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= 0034.0230.p (337 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 372 e-104 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 348 5e-97 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 345 2e-96 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 123 2e-29 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 116 3e-27 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 372 bits (954), Expect = e-104, Method: Compositional matrix adjust. Identities = 180/337 (53%), Positives = 233/337 (69%), Gaps = 2/337 (0%) Query: 2 QITRRTVLKAAASAVGIAAVGAPSVRAQTAVFNYKVATNVPVTHPIYIRLSEAAEKTKAE 61 +ITRR LK A+ A AA G S A A F +K A N+PVTHP+ R E A + Sbjct: 7 KITRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMAAAIAEQ 66 Query: 62 TGGKVDIKVFPNGQLGSDTDLLSQVRSGSVEFLTLPGVILANLVPMASLNSVGFAFHDYP 121 + G+++++++PN QLG+DTD+LSQVR+G+++F TL +IL LVP A ++ +GFAF DY Sbjct: 67 SKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYS 126 Query: 122 AVWKAMDGDLGKYIRSHIE-KTNLHVFDKVWDNGFRHIT-SNKPINTPAELANMKIRVPV 179 VW AMDG+LG ++R IE ++ L F+K+WDNG+R IT S KPI +L MK+RVP Sbjct: 127 QVWPAMDGELGAHVRKQIEARSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPP 186 Query: 180 SPLLLSLFKSLKAAPTPINFNELYSALQTRIVDGQENPFPIITTAKLYEVQKYCAMTSHA 239 SPL S+FK+ AAPT INF E+YSALQT+IV+GQENP II+TAKLYEVQKYC++T+H Sbjct: 187 SPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHM 246 Query: 240 WDGYWLLANKHSFAALPVALQDIITRNFNAAGVNQRADSEKMAADLQQELAAKGLIFSKP 299 WDG+W L NK SF LP LQ+++TR N AGVNQRAD K+ L E+ KGL F+ Sbjct: 247 WDGFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKGLAFNNA 306 Query: 300 ATAQFRQVLQQSGFYKEWKNKFGEEAWAQLEAAVGKL 336 FR L+ +GFY EWK KFG+E WA LE GKL Sbjct: 307 DADSFRAKLRAAGFYAEWKKKFGDEPWALLEKYTGKL 343 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 348 bits (892), Expect = 5e-97, Method: Compositional matrix adjust. Identities = 160/335 (47%), Positives = 225/335 (67%), Gaps = 1/335 (0%) Query: 3 ITRRTVLKAAASAVGIAAVGAPSVRAQTAVFNYKVATNVPVTHPIYIRLSEAAEKTKAET 62 ++RR +LKA A + S A A FNYK AT +HP+ R +A ++ + T Sbjct: 13 VSRRQLLKAGAVGAALPLFSIMSRPANAAEFNYKFATGQDPSHPVNKRAQQAIDRIREAT 72 Query: 63 GGKVDIKVFPNGQLGSDTDLLSQVRSGSVEFLTLPGVILANLVPMASLNSVGFAFHDYPA 122 GG++DIK+FP QLGSDTDL+SQ+R+G VEF V+L+ LVP A + + GFAFHDY Sbjct: 73 GGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFAFHDYKE 132 Query: 123 VWKAMDGDLGKYIRSHIEKTNLHVFDKVWDNGFRHIT-SNKPINTPAELANMKIRVPVSP 181 VW+AMDG LG Y+R+ IEK L K WDNGFR IT S KPI T A+L +K+RVP +P Sbjct: 133 VWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGLKLRVPAAP 192 Query: 182 LLLSLFKSLKAAPTPINFNELYSALQTRIVDGQENPFPIITTAKLYEVQKYCAMTSHAWD 241 +L SLF +L A+PTPINFNE+YS+LQT++V+GQENP II+TA+LYEVQK+C +++H WD Sbjct: 193 MLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWD 252 Query: 242 GYWLLANKHSFAALPVALQDIITRNFNAAGVNQRADSEKMAADLQQELAAKGLIFSKPAT 301 YW+L N+ +F LP +Q+I+ R + A ++RAD ++ + +L KG+ + Sbjct: 253 AYWILGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDLQGKGVQIIEADK 312 Query: 302 AQFRQVLQQSGFYKEWKNKFGEEAWAQLEAAVGKL 336 F++ L + FYK+ + KFG++AW L+ +VG L Sbjct: 313 NSFKEALARGSFYKDLRAKFGDDAWKLLQNSVGSL 347 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 345 bits (886), Expect = 2e-96, Method: Compositional matrix adjust. Identities = 161/336 (47%), Positives = 225/336 (66%), Gaps = 1/336 (0%) Query: 2 QITRRTVLKAAASAVGIAAVGAPSVRAQTAVFNYKVATNVPVTHPIYIRLSEAAEKTKAE 61 Q+TRR +LKA A + S A A F+YK AT +HP+ R EA ++ + Sbjct: 9 QVTRRNMLKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQEAIDRIRNA 68 Query: 62 TGGKVDIKVFPNGQLGSDTDLLSQVRSGSVEFLTLPGVILANLVPMASLNSVGFAFHDYP 121 T G+++IK+FP QLGSDTDL+SQVR+G VEF +L+ LVP A + + GFAFHDY Sbjct: 69 TNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNTGFAFHDYG 128 Query: 122 AVWKAMDGDLGKYIRSHIEKTNLHVFDKVWDNGFRHIT-SNKPINTPAELANMKIRVPVS 180 AVWKAMDG LG ++R+ IEK L K WDNGFR IT S KP+ ++ +K+RVP + Sbjct: 129 AVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLKLRVPAA 188 Query: 181 PLLLSLFKSLKAAPTPINFNELYSALQTRIVDGQENPFPIITTAKLYEVQKYCAMTSHAW 240 P+L SLF +L A+PTPINFNE+YS+LQT++V+GQENP II+TA+LYEVQK+C +++H W Sbjct: 189 PMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVW 248 Query: 241 DGYWLLANKHSFAALPVALQDIITRNFNAAGVNQRADSEKMAADLQQELAAKGLIFSKPA 300 D YW+L N+ +F LP +Q+I+ R + A ++RAD + + +LA+KGL + Sbjct: 249 DAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASKGLQIVEAD 308 Query: 301 TAQFRQVLQQSGFYKEWKNKFGEEAWAQLEAAVGKL 336 F++ L ++ FYK+ + KFGE+AW LE +VG L Sbjct: 309 KDSFKEALARANFYKDMRAKFGEDAWKLLEGSVGAL 344 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 123 bits (309), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 81/258 (31%), Positives = 136/258 (52%), Gaps = 21/258 (8%) Query: 9 LKAAASAVGIAAVGAPSVRAQTAV---FNYKVATNVPVTHPIYIRLSEAAEKTKAETGGK 65 LK+ A+ AA+ + + AQ + F++ VA + P R E AEK T G+ Sbjct: 3 LKSILLAMTAAAIVSTNAFAQQPIVIKFSHVVANDTPKGKAAE-RFKELAEKA---TKGR 58 Query: 66 VDIKVFPNGQLGSDTDLLSQVRSGSVEFLTLPGVILANLVPMASLNSVGFAFHDYPAV-- 123 V I+V+PN L D + L ++ G+V+ L +L L F D P + Sbjct: 59 VKIEVYPNSTLYKDKEELEALQLGAVQMLA------PSLAKFGPLGVKEFEVFDLPYIFP 112 Query: 124 -----WKAMDGDLGKYIRSHIEKTNLHVFDKVWDNGFRHITSNKPINTPAELANMKIRVP 178 ++ +G +GK + +E + WDNGF+ +++NKP++ PA+ +K+R+ Sbjct: 113 TKEVLYRVTEGPIGKDLFKKLEPKGITGL-AYWDNGFKVMSANKPLHHPADFRGLKMRIQ 171 Query: 179 VSPLLLSLFKSLKAAPTPINFNELYSALQTRIVDGQENPFPIITTAKLYEVQKYCAMTSH 238 S +L + ++L A P + F+E+Y ALQT +VDG ENP + T K++EVQK+ +++H Sbjct: 172 SSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNH 231 Query: 239 AWDGYWLLANKHSFAALP 256 + GY ++ NK + LP Sbjct: 232 GYLGYAVIVNKKFWDGLP 249 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 116 bits (290), Expect = 3e-27, Method: Compositional matrix adjust. Identities = 80/263 (30%), Positives = 137/263 (52%), Gaps = 16/263 (6%) Query: 6 RTVLKAAA-SAVGIAAVGAPSVRAQTAV---FNYKVATNVPVTHPIYIRLSEAAEKTKAE 61 RT L A A +G+ A + + Q + F++ VA + P R E AEK Sbjct: 7 RTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDTPKGKGAE-RFKELAEKA--- 62 Query: 62 TGGKVDIKVFPNGQLGSDTDLLSQVRSGSVEFLTLPGVILANLVPMASLN----SVGFAF 117 T G+V ++V+PN L D + L ++ GSV+ L P LA P+ + + + F Sbjct: 63 TQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLA-PS--LAKFGPLGAREFEVFDLPYIF 119 Query: 118 HDYPAVWKAMDGDLGKYIRSHIEKTNLHVFDKVWDNGFRHITSNKPINTPAELANMKIRV 177 D + + +G +G+ + +E + WDNG + +T+N+P++ A+ +K+R+ Sbjct: 120 PDKAVLKRVTEGPIGQGLFQKLEGKGIKGL-AYWDNGMKVMTANRPLHKVADFRALKMRI 178 Query: 178 PVSPLLLSLFKSLKAAPTPINFNELYSALQTRIVDGQENPFPIITTAKLYEVQKYCAMTS 237 S +L F++LKA P + F+E+Y A+QT +VDG EN + T K++EVQ ++ Sbjct: 179 QSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSD 238 Query: 238 HAWDGYWLLANKHSFAALPVALQ 260 H + GY ++ NK + ALP ++ Sbjct: 239 HGYIGYAVIVNKKFWEALPADIR 261 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 0.318 0.132 0.385 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: 915,394 Number of extensions: 34321 Number of successful extensions: 124 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 118 Number of HSP's successfully gapped: 6 Length of query: 337 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 251 Effective length of database: 1,212,660 Effective search space: 304377660 Effective search space used: 304377660 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 131 (55.1 bits)