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= 0001.0934.p (298 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 494 e-141 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 124 7e-30 gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 124 9e-30 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 111 8e-26 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 61 1e-10 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 494 bits (1272), Expect = e-141, Method: Compositional matrix adjust. Identities = 272/298 (91%), Positives = 279/298 (93%), Gaps = 5/298 (1%) Query: 1 MKALHDSTATEAAGSIPDAIAPAPTTAPKRVRRHSNMAWIGMGIVGFWILMAILGPSISP 60 MKALHDST GS A APA + KRVRRHS MAWIGM IVGFWILMAILGPSISP Sbjct: 1 MKALHDST-----GSQAGAPAPAASAPAKRVRRHSTMAWIGMAIVGFWILMAILGPSISP 55 Query: 61 YDATAIVDTDVFTGMSHKFLLGTDYLGRDMLSRILFGTRATIGLALVSTVLASLSGTAIA 120 YDATAIVDTDVF+GMSHKFLLG+DYLGRDMLSRILFGTRATIGLAL +TVLAS +GTAIA Sbjct: 56 YDATAIVDTDVFSGMSHKFLLGSDYLGRDMLSRILFGTRATIGLALAATVLASATGTAIA 115 Query: 121 LFAAFSGGWRDALISRALDALISIPSKMFALMMVATFGSSMGLLVLTAAITYMPGAFRIA 180 LFAAFSGGWRDA+ISRALDALISIPSKMFALMMVATFGSSM LLVLTAAITYMPGA+RIA Sbjct: 116 LFAAFSGGWRDAVISRALDALISIPSKMFALMMVATFGSSMLLLVLTAAITYMPGAYRIA 175 Query: 181 RSLAVNVQAMEYVQAARARGEGVWYIMTVEMLPNMIRPVLADFGLRFVYVVLLLSGLSFL 240 RSLAVNVQAMEYVQAARARGEGVWYIMTVEMLPNMIRPVLADFGLRFVYVVLLLSGLSFL Sbjct: 176 RSLAVNVQAMEYVQAARARGEGVWYIMTVEMLPNMIRPVLADFGLRFVYVVLLLSGLSFL 235 Query: 241 SLGVQPPDADWGSLVRENISGLGEGALAVIMPALAIASLTIGVNLLIDNLRGKRAAKE 298 SLGVQPPDADWGSLVRENISGLGEGALAVIMPALAIASLTIGVNLLIDNLR KRAAKE Sbjct: 236 SLGVQPPDADWGSLVRENISGLGEGALAVIMPALAIASLTIGVNLLIDNLRSKRAAKE 293 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 124 bits (312), Expect = 7e-30, Method: Compositional matrix adjust. Identities = 83/276 (30%), Positives = 147/276 (53%), Gaps = 13/276 (4%) Query: 29 KRVRRHSNMAWIGMGIVGFWILMAILGPSISPYDATAIVDTDVFTGM---------SHKF 79 +R+ H + IG ++ +L AI P ++P+D D DV + S + Sbjct: 29 RRLLGHRGLM-IGAAVLAVIVLAAIFAPLLAPHDP---FDQDVTARLIPPVWQAQGSWEH 84 Query: 80 LLGTDYLGRDMLSRILFGTRATIGLALVSTVLASLSGTAIALFAAFSGGWRDALISRALD 139 +LGTD LGRD SR+++G R ++ + L + +++ L GT + + A + GG DA+IS + Sbjct: 85 ILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVISYLIT 144 Query: 140 ALISIPSKMFALMMVATFGSSMGLLVLTAAITYMPGAFRIARSLAVNVQAMEYVQAARAR 199 +++P + AL M + G S+ ++++ + + RS ++ E++ AA+A Sbjct: 145 TRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAKAI 204 Query: 200 GEGVWYIMTVEMLPNMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSLVRENI 259 G YI+ E+LPN++ ++ L + +LL + LSFL LGVQPP WG +V E Sbjct: 205 GASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAEGK 264 Query: 260 SGLGEGALAVIMPALAIASLTIGVNLLIDNLRGKRA 295 + + +++P +A+A L + +NL+ D LR A Sbjct: 265 TYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNA 300 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 124 bits (311), Expect = 9e-30, Method: Compositional matrix adjust. Identities = 77/266 (28%), Positives = 132/266 (49%), Gaps = 6/266 (2%) Query: 29 KRVRRHSNMAWIGMGIVGFWILMAILGPSISPYDATAIVDTDVFTG---MSHKFLLGTDY 85 ++ ++ + G+ I+ F + +AIL P I P+D D D H F G D Sbjct: 38 RKFKKQHLAVYAGVFIL-FLVAVAILAPWIVPFDPENFFDYDALNSPPTWVHWF--GVDS 94 Query: 86 LGRDMLSRILFGTRATIGLALVSTVLASLSGTAIALFAAFSGGWRDALISRALDALISIP 145 LGRD+ SRI+ GTR ++ S + ++ GT L A + GW D + R D L + P Sbjct: 95 LGRDIFSRIVMGTRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWDRITMRICDVLFAFP 154 Query: 146 SKMFALMMVATFGSSMGLLVLTAAITYMPGAFRIARSLAVNVQAMEYVQAARARGEGVWY 205 + A+ +VA G M ++++ ++ +P R+ R + ++ + Y++A R+ G Sbjct: 155 GILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEATRSIGASDMT 214 Query: 206 IMTVEMLPNMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSLVRENISGLGEG 265 IM + P I ++ F +R ++ +GLSFL LG Q P +WG ++ E + + Sbjct: 215 IMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLMLNEARADMVTS 274 Query: 266 ALAVIMPALAIASLTIGVNLLIDNLR 291 ++P++AI + NLL D LR Sbjct: 275 PHVALVPSIAIFLTVLAFNLLGDGLR 300 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 111 bits (277), Expect = 8e-26, Method: Compositional matrix adjust. Identities = 91/287 (31%), Positives = 146/287 (50%), Gaps = 18/287 (6%) Query: 21 APAPTTAPKRVRRH---SNMAWIGMGIVGFWILMAILGPSISPYDATAIVDTDVFTGMSH 77 AP + +RV RH S A +G+ IV I+ AI P I+P + ++ DV H Sbjct: 27 APRRESPWRRVMRHFVASRSAMLGLVIVLLLIVGAIAAPWITPQNPYDLMQLDVLDARLH 86 Query: 78 ----------KFLLGTDYLGRDMLSRILFGTRATIGLALVSTVLASLSGTAIALFAAFSG 127 + LGTD GRD++S IL+G R ++G+ + S ++A + GT I L AA++G Sbjct: 87 PGTLNGAGTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSALIAGVIGTLIGLLAAYAG 146 Query: 128 GWRDALISRALDALISIPSKMFALMMVATFGSSMGLLVLTAAITYMPGAF--RIARSLAV 185 G D L+ R D ++S PS + A++++A G G+ + A + + A+ R AR A+ Sbjct: 147 GKLDTLLMRFADLVLSFPSILVAMLILAYVGK--GIFNVMATLVVLEWAYYARTARGQAL 204 Query: 186 NVQAMEYVQAARARGEGVWYIMTVEMLPNMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQ 245 + EYV+AAR W IM +LPN + P++ L+ + L + LSFL LGV Sbjct: 205 VERRKEYVEAARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVARAITLEATLSFLGLGVP 264 Query: 246 PPDADWGSLVRENISGLGEGALAV-IMPALAIASLTIGVNLLIDNLR 291 + G L+ + G + P + + + + +NL+ D LR Sbjct: 265 ITEPSLGLLISNGYQYMLSGEYWISFYPGITLLVVIVAINLVGDRLR 311 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 60.8 bits (146), Expect = 1e-10, Method: Compositional matrix adjust. Identities = 53/187 (28%), Positives = 88/187 (47%) Query: 76 SHKFLLGTDYLGRDMLSRILFGTRATIGLALVSTVLASLSGTAIALFAAFSGGWRDALIS 135 S + LGTD GRD+ +R+L+G R ++ + T + + G A + G D Sbjct: 125 SSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDLFTQ 184 Query: 136 RALDALISIPSKMFALMMVATFGSSMGLLVLTAAITYMPGAFRIARSLAVNVQAMEYVQA 195 R L+ S+P ++ + F S+GLL++ ++ R+ + + +EY+QA Sbjct: 185 RLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLEYIQA 244 Query: 196 ARARGEGVWYIMTVEMLPNMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSLV 255 ARA G I+ +LPN + V+ R +L L+ L FL LGV P G L+ Sbjct: 245 ARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLGELL 304 Query: 256 RENISGL 262 + + L Sbjct: 305 AQGKNNL 311 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 0.325 0.137 0.400 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: 767,114 Number of extensions: 27056 Number of successful extensions: 192 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 189 Number of HSP's successfully gapped: 6 Length of query: 298 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 213 Effective length of database: 1,217,395 Effective search space: 259305135 Effective search space used: 259305135 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 130 (54.7 bits)