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= 0025.0195.p (333 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... 108 5e-25 gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter peripl... 87 2e-18 gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasm... 86 3e-18 gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasm... 77 3e-15 gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasm... 66 4e-12 >gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 108 bits (271), Expect = 5e-25, Method: Compositional matrix adjust. Identities = 79/268 (29%), Positives = 137/268 (51%), Gaps = 11/268 (4%) Query: 8 AVLCGLGLT-LSLSVHAQDRPLRIGAAVYGLKGEFMQMWSNHLKAHPAVKDGSVQITIFD 66 A+ LG + +SL A D+PL +G + G + E+ +N + A K V + D Sbjct: 12 AICLSLGSSAMSLPAFAADKPLTMGFSQVGAESEWRT--ANTVSIKDAAKQAGVNLKFAD 69 Query: 67 GNYDALTQSNQFDTMITQKYDAIIFVPIDLKAGAAPVQKAIKAGIPVIGSNARV-LGD-- 123 Q + I QK D I F P+ +++A A IPVI ++ V + D Sbjct: 70 AQQKQENQVKAIRSFIAQKVDVIAFSPVVESGWETVLREAKAAKIPVILTDRAVNVSDKS 129 Query: 124 VLTSYVGNDDVVAGRMEAEALMKAI----GGKGNIVMIEGPIGQSAQIERAKGNDEILSK 179 + +++G+D V GR L++ G NIV ++G +G + I+R G +E++ Sbjct: 130 LYVTFIGSDFVEEGRRAGRWLLEKAKSMPAGDINIVELQGTVGSAPAIDRKAGFEEVIKG 189 Query: 180 YKDVKVLARKTGNWSRAESMSLMENWLTAYPGKINGVIAQNDDEALGAVQAIKSKGIDI- 238 +K++ +TG+++RA+ +ME +L A KIN + A NDD A+GA+QAI+ G+ Sbjct: 190 EPRLKIIRSQTGDFTRAKGKEVMEAFLKAEGKKINVLYAHNDDMAIGAIQAIEEAGMKPG 249 Query: 239 KTIPVVGVDGIAAAIQAVKRGEMTTNFQ 266 K I ++ +DG+ A +A+ G++ + Sbjct: 250 KDIIIISIDGVKGAFEAMMAGKLNVTVE 277 >gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 87.0 bits (214), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 61/194 (31%), Positives = 110/194 (56%), Gaps = 8/194 (4%) Query: 74 QSNQFDTMITQKYDAIIFVPIDLKAGAAPVQKAIKAGIPVIGSNARVLGDVLTSYVGNDD 133 Q +Q + +I++ D I+ VP + +++A KAGI V+ + +L + +Y+ D+ Sbjct: 76 QISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDRLILNADVDAYISFDN 135 Query: 134 VVAGRMEAEALMKAIGGKGNIVMIEG-PIGQSAQIERAKGNDEILSKY---KDVKVLARK 189 G M+AE ++K + KGN ++ G P +A++ R +G + L Y D+K++ ++ Sbjct: 136 EKVGEMQAEGILK-VKNKGNFFLLGGSPTDNNAKMFR-EGQMKALKPYIDKGDIKIVGQQ 193 Query: 190 -TGNWSRAESMSLMENWLTAYPGKINGVIAQNDDEALGAVQAIKSKGIDIKTIPVVGVDG 248 W+ E++S++EN LTA KI+ ++A ND A GA+QA+ ++ + K +PV G D Sbjct: 194 WVKEWNPTEALSIVENALTANNNKIDAIVASNDGTAGGAIQALAAQKLAGK-VPVSGQDA 252 Query: 249 IAAAIQAVKRGEMT 262 AA++ V G T Sbjct: 253 DLAAVKRVVAGTQT 266 >gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 302 Score = 86.3 bits (212), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 81/294 (27%), Positives = 136/294 (46%), Gaps = 26/294 (8%) Query: 28 LRIGAAVYGLKGEFMQMWSNHLKAHPAVKDGSVQITIFDGNYDALTQSNQFDTMITQKYD 87 L+IG + + + L A K ++ D ++ Q + M+ Q D Sbjct: 26 LKIGMSFQEMNNPYFVSMKKAL--DEAAKSLGAKVIATDAAHNVAKQIADIEDMLQQNID 83 Query: 88 AIIFVPIDLKAGAAPVQKAIKAGIPVIGSNARVLGDVLTSYVGNDDVVAGRMEAEALMKA 147 ++ P D A V+ A + V+ +A G V +VG+ + AG AL A Sbjct: 84 ILLINPTDSAGVEAAVKAAKARNVIVVAVDANASGPV-DMFVGSKNKDAGYQSCRALADA 142 Query: 148 IGGKGNIVMIEG----PIGQSAQIERAKGNDEILSKYKDVKVLARKTGNWSRAESMSLME 203 IGGKG + +++G PI ++R +G + L++YKD+K++A + G R+ ++ ++E Sbjct: 143 IGGKGEVAILDGIPVVPI-----LQRVEGCKQALAEYKDIKLVATQNGRQDRSVALGVVE 197 Query: 204 NWLTAYPGKINGVIAQNDDEALGAVQAIKSKGIDIKTIPVVGVDGIAAAIQAVKRG---- 259 N + + P + G+ + ND A+GA+ AI+ G DIK + VDG A++A+ G Sbjct: 198 NMIQSRP-NLKGIFSVNDGGAMGALAAIQGSGKDIK---LTSVDGAPEAVKAIADGGPFV 253 Query: 260 EMTTNFQDAQAQAQGALDVALRTLKGTSYQPRSPIWREYIDTMPWGDGTAKSYS 313 E T F + Q + L +AL G P+ ID MP A +S Sbjct: 254 ETTAQF--PRDQVRVGLAMALAKKWGARVVPK----EVPIDVMPVTKKNAAGFS 301 >gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 316 Score = 76.6 bits (187), Expect = 3e-15, Method: Compositional matrix adjust. Identities = 79/236 (33%), Positives = 117/236 (49%), Gaps = 9/236 (3%) Query: 25 DRPLR-IGAAVYGLKGEFMQMWSNHLKAHPAVKDGSVQITIFDGNYDALTQSNQFDTMIT 83 D+PL+ +G V L F + ++ + ++T+ YD TQ Q + I Sbjct: 26 DKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPDAKVTVVSSKYDLNTQVGQIENFIA 85 Query: 84 QKYDAIIFVPIDLKAGAAPVQKAIKAGIPVIGSNARVLGDVLTSYVGNDDVVAGRMEAEA 143 K D I+ D K V+KA KAGI V+ + G +T V +D+ +AG + Sbjct: 86 NKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDVAAAGADVT--VMSDNTMAGAESCKF 143 Query: 144 LMKAIGGKGNIVMIEGPIGQSAQIERAKGNDEILSKYKDVKVLA-RKTGNWSRAESMSLM 202 L + + GKGN+V++ GP SA ++R G K +K+L+ + SR M+ M Sbjct: 144 LAEKLQGKGNVVIVNGP-PVSAVMDRVTGCKAEFKKSPGIKILSDNQNAGGSRDGGMTTM 202 Query: 203 ENWLTAYPGKINGVIAQNDDEALGAVQAIK-SKGIDIKTIPVVGVDGIAAAIQAVK 257 N L A P KI+ V A ND A+GA AI+ +K DIK I GVDG A +A+K Sbjct: 203 SNLLAAQP-KIDAVFAINDPTAIGAELAIRQAKRSDIKWIS--GVDGAPDAERALK 255 >gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 65.9 bits (159), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 77/279 (27%), Positives = 128/279 (45%), Gaps = 22/279 (7%) Query: 29 RIGAAVYGLKGEFMQMWSNHLKAHPAVKDGSVQITIFDGNYDALTQSNQF---DTMITQK 85 ++ + L EF N + + + I +G D +NQ + MI K Sbjct: 32 KVALVMKSLANEFFLNMENGAREYQKANASKFDL-IANGIKDEQDTANQIKIVEQMIVSK 90 Query: 86 YDAIIFVPIDLKAGAAPVQKAIKAGIPVIGSNARVLGD-------VLTSYVGNDDVVAGR 138 +A++ P D KA V+KAI AGI V+ + + L D + +VG D+ + Sbjct: 91 VNALVIAPADSKALVPVVKKAIDAGIIVVNIDNK-LDDAALKEKGITVPFVGPDNRKGAK 149 Query: 139 MEAEALMKAIGGKGNIVMIEGPIGQSAQIERAKGNDEILSKYKDV--KVLARKTGNWSRA 196 + + L K + + +IEG +R G + + KDV V+ ++G W Sbjct: 150 LAGDYLGKQLQKGDKVAIIEGVSTTFNAQQRTLGFQDAM---KDVGANVVTVQSGQWEID 206 Query: 197 ESMSLMENWLTAYPGKINGVIAQNDDEALGAVQAIKSKGIDIKTIPVVGVDGIAAAIQAV 256 + + + L A+P I ++A ND+ ALGAV AI++ G K + +VG D I A + Sbjct: 207 QGNKVAASILNAHP-DIKAILAGNDNMALGAVAAIRAAGKTGK-VQLVGYDNINAIKPML 264 Query: 257 KRGE-MTTNFQDAQAQAQGALDVALRTLKGTSYQPRSPI 294 K G + T Q AQ QA ++ AL+ L + +P+S + Sbjct: 265 KDGRVLATVDQFAQQQAVFGIETALKAL--SEKKPQSAL 301 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 0.133 0.383 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: 999,501 Number of extensions: 40711 Number of successful extensions: 180 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 171 Number of HSP's successfully gapped: 8 Length of query: 333 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 247 Effective length of database: 1,212,660 Effective search space: 299527020 Effective search space used: 299527020 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)