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= 0001.0113.p (330 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... 100 2e-22 gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasm... 81 1e-16 gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter peripl... 80 2e-16 gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasm... 74 2e-14 gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasm... 72 7e-14 >gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 100 bits (248), Expect = 2e-22, Method: Compositional matrix adjust. Identities = 76/249 (30%), Positives = 126/249 (50%), Gaps = 14/249 (5%) Query: 20 AQNKPLRIGAAVYGLKGEFMQMWSNQLKAHPAVQDGSVQVTVFDGNYDALTQSNQFDTMI 79 A +KPL +G + G + E+ +N + A + V + D Q + I Sbjct: 28 AADKPLTMGFSQVGAESEWRT--ANTVSIKDAAKQAGVNLKFADAQQKQENQVKAIRSFI 85 Query: 80 LQKYDAIIFVPIDLKAGAAPVQKAVKAGIPVIGSNTRVQ---GDVLTSYVGNDDVVAGR- 135 QK D I F P+ +++A A IPVI ++ V + +++G+D V GR Sbjct: 86 AQKVDVIAFSPVVESGWETVLREAKAAKIPVILTDRAVNVSDKSLYVTFIGSDFVEEGRR 145 Query: 136 -----LEAEALMKAIGGKGNIVMIEGPIGQSAQIERARGNDEVLARNKDVKVLARKTGNW 190 LE M A G NIV ++G +G + I+R G +EV+ +K++ +TG++ Sbjct: 146 AGRWLLEKAKSMPA--GDINIVELQGTVGSAPAIDRKAGFEEVIKGEPRLKIIRSQTGDF 203 Query: 191 SRAESMALMENWLTAHPGQIKGVLAQNDDEALGALQAIKAKGIDP-KTIPVVGIDGIADA 249 +RA+ +ME +L A +I + A NDD A+GA+QAI+ G+ P K I ++ IDG+ A Sbjct: 204 TRAKGKEVMEAFLKAEGKKINVLYAHNDDMAIGAIQAIEEAGMKPGKDIIIISIDGVKGA 263 Query: 250 IAAVKRGEM 258 A+ G++ Sbjct: 264 FEAMMAGKL 272 >gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 302 Score = 81.3 bits (199), Expect = 1e-16, Method: Compositional matrix adjust. Identities = 66/227 (29%), Positives = 111/227 (48%), Gaps = 18/227 (7%) Query: 58 QVTVFDGNYDALTQSNQFDTMILQKYDAIIFVPIDLKAGAAPVQKAVKAGIPVIGSNTRV 117 +V D ++ Q + M+ Q D ++ P D A V+ A + V+ + Sbjct: 57 KVIATDAAHNVAKQIADIEDMLQQNIDILLINPTDSAGVEAAVKAAKARNVIVVAVDANA 116 Query: 118 QGDVLTSYVGNDDVVAGRLEAEALMKAIGGKGNIVMIEG----PIGQSAQIERARGNDEV 173 G V +VG+ + AG AL AIGGKG + +++G PI ++R G + Sbjct: 117 SGPV-DMFVGSKNKDAGYQSCRALADAIGGKGEVAILDGIPVVPI-----LQRVEGCKQA 170 Query: 174 LARNKDVKVLARKTGNWSRAESMALMENWLTAHPGQIKGVLAQNDDEALGALQAIKAKGI 233 LA KD+K++A + G R+ ++ ++EN + + P +KG+ + ND A+GAL AI+ G Sbjct: 171 LAEYKDIKLVATQNGRQDRSVALGVVENMIQSRP-NLKGIFSVNDGGAMGALAAIQGSG- 228 Query: 234 DPKTIPVVGIDGIADAIAAVKRG----EMVTQFQDAQAQAQGALDVA 276 K I + +DG +A+ A+ G E QF Q + A+ +A Sbjct: 229 --KDIKLTSVDGAPEAVKAIADGGPFVETTAQFPRDQVRVGLAMALA 273 >gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 80.5 bits (197), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 76/265 (28%), Positives = 138/265 (52%), Gaps = 19/265 (7%) Query: 1 MIKKTLASLL----LMAVATGVSAQNKPLRIGAAVYGLKGEFMQMWSNQLKAHPAVQDG- 55 M+KKT+ +L+ L VA A K +IG ++ L+ ++ W+ A + Sbjct: 4 MLKKTVLALMTVTTLSMVAGSAMADAKNPKIGFSIDDLR---VERWARDRDFFTAAAEKL 60 Query: 56 SVQVTVFDGNYDALTQSNQFDTMILQKYDAIIFVPIDLKAGAAPVQKAVKAGIPVIGSNT 115 +V V + Q +Q + +I + D I+ VP + +++A KAGI V+ + Sbjct: 61 GAKVYVQSADASEQRQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDR 120 Query: 116 RVQGDVLTSYVGNDDVVAGRLEAEALMKAIGGKGNIVMIEG-PIGQSAQIERARGNDEVL 174 + + +Y+ D+ G ++AE ++K + KGN ++ G P +A++ R G + L Sbjct: 121 LILNADVDAYISFDNEKVGEMQAEGILK-VKNKGNFFLLGGSPTDNNAKMFR-EGQMKAL 178 Query: 175 A---RNKDVKVLARK-TGNWSRAESMALMENWLTAHPGQIKGVLAQNDDEALGALQAIKA 230 D+K++ ++ W+ E+++++EN LTA+ +I ++A ND A GA+QA+ A Sbjct: 179 KPYIDKGDIKIVGQQWVKEWNPTEALSIVENALTANNNKIDAIVASNDGTAGGAIQALAA 238 Query: 231 KGIDPKTIPVVGIDGIADAIAAVKR 255 + + K +PV G D AD +AAVKR Sbjct: 239 QKLAGK-VPVSGQD--AD-LAAVKR 259 >gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 316 Score = 73.9 bits (180), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 81/248 (32%), Positives = 119/248 (47%), Gaps = 9/248 (3%) Query: 22 NKPLR-IGAAVYGLKGEFMQMWSNQLKAHPAVQDGSVQVTVFDGNYDALTQSNQFDTMIL 80 +KPL+ +G V L F + ++ + +VTV YD TQ Q + I Sbjct: 26 DKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPDAKVTVVSSKYDLNTQVGQIENFIA 85 Query: 81 QKYDAIIFVPIDLKAGAAPVQKAVKAGIPVIGSNTRVQGDVLTSYVGNDDVVAGRLEAEA 140 K D I+ D K V+KA KAGI V+ + G +T V +D+ +AG + Sbjct: 86 NKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDVAAAGADVT--VMSDNTMAGAESCKF 143 Query: 141 LMKAIGGKGNIVMIEGPIGQSAQIERARGNDEVLARNKDVKVLA-RKTGNWSRAESMALM 199 L + + GKGN+V++ GP SA ++R G ++ +K+L+ + SR M M Sbjct: 144 LAEKLQGKGNVVIVNGP-PVSAVMDRVTGCKAEFKKSPGIKILSDNQNAGGSRDGGMTTM 202 Query: 200 ENWLTAHPGQIKGVLAQNDDEALGALQAIK-AKGIDPKTIPVVGIDGIADAIAAVKRGEM 258 N L A P +I V A ND A+GA AI+ AK D K I G+DG DA A+K + Sbjct: 203 SNLLAAQP-KIDAVFAINDPTAIGAELAIRQAKRSDIKWIS--GVDGAPDAERALKDSKS 259 Query: 259 VTQFQDAQ 266 + AQ Sbjct: 260 LFAASPAQ 267 >gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 72.0 bits (175), Expect = 7e-14, Method: Compositional matrix adjust. Identities = 71/234 (30%), Positives = 113/234 (48%), Gaps = 16/234 (6%) Query: 67 DALTQSNQFDTMILQKYDAIIFVPIDLKAGAAPVQKAVKAGIPVIGSNTRVQGDVLTS-- 124 D Q + MI+ K +A++ P D KA V+KA+ AGI V+ + ++ L Sbjct: 75 DTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVNIDNKLDDAALKEKG 134 Query: 125 ----YVGNDDVVAGRLEAEALMKAIGGKGNIVMIEGPIGQSAQIERARGNDEVLARNKDV 180 +VG D+ +L + L K + + +IEG +R G + + KDV Sbjct: 135 ITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQRTLGFQDAM---KDV 191 Query: 181 --KVLARKTGNWSRAESMALMENWLTAHPGQIKGVLAQNDDEALGALQAIKAKGIDPKTI 238 V+ ++G W + + + L AHP IK +LA ND+ ALGA+ AI+A G K + Sbjct: 192 GANVVTVQSGQWEIDQGNKVAASILNAHP-DIKAILAGNDNMALGAVAAIRAAGKTGK-V 249 Query: 239 PVVGIDGIADAIAAVKRGE-MVTQFQDAQAQAQGALDVALRAIKGPSYQPRSTI 291 +VG D I +K G + T Q AQ QA ++ AL+A+ +P+S + Sbjct: 250 QLVGYDNINAIKPMLKDGRVLATVDQFAQQQAVFGIETALKAL--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 0.315 0.132 0.377 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: 919,127 Number of extensions: 35113 Number of successful extensions: 157 Number of sequences better than 1.0e-08: 9 Number of HSP's gapped: 152 Number of HSP's successfully gapped: 9 Length of query: 330 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 244 Effective length of database: 1,212,660 Effective search space: 295889040 Effective search space used: 295889040 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)