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= 0001.1711.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... 213 2e-56 gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter perip... 111 1e-25 gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter perip... 99 8e-22 gi|300310463|ref|YP_003774555.1| dipeptide ABC transporter perip... 94 2e-20 gi|300310860|ref|YP_003774952.1| dipeptide ABC transporter perip... 72 7e-14 >gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 523 Score = 213 bits (543), Expect = 2e-56, Method: Compositional matrix adjust. Identities = 149/501 (29%), Positives = 259/501 (51%), Gaps = 20/501 (3%) Query: 10 LCAMSSTVLAACSLPTLAVTLNISLDADPGKLDPTQSSMLNERILYQSIFDKLVDLDGEG 69 + A+ +T+ A + A T+ +++ + LDP ++ + +S + L D + Sbjct: 18 VAALGTTLQFAAAHAFAAKTVTLAVYSTFTTLDPYDANDTLSLSMAKSFYQGLFGFDKDM 77 Query: 70 KIVPMLAERWTVSDDQKTYTLYLRKGVKFQDGTPFDAKAVE--FNLLRGQEKTSLRRNEL 127 K++P+LAE + VS D YT+ L++GVKFQDGT F A AV+ F+ + + R N Sbjct: 78 KLIPVLAEGYLVSKDGLEYTIRLKQGVKFQDGTVFKADAVKAVFDRVTNPDNKLKRYNLF 137 Query: 128 KYVSKITVVDDHTIKLDLSTPFAPFLSILTDRAGMMSSPTAVKKYG-EDYVNHPVGTGPF 186 ++K +++D+T+K+ L PF+ F+++L + +M SPTA+K+YG +D HPVGTGPF Sbjct: 138 NRIAKTEILNDYTVKVVLKEPFSAFINVLAHPSAVMISPTALKQYGNKDIAFHPVGTGPF 197 Query: 187 IYEGRLKGATLTLKKNPDYWRAGLPKVDEVVYKIMPDVNVAFNNLRSGQVDISNRFPYKE 246 + + + + K YW+ G PKVDE+++K + D N +++G+ + PY++ Sbjct: 198 KFVEWKQTDYVKVAKFDGYWKPGYPKVDEIIWKPVVDNNARSAMMQTGEAQFTYPLPYEQ 257 Query: 247 ITNVPANANYTVLNKPSLGFRGFYLNTTKPPFDKKEVREAVDILIDRNAIAKVVYNNAVA 306 + + +N V+ PS+ R +NT + PFD +VREA++ I++ A+ KV +N Sbjct: 258 ADLLKSKSNLDVVAAPSIIQRYMSMNTKQKPFDNPKVREAINYAINKQALVKVAFNGYAV 317 Query: 307 P--GHSPFSKAQFANGPGDVPPKVDVARAKALLKAAGKEGGFSFKL-TLPTTADELQAGQ 363 P G P +A G P DV +AKALL AG GF +L + T + ++ Q Sbjct: 318 PMDGVVP-QGVDYAYKTGPWP--YDVKKAKALLAEAGYPNGFETELWSAYTHSTAVKIVQ 374 Query: 364 MIQGMLRPAGITVTLEKTEIASQVEAGK------TGAFEGLFLGWSGRP-DPDQNIFDFV 416 +Q L GI ++ E +VE + T L++GWS + D + + Sbjct: 375 FLQQQLAQVGIKAKIQALEAGQRVERVESWQDPATAPVRLLYIGWSSSTGEADWALRPLL 434 Query: 417 NSGGS----MNYSHIAAKEVDDLLQQARVEGDQAKRKVLYDQAMAILVKEVPYIYLVHDN 472 S N ++ +VD + +A ++ ++ LY A + K+ P+ +LV + Sbjct: 435 ASESFPPRLYNTAYYKNDKVDADIAKALTLTERKDKEALYKDAQQEIWKDAPWAFLVTEK 494 Query: 473 VLFGIAKSVKGFQYVPDGVIR 493 +L+ K++KG +PD I Sbjct: 495 LLYARNKNLKGVYVMPDQAIE 515 >gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 528 Score = 111 bits (277), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 131/493 (26%), Positives = 203/493 (41%), Gaps = 54/493 (10%) Query: 30 LNISLDADP-GKLDPTQSSMLNERILYQSIFDKLVDLDGEGKIVPMLAERWTVSDDQKTY 88 LNI+ ADP LDP ++ +R + +D LV D K+VP LA W + D KT+ Sbjct: 31 LNIAF-ADPLSSLDPQLNNHAGDRSVDLHFWDLLVQND-YNKLVPGLAVSWK-NIDPKTW 87 Query: 89 TLYLRKGVKFQDGTPFDAKAVEFNLLRGQE---KTSLRRNELKYVSKITVVDDHTIKLDL 145 LR VK+QDG PF A V F+ R + + L+ V +T D T+ + Sbjct: 88 EFKLRPNVKWQDGKPFTADDVIFSYQRARAVPGSVATFAGYLRTVESVTAKDPLTLVIKT 147 Query: 146 STPFAPFLSILTDRAGMMSSPTAVKKYGEDYVNHP--VGTGPFIYEGRLKGATLTLKKNP 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 NYTVLNKPSL--GFRGFYLNTTKPPFDKK-----EVREAVDILIDRNAIAKVVYNNAVAP 307 +L +PS G F + DK VR A+ + I+R A+ + A Sbjct: 266 LRVLLIQPSFHQGPSPFITDNNGKQLDKNPLLDVRVRRAMSLAINRKALIDRILQGAATE 325 Query: 308 GHSPFSKAQFANGPGDVPPKVDVARAKALLKAAGKEGGFSFKLTLPTTADEL-QAGQMIQ 366 + F P D A+AK LL AG GF KLT+ D QA + +Q Sbjct: 326 ANQWMPADTFGYNPEIKNIPFDAAQAKKLLADAGFPDGF--KLTIHVPNDRYPQAPETMQ 383 Query: 367 GMLR---PAGITVTLEKTEIASQVEAGKTGAFEGLFLGWS--------------GRPDPD 409 + + GI +E A+ F L W G DP Sbjct: 384 AVAQFWTRIGIKTQVEVLPWAAYSSRANKNEFAVSVLAWGNGTGEASYALVNVLGSVDPK 443 Query: 410 QNIFDFVNSGGSMNYSHIAAKEVDDLLQQARVEGDQAKRKVLYDQAMAILVKEVPYIYLV 469 + I G+ N++H ++ VD L + E D AKR+ + A + +EV I L Sbjct: 444 KGI-------GASNWNHYSSPAVDKALADSTAEFDAAKREAILRGAAKTVSEEVGVIPLY 496 Query: 470 HDNVLFGIAKSVK 482 H ++ K +K Sbjct: 497 HYQNIWAAKKGLK 509 >gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 512 Score = 99.0 bits (245), Expect = 8e-22, Method: Compositional matrix adjust. Identities = 122/480 (25%), Positives = 200/480 (41%), Gaps = 24/480 (5%) Query: 29 TLNISLDADPGKLDPTQSSMLNERILYQSIFDKLVDLDGE-GKIVPMLAERWTVSDDQKT 87 TL + D++ + +++ IL I+D L+ D + + P LA W + Sbjct: 35 TLVYASDSEVENISQYHNNLREGVILAHLIWDTLIYRDPKTNEYKPQLATAWKW-ESPTA 93 Query: 88 YTLYLRKGVKFQDGTPFDAKAV--EFNLLRGQEKTSLRRNELKYVSKITVVDDHTIKLDL 145 L LR+GV+FQ+G F A V FN E ++ R ++ + + D+ ++++L Sbjct: 94 LVLDLRQGVQFQNGDKFSADDVVFTFNYAVSPESKAVTRQNTDWIKSVDKLADYKVRINL 153 Query: 146 STPFAPFLSILTDRAGMMS-SPTA-VKKYG-EDYVNHPVGTGPFIYEGRLKGATLTLKKN 202 PF L L AG + P A KK G E + P+GTGP+ G +TL KN Sbjct: 154 KGPFPAALEYL---AGPLPIYPAAYFKKVGLEGFSKAPIGTGPYKVTSVTPGQGVTLVKN 210 Query: 203 PDYWR---AGLPKVDEVVYKIMPDVNVAFNNLRSGQVDISNRFPYKEITNVPANANYTVL 259 P Y++ G P + + + ++PD L +G +D R P + ++ N V Sbjct: 211 PGYFKDSPQGQPTIGNIKFVVIPDPETRAAQLMTGAIDWIWRVPPDQADSLKTNPKLAVQ 270 Query: 260 NKPSLGFRGFYLNTT-----KPPFDKKEVREAVDILIDRNAIAKVVYNNAVAPGHSPFSK 314 + ++ L+TT PF VR+AV+ I+R A + P ++ + Sbjct: 271 SGETMRIGFITLDTTGTSAPNSPFKDVRVRQAVNHAINRKGYADNLMRGGSQPVYTACFR 330 Query: 315 AQF-ANGPGDVPPKVDVARAKALLKAAGKEGGFSFKLTLPTTADELQAGQMIQGMLRPAG 373 QF + + + A+AK LL AAG GF + E + + I G LR G Sbjct: 331 TQFGCDSNAAIKYDYNPAKAKELLAAAGYPNGFDTDI---YAYREREIAEAIIGDLRKVG 387 Query: 374 ITVTLEKTEIASQVEAGKTGAFEGLFLGWSGRPDPDQNIFDFVNSGGSMNYSHIAAKEVD 433 I L + A+ ++G F W D + F V G + ++ Sbjct: 388 IRARLHYMKFAALQTEYRSGKTPMSFYSWGSFSMNDTSAFAGVYFKGGAD-DITKDPQLQ 446 Query: 434 DLLQQARVEGDQAKRKVLYDQAMAILVKEVPYIYLVHDNVLFGIAKSVKGFQYVPDGVIR 493 LQ A D A RK Y +A ++ K+ Y+ + + + FQ PD + R Sbjct: 447 QYLQTADTSIDPAVRKANYSKAQELISKQA-YVAPMFSYSTYYAYNAQLNFQGYPDELPR 505 >gi|300310463|ref|YP_003774555.1| dipeptide ABC transporter periplasmic peptide-binding protein [Herbaspirillum seropedicae SmR1] Length = 540 Score = 94.4 bits (233), Expect = 2e-20, Method: Compositional matrix adjust. Identities = 113/470 (24%), Positives = 185/470 (39%), Gaps = 27/470 (5%) Query: 41 LDPTQSSMLNERILYQSIFDKLVDLDGEGKIVPMLAERWTVSDDQKTYTLYLRKGVKFQD 100 LDP +++ + ++ L LDG+ +LAE +++D T+T+ LRKGV F D Sbjct: 81 LDPAKTAHSTDYTRVHMFYNGLTKLDGKLGPQMVLAEE-MLTNDAVTWTVKLRKGVNFHD 139 Query: 101 GTPFDAKAVEFNLLRGQEKTSLRRNELKYVSKITVVDDHTIKLDLSTPFAPFLSILTDRA 160 G P V ++++R ++ + SK+ VV D + + P + + + A Sbjct: 140 GKPLTPADVVYSIMRHKDPAT--------ASKVKVVADQFESVKATGPNEVQIKLTSANA 191 Query: 161 GM----MSSPTAVKKYGEDYVNHPVGTGPFIYEGRLKGATLTLKKNPDYWRAGLPKVDEV 216 + ++ + + G + P GTG F + G +N +YW+ GLP +DEV Sbjct: 192 DLPVILATAQFLIIRDGTTNFSTPNGTGAFKLKEFTPGVRTIGVRNENYWKPGLPYLDEV 251 Query: 217 VYKIMPDVNVAFNNLRSGQVDISNRFPYKEITNVPANANYTVLNKPSLGFRGFYLNTTKP 276 +PD N L SG V N + V YTV+ S + + Sbjct: 252 ELFGIPDEAARVNALLSGDVHWINDVNSRSTGRVKNTPGYTVMETKSGQYTDLVMRQDVA 311 Query: 277 PFDKKEVREAVDILIDRNAIAKVVYNN-AVAPGHSPFSKAQFANGPGDVPPKVDVARAKA 335 P + + + L+DR I + AV P G D +AK Sbjct: 312 PGNSMDFTLGMKYLLDREQIKMAAFRGYAVIANDQPIDPTNRFYFAGLPQRPYDPDKAKF 371 Query: 336 LLKAAGKEGGFSFKLTLPTTADELQAGQMIQGML---RPAGITVTLEKTEIASQVEAGKT 392 L AG G T+P A G + +L A I + L+ + + + + Sbjct: 372 HLGKAGVLGS-----TIPIVASVAATGSVDMAVLMQQSAAKIGLKLDVKRVPA--DGYWS 424 Query: 393 GAFEGLFLGWSG---RPDPDQNIFDFVNSGGSMNYSHIAAKEVDDLLQQARVEGDQAKRK 449 + + +G+ RP D + F S N S + D L+ AR E D KRK Sbjct: 425 NQWMKVPVGFGNINPRPSADILLTQFFKSDAQWNESGWKNPQFDQLVVAARGETDFTKRK 484 Query: 450 VLYDQAMAILVKEVPYIYLVHDNVLFGIAKSVKGFQYVPDGVIRTATVSK 499 +Y ++ ++ V L GI+ VKG VP G T ++ Sbjct: 485 AMYADLQTMIHEKCGLGIPVFIINLEGISTKVKGIDPVPLGAFMNYTCAE 534 >gi|300310860|ref|YP_003774952.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 72.4 bits (176), Expect = 7e-14, Method: Compositional matrix adjust. Identities = 107/483 (22%), Positives = 193/483 (39%), Gaps = 54/483 (11%) Query: 41 LDPTQSSMLNERILYQSIFDKLVDLDGEGKIVPMLAERWTVSDDQKTYTLYLRKGVKFQD 100 LDPT+S + R+ + + L+++D G++ P +A W+VS D + LR G+++ D Sbjct: 66 LDPTRSGYMFARM---EVLETLLEVDDAGQLQPSVASAWSVSADGLQWRFVLRSGLRYHD 122 Query: 101 GTPFDAKAVEFNLLRGQEKTSLRRNELKYVSKITVVDDHTIKLDLSTPFAPFLSILTDRA 160 G+ ++ L R Q + + R L ++ + V+ T+ + L PF P +LT Sbjct: 123 GSALTPASILACLQRAQARPGVLR--LADIAALR-VEGQTLVVVLRRPFGPLPYLLTHYT 179 Query: 161 GMMSSPTAVKKYGEDYVNHPVGTGPFIYEGRLKGATLTLKKNPDYWRAGLPKVDEVVYKI 220 + +P + G V +G+GPF R++ L P + Sbjct: 180 TQILAPASFDAQGN--VVAIIGSGPF----RIRSIAL-----PQQFEVERVAGSVSGSGA 228 Query: 221 MPDVNVAFNNLR---------------SGQVDISNRFPYKEITNVPANANYTVLNKPSLG 265 DV R SGQ D++ I + + ++L+ Sbjct: 229 GSDVGKVVQRARYISVSRAETRTLLVQSGQADLAFSLDPPSIRALQDSPRASLLSAMLPR 288 Query: 266 FRGFYLNTTKPPFDKKEVREAVDILIDRNAIAKVVYNNA--VAPGHSPFSKAQFANGPGD 323 LN P VR A+ + I+R IA+ + + A P S A++ + Sbjct: 289 TTLLKLNAGHPLLADVRVRRAISLCIEREGIARALLRDPDLGATQLFPPSLARWHDA-AL 347 Query: 324 VPPKVDVARAKALLKAAG---------KEGGFSFKLTLPTTADELQ---AGQMIQGMLRP 371 P + ++ +A++LL AG + G L L T D + +Q +R Sbjct: 348 APLRTNLQQARSLLDQAGWRPGSDGVRRRDGQRMALNLTTFVDRPELPLIATALQEEMRQ 407 Query: 372 AGITVTLEKTEIASQVEAG-KTGAFEGLFLG--WSGRPDPDQNIF-DFVNSGGSMNYSHI 427 G+ V + +S + AG ++G + + PDP ++ DF GG Sbjct: 408 IGMAVRVVIGN-SSDIPAGHRSGQLQMALAARNYGNLPDPVASLLQDFGPQGGDWGAMGW 466 Query: 428 AAKEVDDLLQQARVEGDQAKRKVLYDQA--MAILVKEVPYIYLVHDNVLFGIAKSVKGFQ 485 +EV LL + A K ++A +A+L +++P I +V +++ V+G Sbjct: 467 DNQEVPALLARLAATPADAAAKGNAERARIVALLQEQLPVIPVVWYRQTCAVSRRVRGAS 526 Query: 486 YVP 488 P Sbjct: 527 IDP 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 0.318 0.135 0.390 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: 1,504,379 Number of extensions: 61693 Number of successful extensions: 171 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 160 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 (21.7 bits) S2: 132 (55.5 bits)