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= 0001.0828.p (359 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310368|ref|YP_003774460.1| sugar ABC transporter permease ... 662 0.0 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 134 1e-32 gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galacto... 124 1e-29 gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease ... 96 6e-21 gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease ... 95 1e-20 >gi|300310368|ref|YP_003774460.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 359 Score = 662 bits (1709), Expect = 0.0, Method: Compositional matrix adjust. Identities = 339/359 (94%), Positives = 350/359 (97%) Query: 1 MSASMDSKLIPESSTGSPAPMLAALLRHPLVRPLAALALLLLIDFLLVPGFFKLEIKDGH 60 MSASMDSKLIP+++ + +PMLA LLRHPLVRPL ALA+LLLIDFLLVPGFFKLEIKDGH Sbjct: 1 MSASMDSKLIPDTAASAGSPMLAGLLRHPLVRPLGALAVLLLIDFLLVPGFFKLEIKDGH 60 Query: 61 LYGALIDIINRAAPLMLAALGMTLVIATRGVDISVGAVVAISGAVAAILIGGKMVVVNGV 120 LYGALIDIINRAAPLMLAALGMTLVIATRGVDISVGAVVAISGAVAAILIGGKMVVV+GV Sbjct: 61 LYGALIDIINRAAPLMLAALGMTLVIATRGVDISVGAVVAISGAVAAILIGGKMVVVDGV 120 Query: 121 PEYVSNVPMLWALCAAMSAALLCGAWNGLLVAGLGLQPIIATLILMVAGRGLAQLFTDGQ 180 +YVSNVPM+WALCAAM AALLCGAWNGLLVAGLGLQPIIATLILMVAGRGLAQL TDGQ Sbjct: 121 SQYVSNVPMVWALCAAMGAALLCGAWNGLLVAGLGLQPIIATLILMVAGRGLAQLLTDGQ 180 Query: 181 IVTVYYKPFFFLGGGYLFGLPFSLYIAGAMFLLLALLMKKTALGLFIESVGINPVASRLA 240 IVTVYYKPFFFLGGGYLFGLPFSLYIA AMF+LLALLMKKTALGLFIESVGINPVASRLA Sbjct: 181 IVTVYYKPFFFLGGGYLFGLPFSLYIAAAMFVLLALLMKKTALGLFIESVGINPVASRLA 240 Query: 241 GIRTAALIFFVYMFCSACAGLAGLMIASNIKSADANNAGLLLELDAILAVTLGGTSLAGG 300 GIRTAALIFFVYMFCSACAGLAGLMIASNIKSADANNAGLLLELDAILAVTLGGTSLAGG Sbjct: 241 GIRTAALIFFVYMFCSACAGLAGLMIASNIKSADANNAGLLLELDAILAVTLGGTSLAGG 300 Query: 301 KFSLVGSVIGALIIQTLTYTIYSLGVPPEVNMVVKSIVVFLVCLSQSPEFRRMLRMSKS 359 KFSLVGSVIGALIIQTLTYTIYSLGVPPEVNMVVKSIVVFLVCLSQSP+FRRMLRMSKS Sbjct: 301 KFSLVGSVIGALIIQTLTYTIYSLGVPPEVNMVVKSIVVFLVCLSQSPQFRRMLRMSKS 359 >gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 134 bits (337), Expect = 1e-32, Method: Compositional matrix adjust. Identities = 106/280 (37%), Positives = 156/280 (55%), Gaps = 16/280 (5%) Query: 66 IDIINRAAPLMLAALGMTLVIATRGVDISVGAVVAISGAVAAILIGGKMVVVNGVPEYVS 125 ++I+ + A ++ A GMT VI T G+D+SVG+V+A+S A+L G V + P + Sbjct: 67 MNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVS----AVL--GMQVSLGAAPGWA- 119 Query: 126 NVPMLWALCAAMSAALLCGAWNGLLVAGLGLQPIIATLILMVAGRGLAQLFTDGQIVTVY 185 +PM + + L+ G NG +VA L + + TL M A RG A L DG V Sbjct: 120 -IPMF------IFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNN 172 Query: 186 YKPFF-FLGGGYLFGLPFSLYIAGAMFLLLALLMKKTALGLFIESVGINPVASRLAGIRT 244 P F ++G G +P+ +++A A+ LL ++++KT LG+ I ++G N A+RL GIR Sbjct: 173 DIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRV 232 Query: 245 AALIFFVYMFCSACAGLAGLMIASNIKSADANNAGLLLELDAILAVTLGGTSLAGGKFSL 304 ++ FVY +GLAG M AS + A+ N G ELDAI AV LGGTSL GG S+ Sbjct: 233 GLVLLFVYSISGLFSGLAGAMSASRLYGANG-NWGSGYELDAIAAVVLGGTSLMGGVGSI 291 Query: 305 VGSVIGALIIQTLTYTIYSLGVPPEVNMVVKSIVVFLVCL 344 G+V+GALII + + LG+ V K V+ L + Sbjct: 292 WGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVI 331 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 124 bits (310), Expect = 1e-29, Method: Compositional matrix adjust. Identities = 104/347 (29%), Positives = 185/347 (53%), Gaps = 23/347 (6%) Query: 6 DSKLIPESSTGSPAP-MLAALLRHPLVRPLAALALLLLIDFLLVPGFFKLEIKDGHLYGA 64 D+ +P +S + A +L+ PL PLA L ++ L+ L FF L Sbjct: 4 DANALPAASLHTAASARWRSLIHSPLALPLAGLVVVSLLMGLASDNFFTLS--------N 55 Query: 65 LIDIINRAAPLMLAALGMTLVIATRGVDISVGAVVAISGAVAAILIGGKMVVVNGVPEYV 124 +++ + + + + A+GM+ VI T G+D+SVGA +A++G ++A LI VN Sbjct: 56 WFNVLRQVSIVGILAVGMSFVILTGGIDLSVGAAMALAGTISAGLI------VN------ 103 Query: 125 SNVPMLWALCAAMSAALLCGAWNGLLVAGLGLQPIIATLILMVAGRGLAQLFTDGQIVTV 184 S +P AL + A G NG LVA + II TL M RG+ +++ G ++ Sbjct: 104 SGLPAPLALLCGVGLATCIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISG 163 Query: 185 YYKPFFFLGGGYLFGLPFSLYIAGAMFLLLALLMKKTALGLFIESVGINPVASRLAGIRT 244 + G G + +P + + ++ L LL+++TA G + ++G N +A+RL+G++T Sbjct: 164 LPGWISWFGVGRIGMVPVPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKT 223 Query: 245 AALIFFVYMFCSACAGLAGLMIASNIKSADANNAGLLLELDAILAVTLGGTSLAGGKFSL 304 + VY +GLA +++ + S N AG+ ELDAI AV LGGT++AGG+ + Sbjct: 224 TRIKLAVYAISGFTSGLAAIILTGRLMSGQPN-AGVGFELDAIAAVVLGGTAIAGGRGLV 282 Query: 305 VGSVIGALIIQTLTYTIYSLGVPPEVNMVVKSIVVFLVCLSQSPEFR 351 VG++IGA+++ L + +G+ P + +++ +++ L + + E+R Sbjct: 283 VGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILL-AIYIAREWR 328 >gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 342 Score = 95.5 bits (236), Expect = 6e-21, Method: Compositional matrix adjust. Identities = 97/306 (31%), Positives = 145/306 (47%), Gaps = 27/306 (8%) Query: 25 LLRHPLVRPLAALALLLLIDFLLVPGFFKLEIKDGHLYGALIDIINRAAPLMLAALGMTL 84 LLRH L L+ ++ LL+P FF Y N + M+A L M L Sbjct: 31 LLRHWEALLAILLVLVCAVNGLLLPHFFDP-------YNLADSTFNFSEKAMIA-LPMAL 82 Query: 85 VIATRGVDISVGAVVAISGAVAAILIGGKMVVVNGVPEYVSNVPMLWALCAAMSAALLCG 144 +I R +DISV A++A++ M + N + VP L L A++ CG Sbjct: 83 LIICREIDISVSAIIALASV--------AMGLANQ-----AGVPPLGLLLVAIATGTACG 129 Query: 145 AWNGLLVAGLGLQPIIATLILMVAGRGLAQLFTDGQIVTVYYKPFFFLGGGYLFGL---P 201 NG LV LGL I+ T+ M RGLA + Q T Y + G GY F + P Sbjct: 130 LLNGALVTRLGLPSIVVTIGSMSLFRGLASVVLGDQAFTQYPEVLGDWGQGYFFDVLPRP 189 Query: 202 FSLYIAGAMFLLLALLMKKTALGLFIESVGINPVASRLAGIRTAALIFFVYMFCSACAGL 261 F +++ A ++ A+L+ T G + ++G NPVA+R +G+ +++ A AGL Sbjct: 190 FVVWLLAA--VVFAVLLHVTRWGRRLYAIGNNPVAARFSGVAVDRYRLALFVLTGAMAGL 247 Query: 262 AGLMIASNIKSADANNAGLLLELDAILAVTLGGTSLAGGKFSLVGSVIGALIIQTLTYTI 321 A + I S N A + EL+ I V LGG S+AGG S+ G ++ L++ LTY + Sbjct: 248 AAFFLTGRIGSTRPNIA-MGWELEIITVVILGGVSIAGGTGSIGGVMLSVLVMGMLTYGL 306 Query: 322 YSLGVP 327 +P Sbjct: 307 ALANIP 312 >gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 94.7 bits (234), Expect = 1e-20, Method: Compositional matrix adjust. Identities = 88/295 (29%), Positives = 147/295 (49%), Gaps = 30/295 (10%) Query: 65 LIDIINRAAPLMLAALGMTLVIATRGVDISVGAVVAISGAVAAILIGGKMVVVNGVPEYV 124 I + N PL++ ++GMT ++ G+D+SVG+V+A++ ++ ++ + V G P Y Sbjct: 50 FITLSNDIPPLVVMSVGMTFILIIGGIDLSVGSVMALAASMLSMAM-----VRWGWPLYA 104 Query: 125 SNVPMLWALCAAMSAALLCGAWNGLLVAGLGLQPIIATLILMVAGRGLAQLFTD------ 178 + P+ + A LCG G++ + I +L ++ RGLA T+ Sbjct: 105 A-APL------GVVVAALCGTLTGMVSVHWRIPSFIVSLGVLEIARGLAYQVTNSRTEYI 157 Query: 179 GQIVTVYYKPFFFLGGGYLFGLPFSLYIAGAMFLLLALLMKKTALGLFIESVGINPVASR 238 G V V P LFG+ + A A+ ++ L++ +T LG + +G N A R Sbjct: 158 GSAVDVISSPI-------LFGMSPAFLSAIAIVIIAQLVLTRTVLGRYWIGIGTNEEAVR 210 Query: 239 LAGIRTAALIFFVYMFCSACAGLAGLMIASNIKSADANNAGLLLELDAILAVTLGGTSLA 298 L+G+ + A AG+A L S +++AD N G+ +EL I AV +GGTSL Sbjct: 211 LSGVNPNPSKILAFALMGALAGIAALFQVSRLEAADPNG-GVGMELQVIAAVVIGGTSLM 269 Query: 299 GGKFSLVGSVIGALIIQTLTYTIYSLGV-PPEVNMVVKSIVVFLVCLSQSPEFRR 352 GG+ S+V + IG LII L + +GV P ++ +++V V L +RR Sbjct: 270 GGRGSIVSTFIGVLIISVLEAGLAQVGVSEPMKRIITGAVIVVAVILD---TYRR 321 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 0.142 0.410 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: 740,794 Number of extensions: 23341 Number of successful extensions: 220 Number of sequences better than 1.0e-08: 17 Number of HSP's gapped: 193 Number of HSP's successfully gapped: 18 Length of query: 359 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 273 Effective length of database: 1,212,660 Effective search space: 331056180 Effective search space used: 331056180 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)