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= 0028.0161.p (499 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter perip... 209 6e-55 gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter perip... 116 5e-27 gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter perip... 99 7e-22 gi|300310463|ref|YP_003774555.1| dipeptide ABC transporter perip... 91 2e-19 gi|300310860|ref|YP_003774952.1| dipeptide ABC transporter perip... 77 3e-15 >gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 523 Score = 209 bits (531), Expect = 6e-55, Method: Compositional matrix adjust. Identities = 140/469 (29%), Positives = 245/469 (52%), Gaps = 18/469 (3%) Query: 41 LDPTQSSMLNERIVYQSIFDKLVDLDGEGKIIPMLAERWTVSEDQKIYTLYLRKGVKFQD 100 LDP ++ + +S + L D + K+IP+LAE + VS+D YT+ L++GVKFQD Sbjct: 49 LDPYDANDTLSLSMAKSFYQGLFGFDKDMKLIPVLAEGYLVSKDGLEYTIRLKQGVKFQD 108 Query: 101 GTPFDAKAVE--FNLLRGQEKTSLRRNELKYVSKITVVDEHTIKLDLSTPFAPFLSILTD 158 GT F A AV+ F+ + + R N ++K +++++T+K+ L PF+ F+++L Sbjct: 109 GTVFKADAVKAVFDRVTNPDNKLKRYNLFNRIAKTEILNDYTVKVVLKEPFSAFINVLAH 168 Query: 159 RAGMMSSPAAVKKYG-EDYVNHPVGTGPFVYEGRLKGATITLKKNPDYWRAGLPKVDEVV 217 + +M SP A+K+YG +D HPVGTGPF + + + + K YW+ G PKVDE++ Sbjct: 169 PSAVMISPTALKQYGNKDIAFHPVGTGPFKFVEWKQTDYVKVAKFDGYWKPGYPKVDEII 228 Query: 218 YKIMPDVNVAFNNLRSGQVDISNRFPYKEITNVPANASYTVLNKPSLGFRGFYMNTGKPP 277 +K + D N +++G+ + PY++ + + ++ V+ PS+ R MNT + P Sbjct: 229 WKPVVDNNARSAMMQTGEAQFTYPLPYEQADLLKSKSNLDVVAAPSIIQRYMSMNTKQKP 288 Query: 278 FDKKEVREAVDILIDRNAIAKVVYNN-AVAAGHSPFSKAQFANGPSDVPPKVDVARAKAL 336 FD +VREA++ I++ A+ KV +N AV +A P DV +AKAL Sbjct: 289 FDNPKVREAINYAINKQALVKVAFNGYAVPMDGVVPQGVDYAYKTGPWP--YDVKKAKAL 346 Query: 337 LKAAGKENGFSFKL-TLPTTPDELQVGQMIQGMLRPAGITVTLEKTELATQIEAGK---- 391 L AG NGF +L + T +++ Q +Q L GI ++ E ++E + Sbjct: 347 LAEAGYPNGFETELWSAYTHSTAVKIVQFLQQQLAQVGIKAKIQALEAGQRVERVESWQD 406 Query: 392 --TGNFEGLFVGWSGRS-DPDQNIYDFVTTNGS----LNYSHFGAKEVDDLLQQARVEGD 444 T L++GWS + + D + + + N +++ +VD + +A + Sbjct: 407 PATAPVRLLYIGWSSSTGEADWALRPLLASESFPPRLYNTAYYKNDKVDADIAKALTLTE 466 Query: 445 QGKRKALYDQAMAILVKEVPYVYTVHDNVLFGIAKSVKGFQYVPDGVIR 493 + ++ALY A + K+ P+ + V + +L+ K++KG +PD I Sbjct: 467 RKDKEALYKDAQQEIWKDAPWAFLVTEKLLYARNKNLKGVYVMPDQAIE 515 >gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 528 Score = 116 bits (290), Expect = 5e-27, Method: Compositional matrix adjust. Identities = 127/491 (25%), Positives = 201/491 (40%), Gaps = 50/491 (10%) Query: 30 LNISLDADP-GKLDPTQSSMLNERIVYQSIFDKLVDLDGEGKIIPMLAERWTVSEDQKIY 88 LNI+ ADP LDP ++ +R V +D LV D K++P LA W + D K + Sbjct: 31 LNIAF-ADPLSSLDPQLNNHAGDRSVDLHFWDLLVQND-YNKLVPGLAVSWK-NIDPKTW 87 Query: 89 TLYLRKGVKFQDGTPFDAKAVEFNLLRGQE---KTSLRRNELKYVSKITVVDEHTIKLDL 145 LR VK+QDG PF A V F+ R + + L+ V +T D T+ + Sbjct: 88 EFKLRPNVKWQDGKPFTADDVIFSYQRARAVPGSVATFAGYLRTVESVTAKDPLTLVIKT 147 Query: 146 STPFAPFLSILTDRAGMMSSPAAVKKYGEDYVNHP--VGTGPFVYEGRLKGATITLKKNP 203 + P P L + ++S K E+Y + +GTGP+ + G + +++N Sbjct: 148 NIP-NPDLPLNLASVHIVSKHIGEKSTTENYNSGAAVIGTGPYKFVSYTPGDRVVMQRND 206 Query: 204 DYWRAGLPKVDEVVYKIMPDVNVAFNNLRSGQVDISNRFPYKEITNV---------PANA 254 DYW G P ++V Y+ + + L SG VD+ ++ ++ + P N Sbjct: 207 DYWN-GKPLWEKVNYRYINNGAARTAALLSGDVDVIDKVSVSDLAKLKQSPNVKVYPYNG 265 Query: 255 SYTVLNKPSL--GFRGFYMNTGKPPFDKK-----EVREAVDILIDRNAIAKVVYNNAVAA 307 +L +PS G F + DK VR A+ + I+R A+ + A Sbjct: 266 LRVLLIQPSFHQGPSPFITDNNGKQLDKNPLLDVRVRRAMSLAINRKALIDRILQGAATE 325 Query: 308 GHSPFSKAQFANGPSDVPPKVDVARAKALLKAAGKENGFSFKLTLPTT--PDELQVGQMI 365 + F P D A+AK LL AG +GF + +P P + Q + Sbjct: 326 ANQWMPADTFGYNPEIKNIPFDAAQAKKLLADAGFPDGFKLTIHVPNDRYPQAPETMQAV 385 Query: 366 QGMLRPAGITVTLE------------KTELATQIEAGKTGNFEGLF--VGWSGRSDPDQN 411 GI +E K E A + A G E + V G DP + Sbjct: 386 AQFWTRIGIKTQVEVLPWAAYSSRANKNEFAVSVLAWGNGTGEASYALVNVLGSVDPKKG 445 Query: 412 IYDFVTTNGSLNYSHFGAKEVDDLLQQARVEGDQGKRKALYDQAMAILVKEVPYVYTVHD 471 I G+ N++H+ + VD L + E D KR+A+ A + +EV + H Sbjct: 446 I-------GASNWNHYSSPAVDKALADSTAEFDAAKREAILRGAAKTVSEEVGVIPLYHY 498 Query: 472 NVLFGIAKSVK 482 ++ K +K Sbjct: 499 QNIWAAKKGLK 509 >gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 512 Score = 99.4 bits (246), Expect = 7e-22, Method: Compositional matrix adjust. Identities = 127/484 (26%), Positives = 203/484 (41%), Gaps = 32/484 (6%) Query: 29 TLNISLDADPGKLDPTQSSMLNERIVYQSIFDKLVDLDGE-GKIIPMLAERWTVSEDQKI 87 TL + D++ + +++ I+ I+D L+ D + + P LA W E Sbjct: 35 TLVYASDSEVENISQYHNNLREGVILAHLIWDTLIYRDPKTNEYKPQLATAWKW-ESPTA 93 Query: 88 YTLYLRKGVKFQDGTPFDAKAV--EFNLLRGQEKTSLRRNELKYVSKITVVDEHTIKLDL 145 L LR+GV+FQ+G F A V FN E ++ R ++ + + ++ ++++L Sbjct: 94 LVLDLRQGVQFQNGDKFSADDVVFTFNYAVSPESKAVTRQNTDWIKSVDKLADYKVRINL 153 Query: 146 STPFAPFLSILTDRAGMMS-SPAA-VKKYG-EDYVNHPVGTGPFVYEGRLKGATITLKKN 202 PF L L AG + PAA KK G E + P+GTGP+ G +TL KN Sbjct: 154 KGPFPAALEYL---AGPLPIYPAAYFKKVGLEGFSKAPIGTGPYKVTSVTPGQGVTLVKN 210 Query: 203 PDYWR---AGLPKVDEVVYKIMPDVNVAFNNLRSGQVDISNRFPYKEITNVPANASYTVL 259 P Y++ G P + + + ++PD L +G +D R P + ++ N V Sbjct: 211 PGYFKDSPQGQPTIGNIKFVVIPDPETRAAQLMTGAIDWIWRVPPDQADSLKTNPKLAVQ 270 Query: 260 NKPSLGFRGFYMNTG-----KPPFDKKEVREAVDILIDRNAIAKVVYNNAVAAGHSPFSK 314 + ++ ++T PF VR+AV+ I+R A +N + G P Sbjct: 271 SGETMRIGFITLDTTGTSAPNSPFKDVRVRQAVNHAINRKGYA----DNLMRGGSQPVYT 326 Query: 315 AQFAN---GPSDVPPKVDV--ARAKALLKAAGKENGFSFKLTLPTTPDELQVGQMIQGML 369 A F S+ K D A+AK LL AAG NGF + E ++ + I G L Sbjct: 327 ACFRTQFGCDSNAAIKYDYNPAKAKELLAAAGYPNGFDTDI---YAYREREIAEAIIGDL 383 Query: 370 RPAGITVTLEKTELATQIEAGKTGNFEGLFVGWSGRSDPDQNIYDFVTTNGSLNYSHFGA 429 R GI L + A ++G F W S D + + V G + Sbjct: 384 RKVGIRARLHYMKFAALQTEYRSGKTPMSFYSWGSFSMNDTSAFAGVYFKGGAD-DITKD 442 Query: 430 KEVDDLLQQARVEGDQGKRKALYDQAMAILVKEVPYVYTVHDNVLFGIAKSVKGFQYVPD 489 ++ LQ A D RKA Y +A ++ K+ YV + + + FQ PD Sbjct: 443 PQLQQYLQTADTSIDPAVRKANYSKAQELISKQA-YVAPMFSYSTYYAYNAQLNFQGYPD 501 Query: 490 GVIR 493 + R Sbjct: 502 ELPR 505 >gi|300310463|ref|YP_003774555.1| dipeptide ABC transporter periplasmic peptide-binding protein [Herbaspirillum seropedicae SmR1] Length = 540 Score = 90.9 bits (224), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 113/472 (23%), Positives = 189/472 (40%), Gaps = 31/472 (6%) Query: 41 LDPTQSSMLNERIVYQSIFDKLVDLDGEGKIIPMLAERWTVSEDQKIYTLYLRKGVKFQD 100 LDP +++ + ++ L LDG+ +LAE ++ D +T+ LRKGV F D Sbjct: 81 LDPAKTAHSTDYTRVHMFYNGLTKLDGKLGPQMVLAEE-MLTNDAVTWTVKLRKGVNFHD 139 Query: 101 GTPFDAKAVEFNLLRGQE-----KTSLRRNELKYVSKITVVDEHTIKLDLSTPFAPFLSI 155 G P V ++++R ++ K + ++ + V K T +E IKL + P + Sbjct: 140 GKPLTPADVVYSIMRHKDPATASKVKVVADQFESV-KATGPNEVQIKLTSANADLPVI-- 196 Query: 156 LTDRAGMMSSPAAVKKYGEDYVNHPVGTGPFVYEGRLKGATITLKKNPDYWRAGLPKVDE 215 + ++ + + G + P GTG F + G +N +YW+ GLP +DE Sbjct: 197 ------LATAQFLIIRDGTTNFSTPNGTGAFKLKEFTPGVRTIGVRNENYWKPGLPYLDE 250 Query: 216 VVYKIMPDVNVAFNNLRSGQVDISNRFPYKEITNVPANASYTVLNKPSLGFRGFYMNTGK 275 V +PD N L SG V N + V YTV+ S + M Sbjct: 251 VELFGIPDEAARVNALLSGDVHWINDVNSRSTGRVKNTPGYTVMETKSGQYTDLVMRQDV 310 Query: 276 PPFDKKEVREAVDILIDRNAIAKVVYNN-AVAAGHSPF---SKAQFANGPSDVPPKVDVA 331 P + + + L+DR I + AV A P ++ FA P D Sbjct: 311 APGNSMDFTLGMKYLLDREQIKMAAFRGYAVIANDQPIDPTNRFYFAGLPQR---PYDPD 367 Query: 332 RAKALLKAAGKENGFSFKLTLPTTPDELQVGQM-IQGMLRPAGITVTLEKTELATQIEAG 390 +AK L AG T+P G + + +++ + + L+ + Sbjct: 368 KAKFHLGKAG-----VLGSTIPIVASVAATGSVDMAVLMQQSAAKIGLKLDVKRVPADGY 422 Query: 391 KTGNFEGLFVGWSG---RSDPDQNIYDFVTTNGSLNYSHFGAKEVDDLLQQARVEGDQGK 447 + + + VG+ R D + F ++ N S + + D L+ AR E D K Sbjct: 423 WSNQWMKVPVGFGNINPRPSADILLTQFFKSDAQWNESGWKNPQFDQLVVAARGETDFTK 482 Query: 448 RKALYDQAMAILVKEVPYVYTVHDNVLFGIAKSVKGFQYVPDGVIRTATVSK 499 RKA+Y ++ ++ V L GI+ VKG VP G T ++ Sbjct: 483 RKAMYADLQTMIHEKCGLGIPVFIINLEGISTKVKGIDPVPLGAFMNYTCAE 534 >gi|300310860|ref|YP_003774952.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 77.0 bits (188), Expect = 3e-15, Method: Compositional matrix adjust. Identities = 107/481 (22%), Positives = 205/481 (42%), Gaps = 50/481 (10%) Query: 41 LDPTQSSMLNERIVYQSIFDKLVDLDGEGKIIPMLAERWTVSEDQKIYTLYLRKGVKFQD 100 LDPT+S + R+ + + L+++D G++ P +A W+VS D + LR G+++ D Sbjct: 66 LDPTRSGYMFARM---EVLETLLEVDDAGQLQPSVASAWSVSADGLQWRFVLRSGLRYHD 122 Query: 101 GTPFDAKAVEFNLLRGQEKTSLRRNELKYVSKITVVDEHTIKLDLSTPFAPFLSILTDRA 160 G+ ++ L R Q + + R L ++ + V+ T+ + L PF P +LT Sbjct: 123 GSALTPASILACLQRAQARPGVLR--LADIAALR-VEGQTLVVVLRRPFGPLPYLLTHYT 179 Query: 161 GMMSSPAAVKKYGEDYVNHPVGTGPFVYEGRLKGATITLKKNPDYWRAGLPK-------- 212 + +PA+ G V +G+GPF R++ +I L + + R Sbjct: 180 TQILAPASFDAQGN--VVAIIGSGPF----RIR--SIALPQQFEVERVAGSVSGSGAGSD 231 Query: 213 VDEVVYKIMPDVNVAFNNLR-----SGQVDISNRFPYKEITNVPANASYTVLNKPSLGFR 267 V +VV + ++V+ R SGQ D++ I + + ++L+ Sbjct: 232 VGKVVQRAR-YISVSRAETRTLLVQSGQADLAFSLDPPSIRALQDSPRASLLSAMLPRTT 290 Query: 268 GFYMNTGKPPFDKKEVREAVDILIDRNAIAKVVYNNA--VAAGHSPFSKAQFANGPSDVP 325 +N G P VR A+ + I+R IA+ + + A P S A++ + + P Sbjct: 291 LLKLNAGHPLLADVRVRRAISLCIEREGIARALLRDPDLGATQLFPPSLARWHDA-ALAP 349 Query: 326 PKVDVARAKALLKAAG---------KENGFSFKLTLPT---TPDELQVGQMIQGMLRPAG 373 + ++ +A++LL AG + +G L L T P+ + +Q +R G Sbjct: 350 LRTNLQQARSLLDQAGWRPGSDGVRRRDGQRMALNLTTFVDRPELPLIATALQEEMRQIG 409 Query: 374 ITVTLEKTELATQIEAG-KTGNFEGLFVGWSGRSDPD---QNIYDFVTTNGSLNYSHFGA 429 + V + ++ I AG ++G + + + PD + DF G + Sbjct: 410 MAVRVVIGN-SSDIPAGHRSGQLQMALAARNYGNLPDPVASLLQDFGPQGGDWGAMGWDN 468 Query: 430 KEVDDLLQQARVEGDQGKRKALYDQA--MAILVKEVPYVYTVHDNVLFGIAKSVKGFQYV 487 +EV LL + K ++A +A+L +++P + V +++ V+G Sbjct: 469 QEVPALLARLAATPADAAAKGNAERARIVALLQEQLPVIPVVWYRQTCAVSRRVRGASID 528 Query: 488 P 488 P Sbjct: 529 P 529 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 0.135 0.389 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: 1,511,007 Number of extensions: 63305 Number of successful extensions: 178 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 165 Number of HSP's successfully gapped: 6 Length of query: 499 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 410 Effective length of database: 1,198,455 Effective search space: 491366550 Effective search space used: 491366550 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: 132 (55.5 bits)