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= 0001.0856.p (307 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasm... 541 e-155 gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasm... 119 2e-28 gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasm... 74 1e-14 gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter peripl... 72 4e-14 gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasm... 64 1e-11 >gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 302 Score = 541 bits (1393), Expect = e-155, Method: Compositional matrix adjust. Identities = 276/283 (97%), Positives = 281/283 (99%) Query: 25 AQELSKLKIGMSFQEMNNPYFVSMKKALDDAAKTFGAKVIVTDAAHNVAKQIADIEDMLQ 84 AQE+SKLKIGMSFQEMNNPYFVSMKKALD+AAK+ GAKVI TDAAHNVAKQIADIEDMLQ Sbjct: 20 AQEVSKLKIGMSFQEMNNPYFVSMKKALDEAAKSLGAKVIATDAAHNVAKQIADIEDMLQ 79 Query: 85 QNIDILLINPTDSAGVEAAVKSAKARNVIVVAVDANASGPVDMFVGSKNKDAGYQSCRAL 144 QNIDILLINPTDSAGVEAAVK+AKARNVIVVAVDANASGPVDMFVGSKNKDAGYQSCRAL Sbjct: 80 QNIDILLINPTDSAGVEAAVKAAKARNVIVVAVDANASGPVDMFVGSKNKDAGYQSCRAL 139 Query: 145 ADAIGGKGEVAILDGIPVVPILQRVEGCKQALAEYKDIKLVATQNGRQDRSVALGVVENM 204 ADAIGGKGEVAILDGIPVVPILQRVEGCKQALAEYKDIKLVATQNGRQDRSVALGVVENM Sbjct: 140 ADAIGGKGEVAILDGIPVVPILQRVEGCKQALAEYKDIKLVATQNGRQDRSVALGVVENM 199 Query: 205 IQSRPNLKGIFSVNDGGAMGALAAIQGSGKDIKLTSVDGAPEAIKAIADGGPFVETTAQF 264 IQSRPNLKGIFSVNDGGAMGALAAIQGSGKDIKLTSVDGAPEA+KAIADGGPFVETTAQF Sbjct: 200 IQSRPNLKGIFSVNDGGAMGALAAIQGSGKDIKLTSVDGAPEAVKAIADGGPFVETTAQF 259 Query: 265 PRDQVRVGLAMALAKKWGARVVPKEVPIDVMPVTKKNAAGFSW 307 PRDQVRVGLAMALAKKWGARVVPKEVPIDVMPVTKKNAAGFSW Sbjct: 260 PRDQVRVGLAMALAKKWGARVVPKEVPIDVMPVTKKNAAGFSW 302 >gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 316 Score = 119 bits (299), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 92/286 (32%), Positives = 157/286 (54%), Gaps = 16/286 (5%) Query: 33 IGMSFQEMNNPYFVSMKKALDDAAKTFG--AKVIVTDAAHNVAKQIADIEDMLQQNIDIL 90 +G++ ++ NP+FV++ K + A AKV V + +++ Q+ IE+ + +D++ Sbjct: 32 VGVTVGDLANPFFVAIAKGAESGAHKINPDAKVTVVSSKYDLNTQVGQIENFIANKVDLI 91 Query: 91 LINPTDSAGVEAAVKSAKARNVIVVAVDANASGPVDMFVGSKNKDAGYQSCRALADAIGG 150 ++N DS GV AVK A+ + IVV A+ D+ V S N AG +SC+ LA+ + G Sbjct: 92 VLNAADSKGVGPAVKKAQ-KAGIVVVAVDVAAAGADVTVMSDNTMAGAESCKFLAEKLQG 150 Query: 151 KGEVAILDGIPVVPILQRVEGCKQALAEYKDIKLVA-TQNGRQDRSVALGVVENMIQSRP 209 KG V I++G PV ++ RV GCK + IK+++ QN R + + N++ ++P Sbjct: 151 KGNVVIVNGPPVSAVMDRVTGCKAEFKKSPGIKILSDNQNAGGSRDGGMTTMSNLLAAQP 210 Query: 210 NLKGIFSVNDGGAMGALAAI-QGSGKDIK-LTSVDGAPEAIKAIADGGP-FVETTAQFPR 266 + +F++ND A+GA AI Q DIK ++ VDGAP+A +A+ D F + AQ P Sbjct: 211 KIDAVFAINDPTAIGAELAIRQAKRSDIKWISGVDGAPDAERALKDSKSLFAASPAQDPY 270 Query: 267 ----DQVRVGLAMALAKKWGARVVPKEVPIDVMPVTKKNAAGFS-W 307 + V +G A+ + +V K +P+ + +T+ N A + W Sbjct: 271 GMAAESVAIGYAVMNGRAPQQKV--KLLPVKL--ITRDNVADYQGW 312 >gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 73.9 bits (180), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 77/292 (26%), Positives = 134/292 (45%), Gaps = 24/292 (8%) Query: 2 KKALTVLALTTATLATLTAAPAGAQELSKLKIGMSFQEMNNPYFVSMKKALDDAAKTFGA 61 ++ + AL A L A AQ +K K+ + + + N +F++M+ + K + Sbjct: 6 RRHFAIAALACAVLP----GAAMAQTPAKPKVALVMKSLANEFFLNMENGAREYQKANAS 61 Query: 62 KV-IVTDA---AHNVAKQIADIEDMLQQNIDILLINPTDSAGVEAAVKSAKARNVIVVAV 117 K ++ + + A QI +E M+ ++ L+I P DS + VK A +IVV + Sbjct: 62 KFDLIANGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVNI 121 Query: 118 D-------ANASGPVDMFVGSKNKDAGYQSCRALADAIGGKGEVAILDGIPVV-PILQRV 169 D G FVG N+ + L + +VAI++G+ QR Sbjct: 122 DNKLDDAALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQRT 181 Query: 170 EGCKQALAEYKDI--KLVATQNGRQDRSVALGVVENMIQSRPNLKGIFSVNDGGAMGALA 227 G + A+ KD+ +V Q+G+ + V +++ + P++K I + ND A+GA+A Sbjct: 182 LGFQDAM---KDVGANVVTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVA 238 Query: 228 AIQGSGK--DIKLTSVDGAPEAIKAIADGGPFVETTAQFPRDQVRVGLAMAL 277 AI+ +GK ++L D AIK + G + T QF + Q G+ AL Sbjct: 239 AIRAAGKTGKVQLVGYDNI-NAIKPMLKDGRVLATVDQFAQQQAVFGIETAL 289 >gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 72.4 bits (176), Expect = 4e-14, Method: Compositional matrix adjust. Identities = 77/261 (29%), Positives = 129/261 (49%), Gaps = 17/261 (6%) Query: 6 TVLALTTATLATLTAAPAGAQELSKLKIGMSFQEMNNPYFVSMKKALDDAAKTFGAKVIV 65 TVLAL T T ++ A A A + KIG S ++ + + AA+ GAKV V Sbjct: 8 TVLALMTVTTLSMVAGSAMA-DAKNPKIGFSIDDLRVERWARDRDFFTAAAEKLGAKVYV 66 Query: 66 TDAAHNVAKQIADIEDMLQQNIDILLINPTDSAGVEAAVKSAKARNVIVVAVDA---NAS 122 A + +QI+ IE+++ + +D+++I P ++ + +K AK + V++ D NA Sbjct: 67 QSADASEQRQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDRLILNAD 126 Query: 123 GPVDMFVGSKNKDAGYQSCRALADAIGGKGEVAILDGIPVVPILQRV-EGCKQALAEY-- 179 VD ++ N+ G + + KG +L G P + EG +AL Y Sbjct: 127 --VDAYISFDNEKVGEMQAEGIL-KVKNKGNFFLLGGSPTDNNAKMFREGQMKALKPYID 183 Query: 180 -KDIKLVATQNGRQ-DRSVALGVVENMIQSRPN-LKGIFSVND---GGAMGALAAIQGSG 233 DIK+V Q ++ + + AL +VEN + + N + I + ND GGA+ ALAA + +G Sbjct: 184 KGDIKIVGQQWVKEWNPTEALSIVENALTANNNKIDAIVASNDGTAGGAIQALAAQKLAG 243 Query: 234 KDIKLTSVDGAPEAIKAIADG 254 K + ++ D A+K + G Sbjct: 244 K-VPVSGQDADLAAVKRVVAG 263 >gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 64.3 bits (155), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 63/267 (23%), Positives = 126/267 (47%), Gaps = 15/267 (5%) Query: 2 KKALTVLALTTATLATLTAAPAGAQELSKLKIGMSFQEMNNPYFVSMKKALDDAAKTFGA 61 ++AL A+ + ++ + PA A + L +G S + + + ++ DAAK G Sbjct: 5 RRALLGAAICLSLGSSAMSLPAFAAD-KPLTMGFSQVGAESEWRTANTVSIKDAAKQAGV 63 Query: 62 KVIVTDAAHNVAKQIADIEDMLQQNIDILLINPTDSAGVEAAVKSAKARNVIVV----AV 117 + DA Q+ I + Q +D++ +P +G E ++ AKA + V+ AV Sbjct: 64 NLKFADAQQKQENQVKAIRSFIAQKVDVIAFSPVVESGWETVLREAKAAKIPVILTDRAV 123 Query: 118 DANASGPVDMFVGSKNKDAGYQSCRALADAIGG--KGEVAILD---GIPVVPILQRVEGC 172 + + F+GS + G ++ R L + G++ I++ + P + R G Sbjct: 124 NVSDKSLYVTFIGSDFVEEGRRAGRWLLEKAKSMPAGDINIVELQGTVGSAPAIDRKAGF 183 Query: 173 KQALAEYKDIKLVATQNGRQDRSVALGVVENMIQSR-PNLKGIFSVNDGGAMGALAAIQG 231 ++ + +K++ +Q G R+ V+E +++ + +++ ND A+GA+ AI+ Sbjct: 184 EEVIKGEPRLKIIRSQTGDFTRAKGKEVMEAFLKAEGKKINVLYAHNDDMAIGAIQAIEE 243 Query: 232 S----GKDIKLTSVDGAPEAIKAIADG 254 + GKDI + S+DG A +A+ G Sbjct: 244 AGMKPGKDIIIISIDGVKGAFEAMMAG 270 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 0.363 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: 870,470 Number of extensions: 37060 Number of successful extensions: 165 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 156 Number of HSP's successfully gapped: 8 Length of query: 307 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 222 Effective length of database: 1,217,395 Effective search space: 270261690 Effective search space used: 270261690 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: 130 (54.7 bits)