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= 0234.0004.p (172 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... 146 7e-37 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 131 3e-32 gi|300313778|ref|YP_003777870.1| D-xylose ABC transporter permea... 129 1e-31 gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease ... 126 7e-31 gi|300310372|ref|YP_003774464.1| sugar ABC transporter permease ... 116 1e-27 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 146 bits (369), Expect = 7e-37, Method: Compositional matrix adjust. Identities = 72/148 (48%), Positives = 107/148 (72%) Query: 21 IPYPVVLMFVIAIAISVMLSRTTFGRHIYAVGSNSEAARLSGVKVSSVTLWTYVIAGALA 80 +P PV+LM ++ ++L RT FGRH+YA+G N AARLSGVK + + L Y I+G + Sbjct: 179 VPVPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTS 238 Query: 81 GLTGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLIGGIGSISGTLIGSFVIGILRNG 140 GL +L RL++ QPN GV +ELDAIA+ V+GGT++ GG G + GTLIG+ ++GIL NG Sbjct: 239 GLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNG 298 Query: 141 LNMNGVSSFIQQIIIGLVILLTVWIDQK 168 LN+ G++ ++Q II G++ILL ++I ++ Sbjct: 299 LNLMGINPYLQDIIRGVIILLAIYIARE 326 >gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 131 bits (330), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 70/154 (45%), Positives = 104/154 (67%) Query: 18 FPGIPYPVVLMFVIAIAISVMLSRTTFGRHIYAVGSNSEAARLSGVKVSSVTLWTYVIAG 77 F +P+ + + + + V+L +T G HIYA+G N +AARL+G++V V L+ Y I+G Sbjct: 185 FLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISG 244 Query: 78 ALAGLTGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLIGGIGSISGTLIGSFVIGIL 137 +GL G + SRL A N G YELDAIA+ V+GGTSL+GG+GSI GT++G+ +IG++ Sbjct: 245 LFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVM 304 Query: 138 RNGLNMNGVSSFIQQIIIGLVILLTVWIDQKRNR 171 NGL + G+SSF Q + G VI+L V +D+ R + Sbjct: 305 NNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQK 338 >gi|300313778|ref|YP_003777870.1| D-xylose ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 385 Score = 129 bits (324), Expect = 1e-31, Method: Compositional matrix adjust. Identities = 70/149 (46%), Positives = 97/149 (65%) Query: 18 FPGIPYPVVLMFVIAIAISVMLSRTTFGRHIYAVGSNSEAARLSGVKVSSVTLWTYVIAG 77 + GIP PV+L+ + S + ++T FGR IY+VGSN EA RLSGV V +V LW + I G Sbjct: 230 YDGIPVPVLLLLALLGLFSYVSTQTVFGRRIYSVGSNMEATRLSGVNVQAVKLWVFGIMG 289 Query: 78 ALAGLTGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLIGGIGSISGTLIGSFVIGIL 137 + L G V +RL P+ G M ELDAIA+ IGGTS+ GG G+I G LIG+ V+ L Sbjct: 290 VMCALAGLVNTARLAAGSPSAGNMGELDAIAACFIGGTSMRGGSGTIYGALIGALVMASL 349 Query: 138 RNGLNMNGVSSFIQQIIIGLVILLTVWID 166 NG++M V ++ Q I+ G +++L VW+D Sbjct: 350 DNGMSMLDVGTYWQMIVKGSILVLAVWVD 378 >gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 347 Score = 126 bits (317), Expect = 7e-31, Method: Compositional matrix adjust. Identities = 76/158 (48%), Positives = 112/158 (70%), Gaps = 2/158 (1%) Query: 17 LFPGIPYP--VVLMFVIAIAISVMLSRTTFGRHIYAVGSNSEAARLSGVKVSSVTLWTYV 74 L P +P P V+++F++AI S++L++T FGR+ +A+GSN EA RLSGVKV + Y Sbjct: 188 LIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYT 247 Query: 75 IAGALAGLTGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLIGGIGSISGTLIGSFVI 134 +GA+ G+ G ++ SRL +AQP G YELDAIA+ VIGGTSL GG G+I GT+IG+F++ Sbjct: 248 FSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIM 307 Query: 135 GILRNGLNMNGVSSFIQQIIIGLVILLTVWIDQKRNRR 172 +L NGL + V+ Q ++ G++I+L V++D R RR Sbjct: 308 SVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRRR 345 >gi|300310372|ref|YP_003774464.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 405 Score = 116 bits (290), Expect = 1e-27, Method: Compositional matrix adjust. Identities = 65/155 (41%), Positives = 102/155 (65%), Gaps = 1/155 (0%) Query: 18 FPGIPYPVVLMFVIAIAISVMLSRTTFGRHIYAVGSNSEAARLSGVKVSSVTLWTYVIAG 77 + G+P +++MF + + + + SRTT GR +YAVG N +AA+LSG+K V+ +T+V G Sbjct: 251 YRGMPNVLIIMFALMVLYTFITSRTTLGRRVYAVGGNEKAAKLSGIKTERVSFFTFVNMG 310 Query: 78 ALAGLTGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLIGGIGSISGTLIGSFVIGIL 137 LA L G + +RL TA P G+ +ELD IA+ IGG S GG+G + G +IG+FV+G++ Sbjct: 311 VLAALAGLIFAARLNTATPKAGLGFELDVIAACFIGGASASGGVGKVMGAVIGAFVMGVM 370 Query: 138 RNGLNMNGVSSFIQQIIIGLVILLTVWID-QKRNR 171 NG+++ G+ QQ+I G V+L+ V D +N+ Sbjct: 371 NNGMSIMGIGIDYQQMIKGFVLLMAVCFDVYNKNK 405 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 0.142 0.412 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: 393,461 Number of extensions: 12638 Number of successful extensions: 116 Number of sequences better than 1.0e-08: 17 Number of HSP's gapped: 121 Number of HSP's successfully gapped: 17 Length of query: 172 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 93 Effective length of database: 1,245,805 Effective search space: 115859865 Effective search space used: 115859865 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: 127 (53.5 bits)