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= 0034.0378.p (258 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... 171 4e-44 gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 166 2e-42 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 162 3e-41 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 111 5e-26 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 97 2e-21 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 171 bits (434), Expect = 4e-44, Method: Compositional matrix adjust. Identities = 95/256 (37%), Positives = 149/256 (58%), Gaps = 1/256 (0%) Query: 1 VLLLLVVLMALSSPLLFPGDPLDMVAEPFLHPGVDAAHLLGSDMLGRDLLSGIFHGARVS 60 V +L +V +A+ +P + P DP + L+ H G D LGRD+ S I G R+S Sbjct: 51 VFILFLVAVAILAPWIVPFDPENFFDYDALNSPPTWVHWFGVDSLGRDIFSRIVMGTRIS 110 Query: 61 LLIAVVSTLLALVLGISGGLLAGYYGGLADAVLMRVTEFFQTIPSFLFALAIVAVVQPNL 120 L S + V+G GLLAGYY G D + MR+ + P L A+ IVA++ + Sbjct: 111 LAAGFFSVAIGAVIGTVFGLLAGYYEGWWDRITMRICDVLFAFPGILLAIGIVAILGGGM 170 Query: 121 ATIALAIGVTAWPSLARLVRAEVLKLRHSEMVQASAALGATDLRIMLRDILPNTLTPILV 180 + +++ V + P+ ARLVR L+L++ ++A+ ++GA+D+ IM + I P T++ I+V Sbjct: 171 INVIISVSVFSIPAFARLVRGNTLQLKNLTYIEATRSIGASDMTIMWKHIFPGTISAIVV 230 Query: 181 STSLMVATAILTESSLAFLGLGDPNAV-SWGNMVGSGREVIRTDWYITTIPGIAIVITVL 239 ++ + T+I+T + L+FLGLG + WG M+ R + T ++ +P IAI +TVL Sbjct: 231 YFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLMLNEARADMVTSPHVALVPSIAIFLTVL 290 Query: 240 ALNLLGDGLADVLDPR 255 A NLLGDGL D LDP+ Sbjct: 291 AFNLLGDGLRDALDPK 306 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 166 bits (419), Expect = 2e-42, Method: Compositional matrix adjust. Identities = 105/263 (39%), Positives = 161/263 (61%), Gaps = 6/263 (2%) Query: 2 LLLLVVLMALSSPLLFPGDPLDMVAEPFLHPGVDAA-----HLLGSDMLGRDLLSGIFHG 56 +L ++VL A+ +PLL P DP D L P V A H+LG+D LGRD S + +G Sbjct: 43 VLAVIVLAAIFAPLLAPHDPFDQDVTARLIPPVWQAQGSWEHILGTDKLGRDYFSRLIYG 102 Query: 57 ARVSLLIAVVSTLLALVLGISGGLLAGYYGGLADAVLMRVTEFFQTIPSFLFALAIVAVV 116 ARVSL I + + L++ ++G + G+LAGY+GG DAV+ + +P L ALA+ ++V Sbjct: 103 ARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVISYLITTRLAMPVVLVALAMASLV 162 Query: 117 QPNLATIALAIGVTAWPSLARLVRAEVLKLRHSEMVQASAALGATDLRIMLRDILPNTLT 176 +L + + +G+ W A + R+ +LR +E + A+ A+GA+ I+LR+ILPN + Sbjct: 163 GGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAKAIGASTPYILLREILPNIMG 222 Query: 177 PILVSTSLMVATAILTESSLAFLGLG-DPNAVSWGNMVGSGREVIRTDWYITTIPGIAIV 235 ++V +L +A AIL E++L+FLGLG P SWG MV G+ + ++ IPG+A+ Sbjct: 223 ALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAEGKTYMFFKPWVIVIPGVALA 282 Query: 236 ITVLALNLLGDGLADVLDPRDRK 258 + VLA+NL+GDGL DV P R Sbjct: 283 LLVLAINLVGDGLRDVNAPDGRN 305 >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 = 100/260 (38%), Positives = 154/260 (59%), Gaps = 11/260 (4%) Query: 10 ALSSPLLFPGDPLDM----VAEPFLHPGV-----DAAHLLGSDMLGRDLLSGIFHGARVS 60 A+++P + P +P D+ V + LHPG + LG+D GRDL+S I +G R+S Sbjct: 61 AIAAPWITPQNPYDLMQLDVLDARLHPGTLNGAGTYTYWLGTDGQGRDLVSAILYGLRIS 120 Query: 61 LLIAVVSTLLALVLGISGGLLAGYYGGLADAVLMRVTEFFQTIPSFLFALAIVAVVQPNL 120 + I V S L+A V+G GLLA Y GG D +LMR + + PS L A+ I+A V + Sbjct: 121 VGIGVGSALIAGVIGTLIGLLAAYAGGKLDTLLMRFADLVLSFPSILVAMLILAYVGKGI 180 Query: 121 ATIALAIGVTAWPSLARLVRAEVLKLRHSEMVQASAALGATDLRIMLRDILPNTLTPILV 180 + + V W AR R + L R E V+A+ L + RIM+R ILPN L P++V Sbjct: 181 FNVMATLVVLEWAYYARTARGQALVERRKEYVEAARGLNLSSWRIMVRHILPNCLPPLIV 240 Query: 181 STSLMVATAILTESSLAFLGLGDP-NAVSWGNMVGSGREVIRT-DWYITTIPGIAIVITV 238 +L VA AI E++L+FLGLG P S G ++ +G + + + +++I+ PGI +++ + Sbjct: 241 IGTLQVARAITLEATLSFLGLGVPITEPSLGLLISNGYQYMLSGEYWISFYPGITLLVVI 300 Query: 239 LALNLLGDGLADVLDPRDRK 258 +A+NL+GD L D+L+PR +K Sbjct: 301 VAINLVGDRLRDILNPRWQK 320 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 111 bits (278), Expect = 5e-26, Method: Compositional matrix adjust. Identities = 70/223 (31%), Positives = 127/223 (56%), Gaps = 2/223 (0%) Query: 36 AAHLLGSDMLGRDLLSGIFHGARVSLLIAVVSTLLALVLGISGGLLAGYYGGLADAVLMR 95 + + LG+D GRD+ + + +G RVS+L + T + +VLG++ G + GY+ G D R Sbjct: 126 SENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDLFTQR 185 Query: 96 VTEFFQTIPSFLFALAIVAVVQPNLATIALAIGVTAWPSLARLVRAEVLKLRHSEMVQAS 155 + E + ++P + ++ QP+L + + + + W SL+ VRA+ L+ R+ E +QA+ Sbjct: 186 LLEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLEYIQAA 245 Query: 156 AALGATDLRIMLRDILPNTLTPILVSTSLMVATAILTESSLAFLGLG-DPNAVSWGNMVG 214 A+G D I+ R +LPN++T ++ ++ AIL +SL FLGLG P+ S G ++ Sbjct: 246 RAMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLGELLA 305 Query: 215 SGREVIRTDWYITTIPGIAIVITVLALNLLGDGLADVLDPRDR 257 G+ + W+I + + +T+L L +G+ L + LD R + Sbjct: 306 QGKNNLDA-WWIALSTFVVLTVTLLLLTNIGNALRNALDVRRK 347 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 96.7 bits (239), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 76/243 (31%), Positives = 119/243 (48%), Gaps = 2/243 (0%) Query: 7 VLMALSSPLLFPGDPLDMVAEPFLHPGVDAAHLLGSDMLGRDLLSGIFHGARVSLLIAVV 66 +LMA+ P + P D +V + + G+ LLGSD LGRD+LS I G R ++ +A+ Sbjct: 44 ILMAILGPSISPYDATAIV-DTDVFSGMSHKFLLGSDYLGRDMLSRILFGTRATIGLALA 102 Query: 67 STLLALVLGISGGLLAGYYGGLADAVLMRVTEFFQTIPSFLFALAIVAVVQPNLATIALA 126 +T+LA G + L A + GG DAV+ R + +IPS +FAL +VA ++ + L Sbjct: 103 ATVLASATGTAIALFAAFSGGWRDAVISRALDALISIPSKMFALMMVATFGSSMLLLVLT 162 Query: 127 IGVTAWPSLARLVRAEVLKLRHSEMVQASAALGATDLRIMLRDILPNTLTPILVSTSL-M 185 +T P R+ R+ + ++ E VQA+ A G IM ++LPN + P+L L Sbjct: 163 AAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGVWYIMTVEMLPNMIRPVLADFGLRF 222 Query: 186 VATAILTESSLAFLGLGDPNAVSWGNMVGSGREVIRTDWYITTIPGIAIVITVLALNLLG 245 V +L P WG++V + +P +AI + +NLL Sbjct: 223 VYVVLLLSGLSFLSLGVQPPDADWGSLVRENISGLGEGALAVIMPALAIASLTIGVNLLI 282 Query: 246 DGL 248 D L Sbjct: 283 DNL 285 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 0.141 0.405 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: 645,687 Number of extensions: 23410 Number of successful extensions: 194 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 192 Number of HSP's successfully gapped: 7 Length of query: 258 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 175 Effective length of database: 1,226,865 Effective search space: 214701375 Effective search space used: 214701375 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: 129 (54.3 bits)