRT FGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGL Sbjct: 181 VPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGL 240 Query: 241 AAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLN 300 AAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLN Sbjct: 241 AAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLN 300 Query: 301 LMGINPYLQDIIRGVIILLAIYIAREWR 328 LMGINPYLQDIIRGVIILLAIYIAREWR Sbjct: 301 LMGINPYLQDIIRGVIILLAIYIAREWR 328 >gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 197 bits (500), Expect = 1e-51, Method: Compositional matrix adjust. Identities = 122/291 (41%), Positives = 184/291 (63%), Gaps = 10/291 (3%) Query: 42 LMGLASDNFFTVSNWLNVLRQVSIVGILAVGMTFVILTGGIDLSVGAAMALAGTL--SAG 99 L G + NF + N +N+LRQV+I +LA GMTFVILT GIDLSVG+ +A++ L Sbjct: 52 LSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVS 111 Query: 100 LIVNSGLPAPVALLAGIALAVGIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGY 159 L G P+ + +G+ + G++NGA+VA + A +VTL TM RG + + G Sbjct: 112 LGAAPGWAIPMFIFSGLVM----GMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGT 167 Query: 160 PI--SGLPGWISWFGVGRIGMIPVPVILMLVVYALAWVLLQRTPFGRHVYAIGGNEMAAR 217 + + +P W G G +P + + + V L+WV+L++T G H+YAIGGN AAR Sbjct: 168 TVLNNDIPS-FEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAAR 226 Query: 218 LSGVKTTRIKLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAG 277 L+G++ + L VY+ISG SGLA + RL N G G+ELDAIAAVVLGGT++ G Sbjct: 227 LTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMG 286 Query: 278 GRGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILLAIYIAREWR 328 G G + GT++GA+++G++NNGL ++G++ + Q + +G +I+LA+ I +WR Sbjct: 287 GVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAV-ILDKWR 336 >gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 347 Score = 186 bits (471), Expect = 3e-48, Method: Compositional matrix adjust. Identities = 125/333 (37%), Positives = 197/333 (59%), Gaps = 12/333 (3%) Query: 3 HEANTLGSAPVRASSQARWRALIHSPLA----LPLVGLVVVSLLMGLASDNFFTVSNWLN 58 H A + + +S RA + +P A L L+++ L AS NF V N ++ Sbjct: 6 HSATSASTTMANTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVS 65 Query: 59 VLRQVSIVGILAVGMTFVILTGGIDLSVGAAMALAGTLSAGLIVNSGLPAPVALLAGIAL 118 +L+ ++ G+LA+ T+VI+T GIDLSVG M ++ ++ N G+P P+ + A I Sbjct: 66 ILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFF 125 Query: 119 AVGIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPI--SGLPGWISWFGVGRI 176 G ++G ++A ++P I TL M + +G+ L+ SG PI + G+ + I Sbjct: 126 GALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLI 185 Query: 177 G----MIPVP--VILMLVVYALAWVLLQRTPFGRHVYAIGGNEMAARLSGVKTTRIKLAV 230 G +P+P V+++ +V A ++L +T FGR+ +A+G NE A RLSGVK K+AV Sbjct: 186 GDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAV 245 Query: 231 YAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAV 290 Y SG G+A +I+ RL S QP G G+ELDAIAAVV+GGT+++GG G ++GT+IGA Sbjct: 246 YTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAF 305 Query: 291 LLGILNNGLNLMGINPYLQDIIRGVIILLAIYI 323 ++ +L NGL +M + Q ++ GVII+LA+Y+ Sbjct: 306 IMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYL 338 >gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 154 bits (388), Expect = 1e-38, Method: Compositional matrix adjust. Identities = 109/331 (32%), Positives = 182/331 (54%), Gaps = 19/331 (5%) Query: 6 NTLGSAPVRASSQARWRALIHSPLALPLVGLVVVSLLMGLASDNFFTVSNWLNVLRQVSI 65 T S P AS QA + A + L L + L+ + ++ S+NF + + ++ + + Sbjct: 2 QTSSSTPA-ASRQAAYLAGFKNYLGL-MAALLAMCVMFAFLSENFLSAATFITLSNDIPP 59 Query: 66 VGILAVGMTFVILTGGIDLSVGAAMALAGTLSAGLIVNSGLPAPVALLAGIALAVGIGLL 125 + +++VGMTF+++ GGIDLSVG+ MALA ++ + +V G P A G+ +A G L Sbjct: 60 LVVMSVGMTFILIIGGIDLSVGSVMALAASMLSMAMVRWGWPLYAAAPLGVVVAALCGTL 119 Query: 126 NGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWISWFGVGRIGMIPVPVIL 185 G + R+P+ IV+L + +ARG+ Y ++ + G + +I P++ Sbjct: 120 TGMVSVHWRIPSFIVSLGVLEIARGLA------YQVTN--SRTEYIG-SAVDVISSPILF 170 Query: 186 --------MLVVYALAWVLLQRTPFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFT 237 + + +A ++L RT GR+ IG NE A RLSGV K+ +A+ G Sbjct: 171 GMSPAFLSAIAIVIIAQLVLTRTVLGRYWIGIGTNEEAVRLSGVNPNPSKILAFALMGAL 230 Query: 238 SGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNN 297 +G+AA+ RL + PN GVG EL IAAVV+GGT++ GGRG +V T IG +++ +L Sbjct: 231 AGIAALFQVSRLEAADPNGGVGMELQVIAAVVIGGTSLMGGRGSIVSTFIGVLIISVLEA 290 Query: 298 GLNLMGINPYLQDIIRGVIILLAIYIAREWR 328 GL +G++ ++ II G +I++A+ + R Sbjct: 291 GLAQVGVSEPMKRIITGAVIVVAVILDTYRR 321 >gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 342 Score = 150 bits (380), Expect = 1e-37, Method: Compositional matrix adjust. Identities = 106/286 (37%), Positives = 164/286 (57%), Gaps = 2/286 (0%) Query: 44 GLASDNFFTVSNWLNVLRQVSIVGILAVGMTFVILTGGIDLSVGAAMALAGTLSAGLIVN 103 GL +FF N + S ++A+ M +I+ ID+SV A +ALA +++ GL Sbjct: 51 GLLLPHFFDPYNLADSTFNFSEKAMIALPMALLIICREIDISVSAIIALA-SVAMGLANQ 109 Query: 104 SGLPAPVALLAGIALAVGIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISG 163 +G+P LL IA GLLNGALV +P+I+VT+ +M + RG+ + G + Sbjct: 110 AGVPPLGLLLVAIATGTACGLLNGALVTRLGLPSIVVTIGSMSLFRGLASVVLGDQAFTQ 169 Query: 164 LPGWISWFGVGRI-GMIPVPVILMLVVYALAWVLLQRTPFGRHVYAIGGNEMAARLSGVK 222 P + +G G ++P P ++ L+ + VLL T +GR +YAIG N +AAR SGV Sbjct: 170 YPEVLGDWGQGYFFDVLPRPFVVWLLAAVVFAVLLHVTRWGRRLYAIGNNPVAARFSGVA 229 Query: 223 TTRIKLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLV 282 R +LA++ ++G +GLAA LTGR+ S +PN +G+EL+ I V+LGG +IAGG G + Sbjct: 230 VDRYRLALFVLTGAMAGLAAFFLTGRIGSTRPNIAMGWELEIITVVILGGVSIAGGTGSI 289 Query: 283 VGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILLAIYIAREWR 328 G ++ +++G+L GL L I + I+ G ++L I I R R Sbjct: 290 GGVMLSVLVMGMLTYGLALANIPGIIMTIVVGALLLATIAIPRLLR 335 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 0.143 0.425 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: 907,598 Number of extensions: 36903 Number of successful extensions: 340 Number of sequences better than 1.0e-08: 26 Number of HSP's gapped: 328 Number of HSP's successfully gapped: 27 Length of query: 328 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 242 Effective length of database: 1,212,660 Effective search space: 293463720 Effective search space used: 293463720 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: 131 (55.1 bits)