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= 0001.0858.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... 568 e-163 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 194 9e-51 gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease ... 186 2e-48 gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease ... 161 5e-41 gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease ... 147 9e-37 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 568 bits (1463), Expect = e-163, Method: Compositional matrix adjust. Identities = 299/328 (91%), Positives = 313/328 (95%) Query: 1 MQHDANALGAAPVRATSQARWRALIHSPLALPLAGLVVVSLLMGLASDNFFTVSNWFNVL 60 M HDANAL AA + + ARWR+LIHSPLALPLAGLVVVSLLMGLASDNFFT+SNWFNVL Sbjct: 1 MPHDANALPAASLHTAASARWRSLIHSPLALPLAGLVVVSLLMGLASDNFFTLSNWFNVL 60 Query: 61 RQVSIVGILAVGMTFVILTGGIDLSVGAAMALAGTLSAGLIVNSGWPAWLALVAGIALAV 120 RQVSIVGILAVGM+FVILTGGIDLSVGAAMALAGT+SAGLIVNSG PA LAL+ G+ LA Sbjct: 61 RQVSIVGILAVGMSFVILTGGIDLSVGAAMALAGTISAGLIVNSGLPAPLALLCGVGLAT 120 Query: 121 LIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWVAWFGVGRIGMIP 180 IGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGW++WFGVGRIGM+P Sbjct: 121 CIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWISWFGVGRIGMVP 180 Query: 181 VPVILMLLVYALAWVLLQRTPFGRHVYAIGGNEMAARLSGVKTTRIKLGVYAISGFTSGL 240 VPVILML+VYALAW+LLQRT FGRHVYAIGGNEMAARLSGVKTTRIKL VYAISGFTSGL Sbjct: 181 VPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGL 240 Query: 241 AAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLN 300 AAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLN Sbjct: 241 AAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLN 300 Query: 301 LMGINPYLQDIVRGVIILLAIYIAREWR 328 LMGINPYLQDI+RGVIILLAIYIAREWR Sbjct: 301 LMGINPYLQDIIRGVIILLAIYIAREWR 328 >gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 194 bits (493), Expect = 9e-51, Method: Compositional matrix adjust. Identities = 125/290 (43%), Positives = 188/290 (64%), Gaps = 8/290 (2%) Query: 42 LMGLASDNFFTVSNWFNVLRQVSIVGILAVGMTFVILTGGIDLSVGAAMALAGTLSAGLI 101 L G + NF + N N+LRQV+I +LA GMTFVILT GIDLSVG+ +A++ L G+ Sbjct: 52 LSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVL--GMQ 109 Query: 102 VNSGW-PAWLALVAGIALAVLIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYP 160 V+ G P W A+ I +++G++NGA+VA + A +VTL TM RG + + G Sbjct: 110 VSLGAAPGW-AIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTT 168 Query: 161 I--SGLPGWVAWFGVGRIGMIPVPVILMLLVYALAWVLLQRTPFGRHVYAIGGNEMAARL 218 + + +P + W G G +P + + + V L+WV+L++T G H+YAIGGN AARL Sbjct: 169 VLNNDIPSF-EWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARL 227 Query: 219 SGVKTTRIKLGVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGG 278 +G++ + L VY+ISG SGLA + RL N G G+ELDAIAAVVLGGT++ GG Sbjct: 228 TGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGG 287 Query: 279 RGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIVRGVIILLAIYIAREWR 328 G + GT++GA+++G++NNGL ++G++ + Q + +G +I+LA+ I +WR Sbjct: 288 VGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAV-ILDKWR 336 >gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 347 Score = 186 bits (473), Expect = 2e-48, Method: Compositional matrix adjust. Identities = 132/340 (38%), Positives = 195/340 (57%), Gaps = 14/340 (4%) Query: 3 HDANALGAAPVRATSQARWRALIHSPLA----LPLAGLVVVSLLMGLASDNFFTVSNWFN 58 H A + S RA + +P A L A L+++ L AS NF V N + Sbjct: 6 HSATSASTTMANTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVS 65 Query: 59 VLRQVSIVGILAVGMTFVILTGGIDLSVGAAMALAGTLSAGLIVNSGWPAWLALVAGIAL 118 +L+ ++ G+LA+ T+VI+T GIDLSVG M ++ ++ N G P L + A I Sbjct: 66 ILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFF 125 Query: 119 AVLIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPI--SGLPGWVAWFGVGRI 176 L G ++G ++A ++P I TL M + +G+ L+ SG PI + G+ A I Sbjct: 126 GALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLI 185 Query: 177 G----MIPVP--VILMLLVYALAWVLLQRTPFGRHVYAIGGNEMAARLSGVKTTRIKLGV 230 G +P+P V+++ LV A ++L +T FGR+ +A+G NE A RLSGVK K+ V 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 LLGILNNGLNLMGINPYLQDIVRGVIILLAIY--IAREWR 328 ++ +L NGL +M + Q +V GVII+LA+Y I R R Sbjct: 306 IMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRRR 345 >gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 161 bits (408), Expect = 5e-41, Method: Compositional matrix adjust. Identities = 107/322 (33%), Positives = 182/322 (56%), Gaps = 18/322 (5%) Query: 15 ATSQARWRALIHSPLALPLAGLVVVSLLMGLASDNFFTVSNWFNVLRQVSIVGILAVGMT 74 A+ QA + A + L L +A L+ + ++ S+NF + + + + + + +++VGMT Sbjct: 10 ASRQAAYLAGFKNYLGL-MAALLAMCVMFAFLSENFLSAATFITLSNDIPPLVVMSVGMT 68 Query: 75 FVILTGGIDLSVGAAMALAGTLSAGLIVNSGWPAWLALVAGIALAVLIGLLNGALVAWGR 134 F+++ GGIDLSVG+ MALA ++ + +V GWP + A G+ +A L G L G + R Sbjct: 69 FILIIGGIDLSVGSVMALAASMLSMAMVRWGWPLYAAAPLGVVVAALCGTLTGMVSVHWR 128 Query: 135 MPAIIVTLATMGVARGVGLIYSGGYPISGLPGWVAWFGVGRIGMIPVPVIL--------M 186 +P+ IV+L + +ARG+ Y ++ + G + +I P++ Sbjct: 129 IPSFIVSLGVLEIARGLA------YQVTN--SRTEYIG-SAVDVISSPILFGMSPAFLSA 179 Query: 187 LLVYALAWVLLQRTPFGRHVYAIGGNEMAARLSGVKTTRIKLGVYAISGFTSGLAAIILT 246 + + +A ++L RT GR+ IG NE A RLSGV K+ +A+ G +G+AA+ Sbjct: 180 IAIVIIAQLVLTRTVLGRYWIGIGTNEEAVRLSGVNPNPSKILAFALMGALAGIAALFQV 239 Query: 247 GRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLNLMGINP 306 RL + PN GVG EL IAAVV+GGT++ GGRG +V T IG +++ +L GL +G++ Sbjct: 240 SRLEAADPNGGVGMELQVIAAVVIGGTSLMGGRGSIVSTFIGVLIISVLEAGLAQVGVSE 299 Query: 307 YLQDIVRGVIILLAIYIAREWR 328 ++ I+ G +I++A+ + R Sbjct: 300 PMKRIITGAVIVVAVILDTYRR 321 >gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 342 Score = 147 bits (372), Expect = 9e-37, Method: Compositional matrix adjust. Identities = 106/286 (37%), Positives = 162/286 (56%), Gaps = 2/286 (0%) Query: 44 GLASDNFFTVSNWFNVLRQVSIVGILAVGMTFVILTGGIDLSVGAAMALAGTLSAGLIVN 103 GL +FF N + S ++A+ M +I+ ID+SV A +ALA +++ GL Sbjct: 51 GLLLPHFFDPYNLADSTFNFSEKAMIALPMALLIICREIDISVSAIIALA-SVAMGLANQ 109 Query: 104 SGWPAWLALVAGIALAVLIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISG 163 +G P L+ IA GLLNGALV +P+I+VT+ +M + RG+ + G + Sbjct: 110 AGVPPLGLLLVAIATGTACGLLNGALVTRLGLPSIVVTIGSMSLFRGLASVVLGDQAFTQ 169 Query: 164 LPGWVAWFGVGRI-GMIPVPVILMLLVYALAWVLLQRTPFGRHVYAIGGNEMAARLSGVK 222 P + +G G ++P P ++ LL + VLL T +GR +YAIG N +AAR SGV Sbjct: 170 YPEVLGDWGQGYFFDVLPRPFVVWLLAAVVFAVLLHVTRWGRRLYAIGNNPVAARFSGVA 229 Query: 223 TTRIKLGVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLV 282 R +L ++ ++G +GLAA LTGR+ S +PN +G+EL+ I V+LGG +IAGG G + Sbjct: 230 VDRYRLALFVLTGAMAGLAAFFLTGRIGSTRPNIAMGWELEIITVVILGGVSIAGGTGSI 289 Query: 283 VGTLIGAVLLGILNNGLNLMGINPYLQDIVRGVIILLAIYIAREWR 328 G ++ +++G+L GL L I + IV 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 0.326 0.143 0.434 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: 945,708 Number of extensions: 39965 Number of successful extensions: 358 Number of sequences better than 1.0e-08: 24 Number of HSP's gapped: 343 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 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 131 (55.1 bits)