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= 0001.1709.p (296 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 247 8e-67 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 191 5e-50 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 162 3e-41 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 118 7e-28 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 116 2e-27 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 247 bits (631), Expect = 8e-67, Method: Compositional matrix adjust. Identities = 124/277 (44%), Positives = 178/277 (64%), Gaps = 1/277 (0%) Query: 21 WRTL-RRFSRNRLALIGAVIITVLVLLALAAPVLARYDPIFDQDYGNLLSGPSAEHWLGT 79 WR R+F + LA+ V I LV +A+ AP + +DP DY L S P+ HW G Sbjct: 33 WREFWRKFKKQHLAVYAGVFILFLVAVAILAPWIVPFDPENFFDYDALNSPPTWVHWFGV 92 Query: 80 DDLGRDIYSRMLYGSRISLQAALISVGLAFSLGVPIGILSGYYRGAVDAIVMRVVDALQA 139 D LGRDI+SR++ G+RISL A SV + +G G+L+GYY G D I MR+ D L A Sbjct: 93 DSLGRDIFSRIVMGTRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWDRITMRICDVLFA 152 Query: 140 FPSLILALALAAALGGGFYNAMVAVGIGFTSSFVRLARGQAMTIRNLDYVMAARSIGAGH 199 FP ++LA+ + A LGGG N +++V + +F RL RG + ++NL Y+ A RSIGA Sbjct: 153 FPGILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEATRSIGASD 212 Query: 200 LRIMWRYILPNSLAPLVIQATFAMGTAIIAEAGLSYLGLGAKPEDPSWGSMLHIAQGYLN 259 + IMW++I P +++ +V+ T +GT+II AGLS+LGLGA+ P WG ML+ A+ + Sbjct: 213 MTIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLMLNEARADMV 272 Query: 260 STPMLAMWPGLAIFLVVLGFNLLGDGIREVFDPKLSR 296 ++P +A+ P +AIFL VL FNLLGDG+R+ DPK+ + Sbjct: 273 TSPHVALVPSIAIFLTVLAFNLLGDGLRDALDPKIDQ 309 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 191 bits (486), Expect = 5e-50, Method: Compositional matrix adjust. Identities = 115/287 (40%), Positives = 175/287 (60%), Gaps = 8/287 (2%) Query: 14 ALPAQPRWR-TLRRFSRNRLALIGAVIITVLVLLALAAPVLARYDPIFDQDYGNLLSGP- 71 ALP P WR LRR +R +IGA ++ V+VL A+ AP+LA +DP FDQD L P Sbjct: 17 ALPPLPAWRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPHDP-FDQDVTARLIPPV 75 Query: 72 -----SAEHWLGTDDLGRDIYSRMLYGSRISLQAALISVGLAFSLGVPIGILSGYYRGAV 126 S EH LGTD LGRD +SR++YG+R+SL L + ++ +G +G+L+GY+ G Sbjct: 76 WQAQGSWEHILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRT 135 Query: 127 DAIVMRVVDALQAFPSLILALALAAALGGGFYNAMVAVGIGFTSSFVRLARGQAMTIRNL 186 DA++ ++ A P +++ALA+A+ +GG +V +G+ F + R +R+ Sbjct: 136 DAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDA 195 Query: 187 DYVMAARSIGAGHLRIMWRYILPNSLAPLVIQATFAMGTAIIAEAGLSYLGLGAKPEDPS 246 +++ AA++IGA I+ R ILPN + L++ T M AI+ EA LS+LGLG +P PS Sbjct: 196 EFIAAAKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPS 255 Query: 247 WGSMLHIAQGYLNSTPMLAMWPGLAIFLVVLGFNLLGDGIREVFDPK 293 WG M+ + Y+ P + + PG+A+ L+VL NL+GDG+R+V P Sbjct: 256 WGLMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAPD 302 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 162 bits (410), Expect = 3e-41, Method: Compositional matrix adjust. Identities = 105/290 (36%), Positives = 169/290 (58%), Gaps = 14/290 (4%) Query: 19 PRWRTLRRFSRNRLALIGAVIITVLVLLALAAPVLARYDP-------IFDQDY--GNLLS 69 P R +R F +R A++G VI+ +L++ A+AAP + +P + D G L Sbjct: 33 PWRRVMRHFVASRSAMLGLVIVLLLIVGAIAAPWITPQNPYDLMQLDVLDARLHPGTLNG 92 Query: 70 GPSAEHWLGTDDLGRDIYSRMLYGSRISLQAALISVGLAFSLGVPIGILSGYYRGAVDAI 129 + +WLGTD GRD+ S +LYG RIS+ + S +A +G IG+L+ Y G +D + Sbjct: 93 AGTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSALIAGVIGTLIGLLAAYAGGKLDTL 152 Query: 130 VMRVVDALQAFPSLILALALAAALGGGFYNAMVAVGIGFTSSFVRLARGQAMTIRNLDYV 189 +MR D + +FPS+++A+ + A +G G +N M + + + + R ARGQA+ R +YV Sbjct: 153 LMRFADLVLSFPSILVAMLILAYVGKGIFNVMATLVVLEWAYYARTARGQALVERRKEYV 212 Query: 190 MAARSIGAGHLRIMWRYILPNSLAPLVIQATFAMGTAIIAEAGLSYLGLGAKPEDPSWGS 249 AAR + RIM R+ILPN L PL++ T + AI EA LS+LGLG +PS G Sbjct: 213 EAARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVARAITLEATLSFLGLGVPITEPSLG- 271 Query: 250 MLHIAQGY---LNSTPMLAMWPGLAIFLVVLGFNLLGDGIREVFDPKLSR 296 L I+ GY L+ ++ +PG+ + +V++ NL+GD +R++ +P+ + Sbjct: 272 -LLISNGYQYMLSGEYWISFYPGITLLVVIVAINLVGDRLRDILNPRWQK 320 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 118 bits (295), Expect = 7e-28, Method: Compositional matrix adjust. Identities = 72/205 (35%), Positives = 110/205 (53%), Gaps = 5/205 (2%) Query: 69 SGPSAEHWLGTDDLGRDIYSRMLYGSRISLQAALISVGLAFSLGVPIGILSGYYRGAVDA 128 + PS+E+WLGTDD GRD+++R+LYG R+S+ + + LGV G + GY+ G D Sbjct: 122 AAPSSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDL 181 Query: 129 IVMRVVDALQAFPSLILALALAAALGGGFYNAMVAVGIGFTSSFVRLARGQAMTIRNLDY 188 R+++ + P L L + ++ +V + + S R + RNL+Y Sbjct: 182 FTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLEY 241 Query: 189 VMAARSIGAGHLRIMWRYILPNSLAPLVIQATFAMGTAIIAEAGLSYLGLGAKPEDPSWG 248 + AAR++G I+WR++LPNS+ +V F M AI+A L +LGLG P PS G Sbjct: 242 IQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLG 301 Query: 249 SMLHIAQGYLNSTPMLAMWPGLAIF 273 +L AQG N + A W L+ F Sbjct: 302 ELL--AQGKNN---LDAWWIALSTF 321 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 116 bits (291), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 89/269 (33%), Positives = 144/269 (53%), Gaps = 7/269 (2%) Query: 22 RTLRRFSRNRLALIGAVIITVLVLLALAAPVLARYDP--IFDQDYGNLLSGPSAEHWLGT 79 + +RR S +A IG I+ +L+A+ P ++ YD I D D + SG S + LG+ Sbjct: 24 KRVRRHST--MAWIGMAIVGFWILMAILGPSISPYDATAIVDTD---VFSGMSHKFLLGS 78 Query: 80 DDLGRDIYSRMLYGSRISLQAALISVGLAFSLGVPIGILSGYYRGAVDAIVMRVVDALQA 139 D LGRD+ SR+L+G+R ++ AL + LA + G I + + + G DA++ R +DAL + Sbjct: 79 DYLGRDMLSRILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVISRALDALIS 138 Query: 140 FPSLILALALAAALGGGFYNAMVAVGIGFTSSFVRLARGQAMTIRNLDYVMAARSIGAGH 199 PS + AL + A G ++ I + R+AR A+ ++ ++YV AAR+ G G Sbjct: 139 IPSKMFALMMVATFGSSMLLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGV 198 Query: 200 LRIMWRYILPNSLAPLVIQATFAMGTAIIAEAGLSYLGLGAKPEDPSWGSMLHIAQGYLN 259 IM +LPN + P++ ++ +GLS+L LG +P D WGS++ L Sbjct: 199 WYIMTVEMLPNMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSLVRENISGLG 258 Query: 260 STPMLAMWPGLAIFLVVLGFNLLGDGIRE 288 + + P LAI + +G NLL D +R Sbjct: 259 EGALAVIMPALAIASLTIGVNLLIDNLRS 287 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 0.326 0.141 0.424 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: 899,339 Number of extensions: 35105 Number of successful extensions: 210 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 208 Number of HSP's successfully gapped: 7 Length of query: 296 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 211 Effective length of database: 1,217,395 Effective search space: 256870345 Effective search space used: 256870345 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)