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= 0013.0174.p (201 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... 227 4e-61 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 184 6e-48 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 183 8e-48 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 90 1e-19 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 78 6e-16 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 227 bits (579), Expect = 4e-61, Method: Compositional matrix adjust. Identities = 108/213 (50%), Positives = 141/213 (66%), Gaps = 12/213 (5%) Query: 1 MDGPLGKHIQAAF-LKSNLIAFDKMWDNGFRQALSSAKPIRTPEDFKAFKIRVPPSPLWT 59 MDG LG H++ +S L AF+K+WDNG+RQ +S KPI+ ED K K+RVPPSPLWT Sbjct: 132 MDGELGAHVRKQIEARSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPSPLWT 191 Query: 60 SLFKSLGAAPVSIPWAETYSALQTRMADGIENALATIYFSKMYEISKHLSYTNHMWDGFW 119 S+FK+ AAP SI +AE YSALQT++ +G EN +A I +K+YE+ K+ S TNHMWDGFW Sbjct: 192 SMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFW 251 Query: 120 M-----------XRARDIVVKVMNEAAVKQRTDVEKLNGELAGNLGTKGVQFTKVDRAPF 168 ++++ +++NEA V QR DV KLN L + KG+ F D F Sbjct: 252 FLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKGLAFNNADADSF 311 Query: 169 QEKLRQAGFYGEWKRRMGDEAWSLLEATTGKLA 201 + KLR AGFY EWK++ GDE W+LLE TGKLA Sbjct: 312 RAKLRAAGFYAEWKKKFGDEPWALLEKYTGKLA 344 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 184 bits (466), Expect = 6e-48, Method: Compositional matrix adjust. Identities = 85/211 (40%), Positives = 130/211 (61%), Gaps = 11/211 (5%) Query: 1 MDGPLGKHIQAAFLKSNLIAFDKMWDNGFRQALSSAKPIRTPEDFKAFKIRVPPSPLWTS 60 MDGPLG H++A K L+ K WDNGFRQ +S KP+R D K K+RVP +P+ TS Sbjct: 134 MDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLKLRVPAAPMLTS 193 Query: 61 LFKSLGAAPVSIPWAETYSALQTRMADGIENALATIYFSKMYEISKHLSYTNHMWDGFWM 120 LF +LGA+P I + E YS+LQT++ +G EN LA I +++YE+ K + +NH+WD +W+ Sbjct: 194 LFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWDAYWI 253 Query: 121 XRAR-----------DIVVKVMNEAAVKQRTDVEKLNGELAGNLGTKGVQFTKVDRAPFQ 169 R +IV + +++AA +R D+ +G +L +KG+Q + D+ F+ Sbjct: 254 LGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASKGLQIVEADKDSFK 313 Query: 170 EKLRQAGFYGEWKRRMGDEAWSLLEATTGKL 200 E L +A FY + + + G++AW LLE + G L Sbjct: 314 EALARANFYKDMRAKFGEDAWKLLEGSVGAL 344 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 183 bits (465), Expect = 8e-48, Method: Compositional matrix adjust. Identities = 86/211 (40%), Positives = 130/211 (61%), Gaps = 11/211 (5%) Query: 1 MDGPLGKHIQAAFLKSNLIAFDKMWDNGFRQALSSAKPIRTPEDFKAFKIRVPPSPLWTS 60 MDGPLG +++A K L+ K WDNGFRQ +S KPI+T D K K+RVP +P+ TS Sbjct: 137 MDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGLKLRVPAAPMLTS 196 Query: 61 LFKSLGAAPVSIPWAETYSALQTRMADGIENALATIYFSKMYEISKHLSYTNHMWDGFWM 120 LF +LGA+P I + E YS+LQT++ +G EN LA I +++YE+ K + +NH+WD +W+ Sbjct: 197 LFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWDAYWI 256 Query: 121 XRAR-----------DIVVKVMNEAAVKQRTDVEKLNGELAGNLGTKGVQFTKVDRAPFQ 169 R +IV + +++AA +R D+ L+G +L KGVQ + D+ F+ Sbjct: 257 LGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDLQGKGVQIIEADKNSFK 316 Query: 170 EKLRQAGFYGEWKRRMGDEAWSLLEATTGKL 200 E L + FY + + + GD+AW LL+ + G L Sbjct: 317 EALARGSFYKDLRAKFGDDAWKLLQNSVGSL 347 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 90.1 bits (222), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 41/117 (35%), Positives = 69/117 (58%), Gaps = 2/117 (1%) Query: 2 DGPLGKHIQAAFLKSNLIAFDKMWDNGFRQALSSAKPIRTPEDFKAFKIRVPPSPLWTSL 61 +GP+GK + + WDNGF+ +S+ KP+ P DF+ K+R+ S + + Sbjct: 122 EGPIGKDLFKKLEPKGITGL-AYWDNGFK-VMSANKPLHHPADFRGLKMRIQSSKVLDAQ 179 Query: 62 FKSLGAAPVSIPWAETYSALQTRMADGIENALATIYFSKMYEISKHLSYTNHMWDGF 118 ++LGA P + ++E Y ALQT + DG EN + +Y KM+E+ KH++ +NH + G+ Sbjct: 180 MRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGY 236 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 77.8 bits (190), Expect = 6e-16, Method: Compositional matrix adjust. Identities = 48/149 (32%), Positives = 80/149 (53%), Gaps = 16/149 (10%) Query: 2 DGPLGKHIQAAF--LKSNLIAFDKMWDNGFRQALSSAKPIRTPEDFKAFKIRVPPSPLWT 59 +GP+G Q F L+ I WDNG + +++ +P+ DF+A K+R+ S + Sbjct: 130 EGPIG---QGLFQKLEGKGIKGLAYWDNGMK-VMTANRPLHKVADFRALKMRIQSSKVLD 185 Query: 60 SLFKSLGAAPVSIPWAETYSALQTRMADGIENALATIYFSKMYEISKHLSYTNHMWDG-- 117 F++L A P + ++E Y A+QT + DG EN + +Y KM+E+ +L+ ++H + G Sbjct: 186 EQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHGYIGYA 245 Query: 118 ------FWMXRARDIVVKVMNEAAVKQRT 140 FW DI ++ EAA+KQ T Sbjct: 246 VIVNKKFWEALPADIRSQL--EAAMKQAT 272 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 0.319 0.133 0.409 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: 626,943 Number of extensions: 23183 Number of successful extensions: 73 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 71 Number of HSP's successfully gapped: 5 Length of query: 201 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 120 Effective length of database: 1,236,335 Effective search space: 148360200 Effective search space used: 148360200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 128 (53.9 bits)