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= 0003.0085.p (323 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasm... 595 e-171 gi|300310384|ref|YP_003774476.1| sugar ABC transporter periplasm... 67 2e-12 gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter peripl... 59 4e-10 gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasm... 55 7e-09 >gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 595 bits (1533), Expect = e-171, Method: Compositional matrix adjust. Identities = 292/324 (90%), Positives = 309/324 (95%), Gaps = 1/324 (0%) Query: 1 MKMTRRTLLGAAVCMTLGWSALS-GAVAADKPLTMGFSQVGAESEWRTANTASIKDAAKK 59 M RR LLGAA+C++LG SA+S A AADKPLTMGFSQVGAESEWRTANT SIKDAAK+ Sbjct: 1 MNSKRRALLGAAICLSLGSSAMSLPAFAADKPLTMGFSQVGAESEWRTANTVSIKDAAKQ 60 Query: 60 AGVNLKFADAQQKQENQVKAIRSFIAQKVDVIAFSPVVESGWDTVLREAKAAKIPVILTD 119 AGVNLKFADAQQKQENQVKAIRSFIAQKVDVIAFSPVVESGW+TVLREAKAAKIPVILTD Sbjct: 61 AGVNLKFADAQQKQENQVKAIRSFIAQKVDVIAFSPVVESGWETVLREAKAAKIPVILTD 120 Query: 120 RAVNVSDKSLYVTFIGSDFVEEGRRAARWLLDRAKTLPAGDINIVELQGTVGSAPAIDRK 179 RAVNVSDKSLYVTFIGSDFVEEGRRA RWLL++AK++PAGDINIVELQGTVGSAPAIDRK Sbjct: 121 RAVNVSDKSLYVTFIGSDFVEEGRRAGRWLLEKAKSMPAGDINIVELQGTVGSAPAIDRK 180 Query: 180 AGFEQEIKANPNLKIIRSQTGDFTRAKGKEVMEAFLKADGKKINVLYAHNDDMAIGAIQA 239 AGFE+ IK P LKIIRSQTGDFTRAKGKEVMEAFLKA+GKKINVLYAHNDDMAIGAIQA Sbjct: 181 AGFEEVIKGEPRLKIIRSQTGDFTRAKGKEVMEAFLKAEGKKINVLYAHNDDMAIGAIQA 240 Query: 240 IEEAGLKPGKDILVISIDGVKGAFEAMMAGKLNVTVECSPLLGPQLMSIAKDVKAGKEVP 299 IEEAG+KPGKDI++ISIDGVKGAFEAMMAGKLNVTVECSPLLGPQLM IAKD+KAGKEVP Sbjct: 241 IEEAGMKPGKDIIIISIDGVKGAFEAMMAGKLNVTVECSPLLGPQLMQIAKDIKAGKEVP 300 Query: 300 KRITTEEGVFPAEVAAKEFPNRKY 323 KRITTEEG+FPAEVAAKEFPNRKY Sbjct: 301 KRITTEEGIFPAEVAAKEFPNRKY 324 >gi|300310384|ref|YP_003774476.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 312 Score = 67.0 bits (162), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 84/310 (27%), Positives = 145/310 (46%), Gaps = 27/310 (8%) Query: 3 MTRRTLLGAAVCMT--LGWSALSGAVAADKPLTMGFSQVGAESEWRTANTASIKDAAKKA 60 M + LLGAA+ + +G SA A ++ GF + ++ A A A K Sbjct: 1 MFKNKLLGAALGLAFAMGASAAQAQEAYIPLISKGF-----QHQFWQAVKAGADQAGKDY 55 Query: 61 GVNLKF--ADAQQKQENQVKAIRSFIAQKVDVIAFSPVVESGWDTVLREAKAAKIPVILT 118 V + F + + + Q+ + + +A+K I F+ + +L++A+AAKIPV+ Sbjct: 56 KVKVTFEGPETEAMVDKQIDMLSAALAKKPQAIGFAALDSKAAIPLLKKAQAAKIPVVAF 115 Query: 119 DRAVNVSDKSLYVTFIGSDFVEEGRRAARWLLDRAKTLPA--GDINIVELQGTVGSAPAI 176 D V D + VT +D R AA D+ L G++ +V T S + Sbjct: 116 DSGV---DSDIPVTTATTD----NRAAAALAADKMAELVGKEGEVAVVAHDQT--SRTGV 166 Query: 177 DRKAGFEQEIK-ANPNLKIIRSQTGDFTRAKGKEVMEAFLKADGKKINVLYAHNDDMAIG 235 DR+ GF + IK A P +K++ Q G + K EV ++ L+A KI ++ N+ AIG Sbjct: 167 DRRDGFLERIKSAYPKIKVVSVQYGAGDQLKSTEVTKSILQAY-PKIKGIFGTNEGSAIG 225 Query: 236 AIQAIEEAGLKPGKDILVISIDGVKGAFEAMMAGKLNVTVECSPL-LGPQLMSIAKDVKA 294 + ++E K I++I D K +A+ G + + +P+ +G + + A Sbjct: 226 VVNGVKEMKRK----IIIIGYDSGKQQKDAIREGIMAGAITQNPVGIGYKTVEAAVKAIK 281 Query: 295 GKEVPKRITT 304 G+++PK I T Sbjct: 282 GEKLPKVIDT 291 >gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 59.3 bits (142), Expect = 4e-10, Method: Compositional matrix adjust. Identities = 87/331 (26%), Positives = 137/331 (41%), Gaps = 45/331 (13%) Query: 3 MTRRTLLGAAVCMTLGWSALSGAVAADKPLTMGFSQVGAESEWRTANTASIKDAAKKAGV 62 M ++T+L TL A S A P +GFS E + AA+K G Sbjct: 4 MLKKTVLALMTVTTLSMVAGSAMADAKNP-KIGFSIDDLRVERWARDRDFFTAAAEKLGA 62 Query: 63 NLKFADAQQKQENQVKAIRSFIAQKVDVIAFSPVVESGWDTVLREAKAAKIPVILTDRAV 122 + A ++ Q+ I + I++ VDVI P + ++EAK A I V+ DR + Sbjct: 63 KVYVQSADASEQRQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDRLI 122 Query: 123 NVSDKSLYVTFIGSDFVEEGRRAARWLLDRAKTLPAGDINIVELQGTVGSAPAIDRKAGF 182 +D Y++F D + G A +L K G+ + +G +P + F Sbjct: 123 LNADVDAYISF---DNEKVGEMQAEGIL---KVKNKGNFFL------LGGSPTDNNAKMF 170 Query: 183 -EQEIKA------NPNLKIIRSQ-TGDFTRAKGKEVMEAFLKADGKKINVLYAHNDDMAI 234 E ++KA ++KI+ Q ++ + ++E L A+ KI+ + A ND A Sbjct: 171 REGQMKALKPYIDKGDIKIVGQQWVKEWNPTEALSIVENALTANNNKIDAIVASNDGTAG 230 Query: 235 GAIQAIEEAGLKPGKDILVISIDGVKGAFEAMMAGKLNVTVECSPLLGPQLMSIAKDVKA 294 GAIQA+ A K + V D A + ++AG +TV PL Sbjct: 231 GAIQAL--AAQKLAGKVPVSGQDADLAAVKRVVAGTQTMTV-YKPL-------------- 273 Query: 295 GKEVPKRITTEEGVFPAEVAAKEFP--NRKY 323 K+I TE E+A E P N +Y Sbjct: 274 -----KQIATEAAKLSVELARNEKPTYNAQY 299 >gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 302 Score = 55.1 bits (131), Expect = 7e-09, Method: Compositional matrix adjust. Identities = 57/238 (23%), Positives = 113/238 (47%), Gaps = 14/238 (5%) Query: 32 LTMGFSQVGAESEWRTANTASIKDAAKKAGVNLKFADAQQKQENQVKAIRSFIAQKVDVI 91 L +G S + + + ++ +AAK G + DA Q+ I + Q +D++ Sbjct: 26 LKIGMSFQEMNNPYFVSMKKALDEAAKSLGAKVIATDAAHNVAKQIADIEDMLQQNIDIL 85 Query: 92 AFSPVVESGWDTVLREAKAAKIPVILTDRAVNVSDKSLYVTFIGSDFVEEGRRAARWLLD 151 +P +G + ++ AKA + V+ AV+ + F+GS + G ++ R L D Sbjct: 86 LINPTDSAGVEAAVKAAKARNVIVV----AVDANASGPVDMFVGSKNKDAGYQSCRALAD 141 Query: 152 RAKTLPAGDINIVELQGTVGSAPAIDRKAGFEQEIKANPNLKIIRSQTGDFTRAKGKEVM 211 G++ I++ + P + R G +Q + ++K++ +Q G R+ V+ Sbjct: 142 AIGG--KGEVAILD---GIPVVPILQRVEGCKQALAEYKDIKLVATQNGRQDRSVALGVV 196 Query: 212 EAFLKADGKKINVLYAHNDDMAIGAIQAIEEAGLKPGKDILVISIDGVKGAFEAMMAG 269 E +++ + +++ ND A+GA+ AI+ + GKDI + S+DG A +A+ G Sbjct: 197 ENMIQSR-PNLKGIFSVNDGGAMGALAAIQGS----GKDIKLTSVDGAPEAVKAIADG 249 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 0.316 0.131 0.368 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: 897,240 Number of extensions: 33873 Number of successful extensions: 140 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 137 Number of HSP's successfully gapped: 6 Length of query: 323 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 238 Effective length of database: 1,217,395 Effective search space: 289740010 Effective search space used: 289740010 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 (21.6 bits) S2: 131 (55.1 bits)