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= 0028.0164.p (291 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... 248 4e-67 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 192 3e-50 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 158 6e-40 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 119 3e-28 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 100 2e-22 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 248 bits (633), Expect = 4e-67, Method: Compositional matrix adjust. Identities = 125/277 (45%), Positives = 178/277 (64%), Gaps = 1/277 (0%) Query: 16 WRTL-RRFSRNRLAVIGAVIITVLVLLAITAPVLARYDPIFDQDYGNLLSGPSAEHWLGT 74 WR R+F + LAV V I LV +AI AP + +DP DY L S P+ HW G Sbjct: 33 WREFWRKFKKQHLAVYAGVFILFLVAVAILAPWIVPFDPENFFDYDALNSPPTWVHWFGV 92 Query: 75 DDLGRDIYTRMLYGSRISLQAALISVGLAFSLGVPIGIVSGYYRGAVDAIVMRVVDALQA 134 D LGRDI++R++ G+RISL A SV + +G G+++GYY G D I MR+ D L A Sbjct: 93 DSLGRDIFSRIVMGTRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWDRITMRICDVLFA 152 Query: 135 FPSLILALALAAALGGGFYNAMVAVGIGFTSSFVRLARGQAMTIRNLDYVMAARSIGAGH 194 FP ++LA+ + A LGGG N +++V + +F RL RG + ++NL Y+ A RSIGA Sbjct: 153 FPGILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEATRSIGASD 212 Query: 195 LRIMWRYILPNSLAPLVIQATFAMGTAIIAEAGLSYLGLGAKPEDPSWGSMLHIAQGYLN 254 + IMW++I P +++ +V+ T +GT+II AGLS+LGLGA+ P WG ML+ A+ + Sbjct: 213 MTIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLMLNEARADMV 272 Query: 255 TTPMLAMWPGLAIFLVVLGFNLLGDGIREVFDPKLSR 291 T+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 = 192 bits (488), Expect = 3e-50, Method: Compositional matrix adjust. Identities = 115/287 (40%), Positives = 176/287 (61%), Gaps = 8/287 (2%) Query: 9 ALPALPRWR-TLRRFSRNRLAVIGAVIITVLVLLAITAPVLARYDPIFDQDYGNLLSGP- 66 ALP LP WR LRR +R +IGA ++ V+VL AI AP+LA +DP FDQD L P Sbjct: 17 ALPPLPAWRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPHDP-FDQDVTARLIPPV 75 Query: 67 -----SAEHWLGTDDLGRDIYTRMLYGSRISLQAALISVGLAFSLGVPIGIVSGYYRGAV 121 S EH LGTD LGRD ++R++YG+R+SL L + ++ +G +G+++GY+ G Sbjct: 76 WQAQGSWEHILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRT 135 Query: 122 DAIVMRVVDALQAFPSLILALALAAALGGGFYNAMVAVGIGFTSSFVRLARGQAMTIRNL 181 DA++ ++ A P +++ALA+A+ +GG +V +G+ F + R +R+ Sbjct: 136 DAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDA 195 Query: 182 DYVMAARSIGAGHLRIMWRYILPNSLAPLVIQATFAMGTAIIAEAGLSYLGLGAKPEDPS 241 +++ AA++IGA I+ R ILPN + L++ T M AI+ EA LS+LGLG +P PS Sbjct: 196 EFIAAAKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPS 255 Query: 242 WGSMLHIAQGYLNTTPMLAMWPGLAIFLVVLGFNLLGDGIREVFDPK 288 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 = 158 bits (399), Expect = 6e-40, Method: Compositional matrix adjust. Identities = 103/290 (35%), Positives = 168/290 (57%), Gaps = 14/290 (4%) Query: 14 PRWRTLRRFSRNRLAVIGAVIITVLVLLAITAPVLARYDP-------IFDQDY--GNLLS 64 P R +R F +R A++G VI+ +L++ AI AP + +P + D G L Sbjct: 33 PWRRVMRHFVASRSAMLGLVIVLLLIVGAIAAPWITPQNPYDLMQLDVLDARLHPGTLNG 92 Query: 65 GPSAEHWLGTDDLGRDIYTRMLYGSRISLQAALISVGLAFSLGVPIGIVSGYYRGAVDAI 124 + +WLGTD GRD+ + +LYG RIS+ + S +A +G IG+++ Y G +D + Sbjct: 93 AGTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSALIAGVIGTLIGLLAAYAGGKLDTL 152 Query: 125 VMRVVDALQAFPSLILALALAAALGGGFYNAMVAVGIGFTSSFVRLARGQAMTIRNLDYV 184 +MR D + +FPS+++A+ + A +G G +N M + + + + R ARGQA+ R +YV Sbjct: 153 LMRFADLVLSFPSILVAMLILAYVGKGIFNVMATLVVLEWAYYARTARGQALVERRKEYV 212 Query: 185 MAARSIGAGHLRIMWRYILPNSLAPLVIQATFAMGTAIIAEAGLSYLGLGAKPEDPSWGS 244 AAR + RIM R+ILPN L PL++ T + AI EA LS+LGLG +PS G Sbjct: 213 EAARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVARAITLEATLSFLGLGVPITEPSLG- 271 Query: 245 MLHIAQGY---LNTTPMLAMWPGLAIFLVVLGFNLLGDGIREVFDPKLSR 291 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 = 119 bits (297), Expect = 3e-28, Method: Compositional matrix adjust. Identities = 73/205 (35%), Positives = 109/205 (53%), Gaps = 5/205 (2%) Query: 64 SGPSAEHWLGTDDLGRDIYTRMLYGSRISLQAALISVGLAFSLGVPIGIVSGYYRGAVDA 123 + PS+E+WLGTDD GRD++ R+LYG R+S+ + + LGV G V GY+ G D Sbjct: 122 AAPSSENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDL 181 Query: 124 IVMRVVDALQAFPSLILALALAAALGGGFYNAMVAVGIGFTSSFVRLARGQAMTIRNLDY 183 R+++ + P L L + ++ +V + + S R + RNL+Y Sbjct: 182 FTQRLLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLEY 241 Query: 184 VMAARSIGAGHLRIMWRYILPNSLAPLVIQATFAMGTAIIAEAGLSYLGLGAKPEDPSWG 243 + AAR++G I+WR++LPNS+ +V F M AI+A L +LGLG P PS G Sbjct: 242 IQAARAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLG 301 Query: 244 SMLHIAQGYLNTTPMLAMWPGLAIF 268 +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 = 100 bits (248), Expect = 2e-22, Method: Compositional matrix adjust. Identities = 84/264 (31%), Positives = 138/264 (52%), Gaps = 14/264 (5%) Query: 17 RTLRRFSRNRLAVIGAVIITVLVLLAITAPVLARYDP--IFDQDYGNLLSGPSAEHWLGT 74 + +RR S +A IG I+ +L+AI P ++ YD I D D + SG S + LG+ Sbjct: 24 KRVRRHST--MAWIGMAIVGFWILMAILGPSISPYDATAIVDTD---VFSGMSHKFLLGS 78 Query: 75 DDLGRDIYTRMLYGSRISLQAALISVGLAFSLGVPIGIVSGYYRGAVDAIVMRVVDALQA 134 D LGRD+ +R+L+G+R ++ AL + LA + G I + + + G DA++ R +DAL + Sbjct: 79 DYLGRDMLSRILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVISRALDALIS 138 Query: 135 FPSLILALALAAALGGGFYNAMVAVGIGFTSSFVRLARGQAMTIRNLDYVMAARSIGAGH 194 PS + AL + A G ++ I + R+AR A+ ++ ++YV AAR+ G G Sbjct: 139 IPSKMFALMMVATFGSSMLLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGV 198 Query: 195 LRIMWRYILPNSLAPLVIQATFAMGTAIIAEAGLSYLGLGAKPEDPSWGSMLHIAQGYLN 254 IM +LPN + P++ ++ +GLS+L LG +P D WGS++ L Sbjct: 199 WYIMTVEMLPNMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSLVRENISGLG 258 Query: 255 TTPMLAMWPGLAIF-------LVV 271 + + P LAI L++ Sbjct: 259 EGALAVIMPALAIASLTIGVNLLI 282 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 0.427 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: 874,738 Number of extensions: 37591 Number of successful extensions: 208 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 205 Number of HSP's successfully gapped: 7 Length of query: 291 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 207 Effective length of database: 1,222,130 Effective search space: 252980910 Effective search space used: 252980910 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 130 (54.7 bits)