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= 0003.0083.p (364 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 ... 581 e-167 gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galacto... 133 2e-32 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 130 2e-31 gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease ... 97 2e-21 gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease ... 97 3e-21 >gi|300310368|ref|YP_003774460.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 359 Score = 581 bits (1497), Expect = e-167, Method: Compositional matrix adjust. Identities = 297/361 (82%), Positives = 331/361 (91%), Gaps = 3/361 (0%) Query: 1 MSASMNSNLVSNRNPSSGAAVNRLRRAFFHPLSRPLGALAVLLLIDFFMIPGFFRIEMKD 60 MSASM+S L+ + S+G+ + L HPL RPLGALAVLLLIDF ++PGFF++E+KD Sbjct: 1 MSASMDSKLIPDTAASAGSPM--LAGLLRHPLVRPLGALAVLLLIDFLLVPGFFKLEIKD 58 Query: 61 GHLYGSVIDIVNRAAPLMLAALGMTLVIATRGIDISVGAVVAISGTIAAMLIGGTMVVNN 120 GHLYG++IDI+NRAAPLMLAALGMTLVIATRG+DISVGAVVAISG +AA+LIGG MVV + Sbjct: 59 GHLYGALIDIINRAAPLMLAALGMTLVIATRGVDISVGAVVAISGAVAAILIGGKMVVVD 118 Query: 121 GVPEYVSNIPMGWALAAALGVALLCGAWNGLLVATLGLQPIIATLILMVAGRGLAQLLTD 180 GV +YVSN+PM WAL AA+G ALLCGAWNGLLVA LGLQPIIATLILMVAGRGLAQLLTD Sbjct: 119 GVSQYVSNVPMVWALCAAMGAALLCGAWNGLLVAGLGLQPIIATLILMVAGRGLAQLLTD 178 Query: 181 GQIITVYYKPFFYLGSGYLWGLPFSLFIVAGMFVVLALLMRKTALGLFIQSVGINPVASR 240 GQI+TVYYKPFF+LG GYL+GLPFSL+I A MFV+LALLM+KTALGLFI+SVGINPVASR Sbjct: 179 GQIVTVYYKPFFFLGGGYLFGLPFSLYIAAAMFVLLALLMKKTALGLFIESVGINPVASR 238 Query: 241 LAGIRTAALIFFVYIFCSLCAGLAGLMISANIKSADANNAGLLLELDAILAVTLGGTSLA 300 LAGIRTAALIFFVY+FCS CAGLAGLMI++NIKSADANNAGLLLELDAILAVTLGGTSLA Sbjct: 239 LAGIRTAALIFFVYMFCSACAGLAGLMIASNIKSADANNAGLLLELDAILAVTLGGTSLA 298 Query: 301 GGKFSLVGSVIGALIIQALTYTIYSLGVPPEVNMVVKSVVVFLVCLSQSPEFRR-LRLFK 359 GGKFSLVGSVIGALIIQ LTYTIYSLGVPPEVNMVVKS+VVFLVCLSQSP+FRR LR+ K Sbjct: 299 GGKFSLVGSVIGALIIQTLTYTIYSLGVPPEVNMVVKSIVVFLVCLSQSPQFRRMLRMSK 358 Query: 360 S 360 S Sbjct: 359 S 359 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 133 bits (335), Expect = 2e-32, Method: Compositional matrix adjust. Identities = 110/341 (32%), Positives = 187/341 (54%), Gaps = 34/341 (9%) Query: 19 AAVNRLRRAFFHPLSRPLGALAVLLLI------DFFMIPGFFRIEMKDGHLYGSVIDIVN 72 AA R R PL+ PL L V+ L+ +FF + +F + + S++ I+ Sbjct: 16 AASARWRSLIHSPLALPLAGLVVVSLLMGLASDNFFTLSNWFNVLRQV-----SIVGIL- 69 Query: 73 RAAPLMLAALGMTLVIATRGIDISVGAVVAISGTIAAMLIGGTMVVNNGVPEYVSNIPMG 132 A+GM+ VI T GID+SVGA +A++GTI+A LI VN+G+P P+ Sbjct: 70 --------AVGMSFVILTGGIDLSVGAAMALAGTISAGLI-----VNSGLPA-----PL- 110 Query: 133 WALAAALGVALLCGAWNGLLVATLGLQPIIATLILMVAGRGLAQLLTDGQIITVYYKPFF 192 AL +G+A G NG LVA + II TL M RG+ + + G I+ Sbjct: 111 -ALLCGVGLATCIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWIS 169 Query: 193 YLGSGYLWGLPFSLFIVAGMFVVLALLMRKTALGLFIQSVGINPVASRLAGIRTAALIFF 252 + G G + +P + ++ ++ + LL+++TA G + ++G N +A+RL+G++T + Sbjct: 170 WFGVGRIGMVPVPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKLA 229 Query: 253 VYIFCSLCAGLAGLMISANIKSADANNAGLLLELDAILAVTLGGTSLAGGKFSLVGSVIG 312 VY +GLA ++++ + S N AG+ ELDAI AV LGGT++AGG+ +VG++IG Sbjct: 230 VYAISGFTSGLAAIILTGRLMSGQPN-AGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIG 288 Query: 313 ALIIQALTYTIYSLGVPPEVNMVVKSVVVFLVCLSQSPEFR 353 A+++ L + +G+ P + +++ V++ L + + E+R Sbjct: 289 AVLLGILNNGLNLMGINPYLQDIIRGVIILL-AIYIAREWR 328 >gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 130 bits (327), Expect = 2e-31, Method: Compositional matrix adjust. Identities = 102/282 (36%), Positives = 154/282 (54%), Gaps = 16/282 (5%) Query: 66 SVIDIVNRAAPLMLAALGMTLVIATRGIDISVGAVVAISGTIAAMLIGGTMVVNNGVPEY 125 + ++I+ + A ++ A GMT VI T GID+SVG+V+A+S + G V P Sbjct: 65 NTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVL------GMQVSLGAAP-- 116 Query: 126 VSNIPMGWALAAALGVALLCGAWNGLLVATLGLQPIIATLILMVAGRGLAQLLTDGQIIT 185 GWA+ + L+ G NG +VA L + + TL M A RG A LL DG + Sbjct: 117 ------GWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVL 170 Query: 186 VYYKPFF-YLGSGYLWGLPFSLFIVAGMFVVLALLMRKTALGLFIQSVGINPVASRLAGI 244 P F ++G+G +P+ +++ + ++ +++RKT LG+ I ++G N A+RL GI Sbjct: 171 NNDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGI 230 Query: 245 RTAALIFFVYIFCSLCAGLAGLMISANIKSADANNAGLLLELDAILAVTLGGTSLAGGKF 304 R ++ FVY L +GLAG M ++ + A+ N G ELDAI AV LGGTSL GG Sbjct: 231 RVGLVLLFVYSISGLFSGLAGAMSASRLYGANG-NWGSGYELDAIAAVVLGGTSLMGGVG 289 Query: 305 SLVGSVIGALIIQALTYTIYSLGVPPEVNMVVKSVVVFLVCL 346 S+ G+V+GALII + + LG+ V K V+ L + Sbjct: 290 SIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVI 331 >gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 342 Score = 97.4 bits (241), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 95/289 (32%), Positives = 146/289 (50%), Gaps = 29/289 (10%) Query: 45 IDFFMIPGFFRIEMKDGHLYGSVIDIVNRAAPLMLAALGMTLVIATRGIDISVGAVVAIS 104 ++ ++P FF +L S + +A + AL M L+I R IDISV A++A+ Sbjct: 49 VNGLLLPHFF----DPYNLADSTFNFSEKA----MIALPMALLIICREIDISVSAIIAL- 99 Query: 105 GTIAAMLIGGTMVVNNGVPEYVSNIPMGWALAA-ALGVALLCGAWNGLLVATLGLQPIIA 163 A++ +G + GVP P+G L A A G A CG NG LV LGL I+ Sbjct: 100 ---ASVAMG--LANQAGVP------PLGLLLVAIATGTA--CGLLNGALVTRLGLPSIVV 146 Query: 164 TLILMVAGRGLAQLLTDGQIITVYYKPFFYLGSGYLWGL---PFSLFIVAGMFVVLALLM 220 T+ M RGLA ++ Q T Y + G GY + + PF ++++A VV A+L+ Sbjct: 147 TIGSMSLFRGLASVVLGDQAFTQYPEVLGDWGQGYFFDVLPRPFVVWLLAA--VVFAVLL 204 Query: 221 RKTALGLFIQSVGINPVASRLAGIRTAALIFFVYIFCSLCAGLAGLMISANIKSADANNA 280 T G + ++G NPVA+R +G+ +++ AGLA ++ I S N A Sbjct: 205 HVTRWGRRLYAIGNNPVAARFSGVAVDRYRLALFVLTGAMAGLAAFFLTGRIGSTRPNIA 264 Query: 281 GLLLELDAILAVTLGGTSLAGGKFSLVGSVIGALIIQALTYTIYSLGVP 329 + EL+ I V LGG S+AGG S+ G ++ L++ LTY + +P Sbjct: 265 -MGWELEIITVVILGGVSIAGGTGSIGGVMLSVLVMGMLTYGLALANIP 312 >gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 96.7 bits (239), Expect = 3e-21, Method: Compositional matrix adjust. Identities = 87/289 (30%), Positives = 148/289 (51%), Gaps = 20/289 (6%) Query: 68 IDIVNRAAPLMLAALGMTLVIATRGIDISVGAVVAISGTIAAMLIGGTMVVNNGVPEYVS 127 I + N PL++ ++GMT ++ GID+SVG+V+A++ ++ +M + V G P Y + Sbjct: 51 ITLSNDIPPLVVMSVGMTFILIIGGIDLSVGSVMALAASMLSMAM-----VRWGWPLYAA 105 Query: 128 NIPMGWALAAALGVALLCGAWNGLLVATLGLQPIIATLILMVAGRGLAQLLTDGQIITVY 187 P+G +AA LCG G++ + I +L ++ RGLA +T+ + T Y Sbjct: 106 A-PLGVVVAA------LCGTLTGMVSVHWRIPSFIVSLGVLEIARGLAYQVTNSR--TEY 156 Query: 188 Y-KPFFYLGSGYLWGLPFSLFIVAGMFVVLALLMRKTALGLFIQSVGINPVASRLAGIRT 246 + S L+G+ + + ++ L++ +T LG + +G N A RL+G+ Sbjct: 157 IGSAVDVISSPILFGMSPAFLSAIAIVIIAQLVLTRTVLGRYWIGIGTNEEAVRLSGVNP 216 Query: 247 AALIFFVYIFCSLCAGLAGLMISANIKSADANNAGLLLELDAILAVTLGGTSLAGGKFSL 306 + AG+A L + +++AD N G+ +EL I AV +GGTSL GG+ S+ Sbjct: 217 NPSKILAFALMGALAGIAALFQVSRLEAADPNG-GVGMELQVIAAVVIGGTSLMGGRGSI 275 Query: 307 VGSVIGALIIQALTYTIYSLGV-PPEVNMVVKSVVVFLVCLSQSPEFRR 354 V + IG LII L + +GV P ++ +V+V V L +RR Sbjct: 276 VSTFIGVLIISVLEAGLAQVGVSEPMKRIITGAVIVVAVILD---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 0.328 0.142 0.413 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: 1,012,840 Number of extensions: 42298 Number of successful extensions: 313 Number of sequences better than 1.0e-08: 17 Number of HSP's gapped: 281 Number of HSP's successfully gapped: 17 Length of query: 364 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 278 Effective length of database: 1,212,660 Effective search space: 337119480 Effective search space used: 337119480 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)