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= 0001.2504.p (336 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... 147 1e-36 gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease ... 119 2e-28 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 118 5e-28 gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease ... 108 6e-25 gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease ... 107 2e-24 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 147 bits (371), Expect = 1e-36, Method: Compositional matrix adjust. Identities = 106/289 (36%), Positives = 169/289 (58%), Gaps = 2/289 (0%) Query: 39 LVALVLGFGLFSQFFLSVMNLQNILVQATVLGLLALAVALPLLVGEIDLSLPANLGFSSA 98 LV + L GL S F ++ N N+L Q +++G+LA+ ++ +L G IDLS+ A + + Sbjct: 36 LVVVSLLMGLASDNFFTLSNWFNVLRQVSIVGILAVGMSFVILTGGIDLSVGAAMALAGT 95 Query: 99 IGAWLYATWGGPWWLTMLVGVAVATLIGWFNGLCITRLRMVSLIQTLAMMIVLQGALLAL 158 I A L G P L +L GV +AT IG NG + RM ++I TLA M V +G L Sbjct: 96 ISAGLIVNSGLPAPLALLCGVGLATCIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIY 155 Query: 159 TQGKTITNLDDGYIWIGSATLGGWPLMPVIFVIALLAMS-VLLRRTVLGRSIYAVGGNAL 217 + G I+ L W G +G P +PVI ++ + A++ +LL+RT GR +YA+GGN + Sbjct: 156 SGGYPISGLPGWISWFGVGRIGMVP-VPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEM 214 Query: 218 ASHAAGIRVHRIKIICYALAGAIAGVAGYLLASWQIAITSNQGASYLLYAIAAPIIGGVS 277 A+ +G++ RIK+ YA++G +G+A +L ++ N G + L AIAA ++GG + Sbjct: 215 AARLSGVKTTRIKLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTA 274 Query: 278 VFGGRGSVLGILGGVLLLTVIQVGLAITNVPSFYVGMIGGVMIFIAVAI 326 + GGRG V+G L G +LL ++ GL + + + +I GV+I +A+ I Sbjct: 275 IAGGRGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILLAIYI 323 >gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 347 Score = 119 bits (299), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 101/303 (33%), Positives = 168/303 (55%), Gaps = 10/303 (3%) Query: 39 LVALVLGFGLFSQFFLSVMNLQNILVQATVLGLLALAVALPLLVGEIDLSLPANLGFSSA 98 L+ ++L F S F+ V NL +IL V G+LA+A ++ IDLS+ + F + Sbjct: 43 LLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAV 102 Query: 99 IGAWLYATWGGPWWLTMLVGVAVATLIGWFNGLCITRLRMVSLIQTLAMMIVLQGALLAL 158 + + WG P L + + L GW +G+ I +L++ I TL MM++L+G L + Sbjct: 103 MAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVI 162 Query: 159 TQGKTIT-NLDDGYIWIGSATLGGW--PLMPV------IFVIALLAMSVLLRRTVLGRSI 209 + + I N +G+ I +L G P +P+ +F++A+ A S++L +TV GR Sbjct: 163 SGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGA-SIILNKTVFGRYT 221 Query: 210 YAVGGNALASHAAGIRVHRIKIICYALAGAIAGVAGYLLASWQIAITSNQGASYLLYAIA 269 +A+G N A +G++V K+ Y +GAI G+AG ++AS + G Y L AIA Sbjct: 222 FALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIA 281 Query: 270 APIIGGVSVFGGRGSVLGILGGVLLLTVIQVGLAITNVPSFYVGMIGGVMIFIAVAIDAI 329 A +IGG S+ GG G++LG + G +++V+ GL I +V + ++ GV+I +AV +D + Sbjct: 282 AVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDIL 341 Query: 330 RVR 332 R R Sbjct: 342 RRR 344 >gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 118 bits (296), Expect = 5e-28, Method: Compositional matrix adjust. Identities = 95/285 (33%), Positives = 148/285 (51%), Gaps = 3/285 (1%) Query: 53 FLSVMNLQNILVQATVLGLLALAVALPLLVGEIDLSLPANLGFSSAIGAWLYATWGGPWW 112 F S N NIL Q + +LA + +L IDLS+ + L S+ +G + W Sbjct: 60 FASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWA 119 Query: 113 LTMLVGVAVATLIGWFNGLCITRLRMVSLIQTLAMMIVLQGALLALTQGKTITNLD-DGY 171 + M + + ++G NG + L + + + TL M +GA L G T+ N D + Sbjct: 120 IPMFIFSGL--VMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSF 177 Query: 172 IWIGSATLGGWPLMPVIFVIALLAMSVLLRRTVLGRSIYAVGGNALASHAAGIRVHRIKI 231 WIG+ P + + V +L V+LR+TVLG IYA+GGN A+ GIRV + + Sbjct: 178 EWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLL 237 Query: 232 ICYALAGAIAGVAGYLLASWQIAITSNQGASYLLYAIAAPIIGGVSVFGGRGSVLGILGG 291 Y+++G +G+AG + AS N G+ Y L AIAA ++GG S+ GG GS+ G + G Sbjct: 238 FVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVG 297 Query: 292 VLLLTVIQVGLAITNVPSFYVGMIGGVMIFIAVAIDAIRVRFFVQ 336 L++ V+ GL I + SF+ + G +I +AV +D R + Q Sbjct: 298 ALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQKDAAQ 342 >gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 352 Score = 108 bits (270), Expect = 6e-25, Method: Compositional matrix adjust. Identities = 94/280 (33%), Positives = 150/280 (53%), Gaps = 5/280 (1%) Query: 53 FLSVMNLQNILVQATVLGLLALAVALPLLVGEIDLSLPANLGFSSAIGAWLYATWGG-PW 111 FLS ++ N+L + + +LALA L +L IDLS+ +NL S + A L + P Sbjct: 49 FLSAQSMDNLLTDSAITIMLALAQMLVILTRGIDLSVASNLALSGMMSALLAMHFPALPV 108 Query: 112 WLTMLVGVAVATLIGWFNGLCITRLRMVSLIQTLAMMIVLQGALLALTQGKTIT--NLDD 169 + +L+ V + ++G NG I L + ++ TL M V +G + L+ G ++ N+ Sbjct: 109 GVFILMAVLIGLMLGLLNGWLIGYLELPPIVVTLGSMSVYRGMVFVLSGGAWVSSRNMPA 168 Query: 170 GYIWIGSATLGGWPLMPVIFVIALLAMSVLLRRTVLGRSIYAVGGNALASHAAGIRVHRI 229 +I A LGG + + +A++A+ L R T GR +YA+G + A+ GI Sbjct: 169 DFIAFPLARLGGLTHLVWLGALAVVAIWFLARHTRFGRDLYAIGNDPAAAAYVGIASRGR 228 Query: 230 KIICYALAGAIAGVAGYL-LASWQIAITSNQGASYLLYAIAAPIIGGVSVFGGRGSVLGI 288 + Y L+GA+AG+AGYL +A + +A T + L IAA +IGGVS+ GG G V G Sbjct: 229 LLWTYGLSGAMAGLAGYLWVARYAVAYT-EIAYGFELTVIAACVIGGVSIAGGVGQVSGA 287 Query: 289 LGGVLLLTVIQVGLAITNVPSFYVGMIGGVMIFIAVAIDA 328 + G L L+VI L I + F+ + G++I AV ++A Sbjct: 288 VLGALFLSVINNALPIMRISPFWQSALTGLVILCAVVLNA 327 >gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 107 bits (266), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 92/302 (30%), Positives = 149/302 (49%), Gaps = 17/302 (5%) Query: 39 LVALVLGFGLFSQFFLSVMNLQNILVQATVLGLLALAVALPLLVGEIDLSLPANLGFSSA 98 L+A+ + F S+ FLS + L ++++ + L++G IDLS+ + + +++ Sbjct: 30 LLAMCVMFAFLSENFLSAATFITLSNDIPPLVVMSVGMTFILIIGGIDLSVGSVMALAAS 89 Query: 99 IGAWLYATWGGPWWLTMLVGVAVATLIGWFNGLCITRLRMVSLIQTLAMMIVLQGALLAL 158 + + WG P + +GV VA L G G+ R+ S I +L ++ + +G + Sbjct: 90 MLSMAMVRWGWPLYAAAPLGVVVAALCGTLTGMVSVHWRIPSFIVSLGVLEIARGLAYQV 149 Query: 159 TQGKTITNLDDGYIWIGSAT--------LGGWPLMPVIFVIALLAMSVLLRRTVLGRSIY 210 T +T +IGSA G P I ++A ++L RTVLGR Sbjct: 150 TNSRTE--------YIGSAVDVISSPILFGMSPAFLSAIAIVIIA-QLVLTRTVLGRYWI 200 Query: 211 AVGGNALASHAAGIRVHRIKIICYALAGAIAGVAGYLLASWQIAITSNQGASYLLYAIAA 270 +G N A +G+ + KI+ +AL GA+AG+A S A N G L IAA Sbjct: 201 GIGTNEEAVRLSGVNPNPSKILAFALMGALAGIAALFQVSRLEAADPNGGVGMELQVIAA 260 Query: 271 PIIGGVSVFGGRGSVLGILGGVLLLTVIQVGLAITNVPSFYVGMIGGVMIFIAVAIDAIR 330 +IGG S+ GGRGS++ GVL+++V++ GLA V +I G +I +AV +D R Sbjct: 261 VVIGGTSLMGGRGSIVSTFIGVLIISVLEAGLAQVGVSEPMKRIITGAVIVVAVILDTYR 320 Query: 331 VR 332 R Sbjct: 321 RR 322 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 0.143 0.444 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: 918,581 Number of extensions: 33518 Number of successful extensions: 295 Number of sequences better than 1.0e-08: 22 Number of HSP's gapped: 285 Number of HSP's successfully gapped: 23 Length of query: 336 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 250 Effective length of database: 1,212,660 Effective search space: 303165000 Effective search space used: 303165000 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)