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= 0025.0220.p (320 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasm... 91 2e-19 gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasm... 70 2e-13 gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter peripl... 63 3e-11 gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasm... 61 1e-10 gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasm... 59 7e-10 >gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 316 Score = 90.5 bits (223), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 83/286 (29%), Positives = 135/286 (47%), Gaps = 11/286 (3%) Query: 31 LGVAIPTATHSFTAGIVWWANQAKAELEKAHPDMKV-IVKTAATAPEQANQLQDMLTVNK 89 +GV + + F I A A++ K +PD KV +V + Q Q+++ + NK Sbjct: 32 VGVTVGDLANPFFVAI---AKGAESGAHKINPDAKVTVVSSKYDLNTQVGQIENFIA-NK 87 Query: 90 INALVIFPIESASLTQPVAQVKNKGVYVTVVDRGLTTTEAQNAYIAGDNTAFGKLPAEYL 149 ++ +V+ +S + V + + G+ V V + + DNT G ++L Sbjct: 88 VDLIVLNAADSKGVGPAVKKAQKAGIVVVAV---DVAAAGADVTVMSDNTMAGAESCKFL 144 Query: 150 VKYLNGKGDIVVLRGMPTTLDNERFDAFSAVIKSNPGVKVL-DAKYGNWNRDDAFKVMQD 208 + L GKG++V++ G P + +R A K +PG+K+L D + +RD M + Sbjct: 145 AEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKSPGIKILSDNQNAGGSRDGGMTTMSN 204 Query: 209 YLTRFKHIDAVWAADDDMAIGVQKAIEQAKRTDIKQVFGGAGAKGAVKKIMDGSDKLITA 268 L IDAV+A +D AIG + AI QAKR+DIK + G GA A + + D S L A Sbjct: 205 LLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIKWISGVDGAPDAERALKD-SKSLFAA 263 Query: 269 DVSYSPKFMYDAIKLTAEARLKGAALPPKT-IIPSVLITKENAKQF 313 + P M A + G A K ++P LIT++N + Sbjct: 264 SPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLPVKLITRDNVADY 309 >gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 70.5 bits (171), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 53/180 (29%), Positives = 86/180 (47%), Gaps = 9/180 (5%) Query: 76 EQANQLQ--DMLTVNKINALVIFPIESASLTQPVAQVKNKGVYVTVVDRGLTTTEAQNA- 132 + ANQ++ + + V+K+NALVI P +S +L V + + G+ V +D L + Sbjct: 75 DTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVNIDNKLDDAALKEKG 134 Query: 133 ----YIAGDNTAFGKLPAEYLVKYLNGKGDIVVLRGMPTTLD-NERFDAFSAVIKSNPGV 187 ++ DN KL +YL K L + ++ G+ TT + +R F +K + G Sbjct: 135 ITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQRTLGFQDAMK-DVGA 193 Query: 188 KVLDAKYGNWNRDDAFKVMQDYLTRFKHIDAVWAADDDMAIGVQKAIEQAKRTDIKQVFG 247 V+ + G W D KV L I A+ A +D+MA+G AI A +T Q+ G Sbjct: 194 NVVTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAAIRAAGKTGKVQLVG 253 >gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 63.2 bits (152), Expect = 3e-11, Method: Compositional matrix adjust. Identities = 72/268 (26%), Positives = 129/268 (48%), Gaps = 29/268 (10%) Query: 65 KVIVKTA-ATAPEQANQLQDMLTVNKINALVIFPIESASLTQPVAQVKNKGVYVTVVDRG 123 KV V++A A+ Q +Q++++++ ++ +VI P + LT + + K G+ V DR Sbjct: 63 KVYVQSADASEQRQISQIENLIS-RGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDRL 121 Query: 124 LTTTEAQNAYIAGDNTAFGKLPAEYLVKYLNGKGDIVVLRGMPTTLDNERF-----DAFS 178 + + +AYI+ DN G++ AE ++K N KG+ +L G PT + + F A Sbjct: 122 ILNADV-DAYISFDNEKVGEMQAEGILKVKN-KGNFFLLGGSPTDNNAKMFREGQMKALK 179 Query: 179 AVIKSNPGVKVLDAKY-GNWNRDDAFKVMQDYLT-RFKHIDAVWAADDDMAIGVQKAIEQ 236 I +K++ ++ WN +A ++++ LT IDA+ A++D A G +A+ Sbjct: 180 PYIDKGD-IKIVGQQWVKEWNPTEALSIVENALTANNNKIDAIVASNDGTAGGAIQALAA 238 Query: 237 AKRTDIKQVFGGAGAKGAVKKIMDGSDKLITADVSYSP--KFMYDAIKLTAE-ARLK--- 290 K V G AVK+++ G+ + Y P + +A KL+ E AR + Sbjct: 239 QKLAGKVPVSGQDADLAAVKRVVAGTQTMTV----YKPLKQIATEAAKLSVELARNEKPT 294 Query: 291 -------GAALPPKTIIPSVLITKENAK 311 G ++ +L+TKEN K Sbjct: 295 YNAQYDNGFKKVDSLLLKPILLTKENVK 322 >gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 302 Score = 61.2 bits (147), Expect = 1e-10, Method: Compositional matrix adjust. Identities = 69/256 (26%), Positives = 118/256 (46%), Gaps = 15/256 (5%) Query: 65 KVIVKTAA-TAPEQANQLQDMLTVNKINALVIFPIESASLTQPVAQVKNKGVYVTVVDRG 123 KVI AA +Q ++DML N I+ L+I P +SA + V K + V V VD Sbjct: 57 KVIATDAAHNVAKQIADIEDMLQQN-IDILLINPTDSAGVEAAVKAAKARNVIVVAVD-- 113 Query: 124 LTTTEAQNAYIAGDNTAFGKLPAEYLVKYLNGKGDIVVLRGMPTTLDNERFDAFSAVIKS 183 + + ++ N G L + GKG++ +L G+P +R + + Sbjct: 114 ANASGPVDMFVGSKNKDAGYQSCRALADAIGGKGEVAILDGIPVVPILQRVEGCKQALAE 173 Query: 184 NPGVKVLDAKYGNWNRDDAFKVMQDYLTRFKHIDAVWAADDDMAIGVQKAIEQAKRTDIK 243 +K++ + G +R A V+++ + ++ +++ +D A+G AI Q DIK Sbjct: 174 YKDIKLVATQNGRQDRSVALGVVENMIQSRPNLKGIFSVNDGGAMGALAAI-QGSGKDIK 232 Query: 244 QVFGGAGAKGAVKKIMDGSDKLITADVSYSPKFMYDAIKL---TAEARLKGAALPPKTII 300 + GA AVK I DG V + +F D +++ A A+ GA + PK + Sbjct: 233 -LTSVDGAPEAVKAIADGG-----PFVETTAQFPRDQVRVGLAMALAKKWGARVVPKEVP 286 Query: 301 PSVL-ITKENAKQFYF 315 V+ +TK+NA F + Sbjct: 287 IDVMPVTKKNAAGFSW 302 >gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 58.5 bits (140), Expect = 7e-10, Method: Compositional matrix adjust. Identities = 69/287 (24%), Positives = 127/287 (44%), Gaps = 23/287 (8%) Query: 49 WANQAKAELEKAHPDMKVIVKTAATAPEQANQLQDMLT--VNKINALVIFPIESASLTQP 106 W ++ A V +K A +Q NQ++ + + K++ + P+ + Sbjct: 46 WRTANTVSIKDAAKQAGVNLKFADAQQKQENQVKAIRSFIAQKVDVIAFSPVVESGWETV 105 Query: 107 VAQVKNKGVYVTVVDRGLTTTEAQ--NAYIAGDNTAFGKLPAEYLVKYLN----GKGDIV 160 + + K + V + DR + ++ +I D G+ +L++ G +IV Sbjct: 106 LREAKAAKIPVILTDRAVNVSDKSLYVTFIGSDFVEEGRRAGRWLLEKAKSMPAGDINIV 165 Query: 161 VLRGMPTTLDN-ERFDAFSAVIKSNPGVKVLDAKYGNWNRDDAFKVMQDYL-TRFKHIDA 218 L+G + +R F VIK P +K++ ++ G++ R +VM+ +L K I+ Sbjct: 166 ELQGTVGSAPAIDRKAGFEEVIKGEPRLKIIRSQTGDFTRAKGKEVMEAFLKAEGKKINV 225 Query: 219 VWAADDDMAIGVQKAIEQAKRTDIKQ--VFGGAGAKGAVKKIMDGSDKL-ITADVS--YS 273 ++A +DDMAIG +AIE+A K + G KGA + +M G KL +T + S Sbjct: 226 LYAHNDDMAIGAIQAIEEAGMKPGKDIIIISIDGVKGAFEAMMAG--KLNVTVECSPLLG 283 Query: 274 PKFMYDAIKLTAEARLKGAALPPKTIIPSVLITKENAKQFYFPDSPF 320 P+ M A + A + + I P+ + KE FP+ + Sbjct: 284 PQLMQIAKDIKAGKEVPKRITTEEGIFPAEVAAKE------FPNRKY 324 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 0.317 0.132 0.374 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: 837,250 Number of extensions: 31650 Number of successful extensions: 112 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 111 Number of HSP's successfully gapped: 7 Length of query: 320 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 235 Effective length of database: 1,217,395 Effective search space: 286087825 Effective search space used: 286087825 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 130 (54.7 bits)