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= 0001.1371.p (276 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310862|ref|YP_003774954.1| dipeptide/oligopeptide/nickel A... 288 3e-79 gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 119 3e-28 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 116 2e-27 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 91 1e-19 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 77 1e-15 >gi|300310862|ref|YP_003774954.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 278 Score = 288 bits (738), Expect = 3e-79, Method: Compositional matrix adjust. Identities = 226/266 (84%), Positives = 241/266 (90%) Query: 11 ETRPRRVTPGQWAGLLLLLMIVLFAWLGPLLIEVDPAGQQLSRFLETPSLAHPLGYDQLG 70 + PRR + GQW+GL+LLL++ FA LGPL+I+ DPA QQL+R+LETPSLA PLG+DQLG Sbjct: 13 QAGPRRWSAGQWSGLVLLLLVAGFALLGPLVIDTDPARQQLARYLETPSLAEPLGFDQLG 72 Query: 71 RSMLARLAHGTRLSLSLALVSVLSAAIPGIVIGLLAAWCGGWVERVLAALADAVLALPGL 130 RSMLARLAHG RLSLSLAL+SVLSAAIPG +IGLLAAWCGGW ERVLAALADAVLALPGL Sbjct: 73 RSMLARLAHGARLSLSLALLSVLSAAIPGSLIGLLAAWCGGWTERVLAALADAVLALPGL 132 Query: 131 LLVLLLAAFAPGGFWPLYVGISLALWVEYFRVVRAASRILLASAPVEASRLLGFGPGYIV 190 LLVLLLAAFAPGGFWPLYVGISLALWVEYFRVVRAASRILLAS VEASRLLGFG YIV Sbjct: 133 LLVLLLAAFAPGGFWPLYVGISLALWVEYFRVVRAASRILLASPQVEASRLLGFGALYIV 192 Query: 191 RRHLMPALLPRLFTLMRFGLAGAVLAMSALGFVGVGLQPPTPELGVMMIELLPYYREAPW 250 R HL+PALLPRL TL+RFGLAGAVLAMSALGFVGVGLQPPTPELGVMMIELLPYYREAPW Sbjct: 193 RCHLLPALLPRLLTLVRFGLAGAVLAMSALGFVGVGLQPPTPELGVMMIELLPYYREAPW 252 Query: 251 LVGSPVLVLFLTLLALLLLSPQKENA 276 LV SPVLVLFL LL LLLLS Q E A Sbjct: 253 LVASPVLVLFLGLLGLLLLSSQGEAA 278 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 119 bits (298), Expect = 3e-28, Method: Compositional matrix adjust. Identities = 77/256 (30%), Positives = 131/256 (51%), Gaps = 2/256 (0%) Query: 22 WAGLLLLLMIVLFAWLGPLLIEVDPAGQQLSRFLETP-SLAHPLGYDQLGRSMLARLAHG 80 +AG+ +L ++ + A L P ++ DP L +P + H G D LGR + +R+ G Sbjct: 48 YAGVFILFLVAV-AILAPWIVPFDPENFFDYDALNSPPTWVHWFGVDSLGRDIFSRIVMG 106 Query: 81 TRLSLSLALVSVLSAAIPGIVIGLLAAWCGGWVERVLAALADAVLALPGLLLVLLLAAFA 140 TR+SL+ SV A+ G V GLLA + GW +R+ + D + A PG+LL + + A Sbjct: 107 TRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWDRITMRICDVLFAFPGILLAIGIVAIL 166 Query: 141 PGGFWPLYVGISLALWVEYFRVVRAASRILLASAPVEASRLLGFGPGYIVRRHLMPALLP 200 GG + + +S+ + R+VR + L +EA+R +G I+ +H+ P + Sbjct: 167 GGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEATRSIGASDMTIMWKHIFPGTIS 226 Query: 201 RLFTLMRFGLAGAVLAMSALGFVGVGLQPPTPELGVMMIELLPYYREAPWLVGSPVLVLF 260 + + +++ + L F+G+G Q PTPE G+M+ E +P + P + +F Sbjct: 227 AIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLMLNEARADMVTSPHVALVPSIAIF 286 Query: 261 LTLLALLLLSPQKENA 276 LT+LA LL +A Sbjct: 287 LTVLAFNLLGDGLRDA 302 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 116 bits (291), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 84/252 (33%), Positives = 140/252 (55%), Gaps = 6/252 (2%) Query: 24 GLLLLLMIVLFAWLGPLLIEVDPAGQQLSRFLETP------SLAHPLGYDQLGRSMLARL 77 G +L +IVL A PLL DP Q ++ L P S H LG D+LGR +RL Sbjct: 40 GAAVLAVIVLAAIFAPLLAPHDPFDQDVTARLIPPVWQAQGSWEHILGTDKLGRDYFSRL 99 Query: 78 AHGTRLSLSLALVSVLSAAIPGIVIGLLAAWCGGWVERVLAALADAVLALPGLLLVLLLA 137 +G R+SL++ L + L + + G +G+LA + GG + V++ L LA+P +L+ L +A Sbjct: 100 IYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVISYLITTRLAMPVVLVALAMA 159 Query: 138 AFAPGGFWPLYVGISLALWVEYFRVVRAASRILLASAPVEASRLLGFGPGYIVRRHLMPA 197 + G + V + L LW + V R+A++ L + + A++ +G YI+ R ++P Sbjct: 160 SLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAKAIGASTPYILLREILPN 219 Query: 198 LLPRLFTLMRFGLAGAVLAMSALGFVGVGLQPPTPELGVMMIELLPYYREAPWLVGSPVL 257 ++ L ++ +A A+L + L F+G+G+QPPTP G+M+ E Y PW++ P + Sbjct: 220 IMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAEGKTYMFFKPWVIVIPGV 279 Query: 258 VLFLTLLALLLL 269 L L +LA+ L+ Sbjct: 280 ALALLVLAINLV 291 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 90.9 bits (224), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 61/210 (29%), Positives = 110/210 (52%), Gaps = 1/210 (0%) Query: 64 LGYDQLGRSMLARLAHGTRLSLSLALVSVLSAAIPGIVIGLLAAWCGGWVERVLAALADA 123 LG D GR +++ + +G R+S+ + + S L A + G +IGLLAA+ GG ++ +L AD Sbjct: 100 LGTDGQGRDLVSAILYGLRISVGIGVGSALIAGVIGTLIGLLAAYAGGKLDTLLMRFADL 159 Query: 124 VLALPGLLLVLLLAAFAPGGFWPLYVGISLALWVEYFRVVRAASRILLASAPVEASRLLG 183 VL+ P +L+ +L+ A+ G + + + + W Y R R + + VEA+R L Sbjct: 160 VLSFPSILVAMLILAYVGKGIFNVMATLVVLEWAYYARTARGQALVERRKEYVEAARGLN 219 Query: 184 FGPGYIVRRHLMPALLPRLFTLMRFGLAGAVLAMSALGFVGVGLQPPTPELGVMMIELLP 243 I+ RH++P LP L + +A A+ + L F+G+G+ P LG+++ Sbjct: 220 LSSWRIMVRHILPNCLPPLIVIGTLQVARAITLEATLSFLGLGVPITEPSLGLLISNGYQ 279 Query: 244 YYREAP-WLVGSPVLVLFLTLLALLLLSPQ 272 Y W+ P + L + ++A+ L+ + Sbjct: 280 YMLSGEYWISFYPGITLLVVIVAINLVGDR 309 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 77.4 bits (189), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 73/249 (29%), Positives = 123/249 (49%), Gaps = 4/249 (1%) Query: 13 RPRRVTPGQWAGLLLLLMIVLFAWLGPLLIEVDPAGQQLSRFLETPSLAHPLGYDQLGRS 72 R RR + W G+ ++ +L A LGP + D + S LG D LGR Sbjct: 25 RVRRHSTMAWIGMAIVGFWILMAILGPSISPYDATAIVDTDVFSGMSHKFLLGSDYLGRD 84 Query: 73 MLARLAHGTRLSLSLALVSVLSAAIPGIVIGLLAAWCGGWVERVLAALADAVLALPGLLL 132 ML+R+ GTR ++ LAL + + A+ G I L AA+ GGW + V++ DA++++P + Sbjct: 85 MLSRILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVISRALDALISIPSKMF 144 Query: 133 VLLLAAFAPGGFWPLYVGISLALWVEYFRVVRAASRILLASAPVEASRLLGFGPGYIVRR 192 L++ A L + ++ +R+ R+ + + A V+A+R G G YI+ Sbjct: 145 ALMMVATFGSSMLLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGVWYIMTV 204 Query: 193 HLMPALLPRLFTLMRFGL--AGAVLAMSALGFVGVGLQPPTPELGVMMIELLPYYREAPW 250 ++P ++ + L FGL VL +S L F+ +G+QPP + G ++ E + E Sbjct: 205 EMLPNMIRPV--LADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSLVRENISGLGEGAL 262 Query: 251 LVGSPVLVL 259 V P L + Sbjct: 263 AVIMPALAI 271 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 0.328 0.144 0.443 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: 792,147 Number of extensions: 30375 Number of successful extensions: 246 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 243 Number of HSP's successfully gapped: 6 Length of query: 276 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 192 Effective length of database: 1,222,130 Effective search space: 234648960 Effective search space used: 234648960 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 (21.7 bits) S2: 130 (54.7 bits)