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= 0035.0044.p (355 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, d... 243 1e-65 gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 190 2e-49 gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate tran... 173 2e-44 gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate tran... 100 1e-22 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 243 bits (621), Expect = 1e-65, Method: Compositional matrix adjust. Identities = 137/346 (39%), Positives = 221/346 (63%), Gaps = 2/346 (0%) Query: 1 MSSRLIELLLRMFGRLRGGLNLIMVTAMAFFSGVSGSKLADVAAVGGILMPAVRQTRQNP 60 M+ +++ L + G +RGGLN +++ AM SG+SG+K AD+AAV +L+P +++ + Sbjct: 272 MAKAMVDFLASLLGHVRGGLNYVLLGAMLLVSGISGAKTADMAAVAPVLLPEMKRRGNHE 331 Query: 61 NEAAGLLAASAIMAETIPPCINMIILGFVANLSIGGLFLAGILPALAMAIALCIMAYYTG 120 E LLAAS MAETIPP + +I +G VA +SI LF GI+P + +A+ L I+A + Sbjct: 332 GELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMPGIVLAVLLAILARWRS 391 Query: 121 RKVDVSVVFIKPRPMGKLIGGALVGLIMIVMIGKGVASGVATSTEISSFAVVYAIVVGWL 180 ++ + R + + + AL L++ ++I V GVAT+TE+S+ + Y++V G L Sbjct: 392 AEIMEGIQRAPGRVVLRTLIIALPALLLPILIRTAVVEGVATATEVSTIGIAYSVVAGLL 451 Query: 181 AFRELNRKVLVKLFVDAASMSGMVLFIVAAASSVAYALTVEQIPHALAELMVSLAHDYGS 240 +R+ + K L + VD A++SG +LFI+ A+ +++ALT HALAE M S+ G Sbjct: 452 VYRKFDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQSGFSHALAEAMTSVPG--GK 509 Query: 241 WMFILISVLALILFGAVLEGAPALIIFGPLLTPIAVQLGYNPLHFAIILVISMGIGLFSP 300 + F+L+S+ A I+ G+VLEG PA+++F PLL P+A +G + +H+A+++++SMG+GLF+P Sbjct: 510 YGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHEVHYAMVIILSMGVGLFAP 569 Query: 301 PFGLGMYATCAIAQVRLQDVVKPYLKYLAILLVTLVVIIVWPDLSL 346 PFGLG YA C I +V VK YL L+V L+++ P S+ Sbjct: 570 PFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVPWFSI 615 >gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate transport system dctQ-M fusion permease large permease [Herbaspirillum seropedicae SmR1] Length = 627 Score = 190 bits (482), Expect = 2e-49, Method: Compositional matrix adjust. Identities = 123/333 (36%), Positives = 202/333 (60%), Gaps = 10/333 (3%) Query: 1 MSSRLIELLLRMFGRLRGGLNLIMVTAMAFFSGVSGSKLADVAAVGGILMPAVRQTRQNP 60 ++ LI+ + + G +RGGL +++ AM SG+SGSK AD+AA+ L P +++ P Sbjct: 277 LAKTLIDFMAALLGHVRGGLQYVLLGAMFLVSGISGSKAADMAAIAPALFPEMKKRGSKP 336 Query: 61 NEAAGLLAASAIMAETIPPCINMIILGFVANLSIGGLFLAGILPALAMAIALCIMAYYTG 120 E LL++S M ETIPP + +I +G V ++SI LF+ G++PA IA+ ++ + Sbjct: 337 EELVALLSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPAAIATIAIAVVCWMRA 396 Query: 121 RKVDVSVVFIKPRPMG---KLIGGALVGLIMIVMIGKGVASGVATSTEISSFAVVYAIVV 177 R+ + V K P+ K + A+ L + ++I V GVAT+TE+++ V Y +VV Sbjct: 397 RREPMPDV--KRAPLSLIVKALIAAIPALALPMLIRVAVIEGVATATEVATIGVAYTVVV 454 Query: 178 G---WLAFRELNRKVLVKLFVDAASMSGMVLFIVAAASSVAYALTVEQIPHALAELMVSL 234 G L R L+ K L + +++A++SG +L I+ A+++A+ALT L LM + Sbjct: 455 GLIMHLFMRHLSFKRLYPMLIESAALSGAILLIIGMATAMAWALTQSGFSAKLVALMQGV 514 Query: 235 AHDYGSWMFILISVLALILFGAVLEGAPALIIFGPLLTPIAVQLGYNPLHFAIILVISMG 294 G F+LI+++ I+ G++LEG PA+++FGPLL P+A LG + +H+A++++++MG Sbjct: 515 PG--GGVGFLLITIVIFIVLGSLLEGIPAIVLFGPLLFPVARSLGVHDVHYAMVVILAMG 572 Query: 295 IGLFSPPFGLGMYATCAIAQVRLQDVVKPYLKY 327 IGLF+PPFG+G YA CAI +V V Y Sbjct: 573 IGLFAPPFGVGFYAACAIGKVSPDGVFNRVWGY 605 >gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 426 Score = 173 bits (438), Expect = 2e-44, Method: Compositional matrix adjust. Identities = 120/358 (33%), Positives = 198/358 (55%), Gaps = 19/358 (5%) Query: 2 SSRLIELLLRMFGRLRGGLNLIMVTAMAFFSGVSGSKLADVAAVGGILMPAVRQTRQNPN 61 + R+I M G GGL L V A A F+ VSGS A V A+G I++PA+ + + PN Sbjct: 75 ARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGSIILPAMVK-QGFPN 133 Query: 62 E-AAGLLAASAIMAETIPPCINMIILGFVANLSIGGLFLAGILPALAMAIALCIMAYYTG 120 AG++ S + IPP I M++ N S+G LF+AG++P L +A L + ++ Sbjct: 134 RFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLLLAFLLGVTTWFLA 193 Query: 121 RKVDVSVVFIKPRPMGKLIGGALV--------GLIMIVMIGKGVASGVATSTEISSFAVV 172 RK + PR + K GL +IV++ G+ +GV T TE ++ A V Sbjct: 194 RKNN------YPR-LKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFTPTEAAAMAAV 246 Query: 173 YAIVVGWLAFRELNRKVLVKLFVDAASMSGMVLFIVAAASSVAYALTVEQIPHALAELMV 232 YA + +++L K + K+ +D+ASMS M+L+I+ A ++ +T E IP A+A + Sbjct: 247 YAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIPQAMAAWIT 306 Query: 233 SLAHDYGSWMFILISVLALILFGAVLEGAPALIIFGPLLTPIAVQLGYNPLHFAIILVIS 292 G F+L+ + L+L G V+E + ++I P+L P+A++LG +P+HF I++V++ Sbjct: 307 D--SGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHFGILIVVN 364 Query: 293 MGIGLFSPPFGLGMYATCAIAQVRLQDVVKPYLKYLAILLVTLVVIIVWPDLSLWLPR 350 M +G+ PP GL +Y I ++ + ++ + +L +L L ++ WP LSLWLP Sbjct: 365 MEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGFLALVTYWPALSLWLPN 422 >gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 449 Score = 100 bits (250), Expect = 1e-22, Method: Compositional matrix adjust. Identities = 86/353 (24%), Positives = 171/353 (48%), Gaps = 19/353 (5%) Query: 15 RLRGGLNLIMVTAMAFFSGVSGSKLADVAAVGGILMPAVRQTRQNPNEAAGLLAASAIMA 74 ++ GGL + V A A F+ ++GS A +A+G +P +R+ +P AAG++AA + Sbjct: 93 KVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPEMRRRGYSPGFAAGIIAAGGTLG 152 Query: 75 ETIPPCINMIILGFVANLSIGGLFLAGILPALAMAIALCIMAYYTGRKV----------- 123 +PP I MI+ A S+G LFLAGI P + + + A Y RK Sbjct: 153 ILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVLLFAGYAVYRARKEYRLAHAVYSAG 212 Query: 124 DVSVVFIKPRPMG-----KLIGGALVGLIMIVMIGKGVASGVATSTEISSFAVVYAIVVG 178 ++ +++ L LI+++ + + G+AT +E + + A+V+ Sbjct: 213 GAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVMVALYGGLATPSETAGLGALLALVLI 272 Query: 179 WLAFRELNRKVLVKLFVDAASMSGMVLFIVAAASSVAYALTVEQIPHALAELMVSLAHDY 238 + +R + + SGM+L I+ + +Y ++ I + A+ +V L Sbjct: 273 AVVYRIYKPREIAPFLSSTIKESGMLLLIIGMSLLYSYVMSYLHISQSAAQWVVDL--HL 330 Query: 239 GSWMFILISVLALILFGAVLEGAPALIIFGPLLTPIAVQLGYNPLHFAIILVISMGIGLF 298 W+ + + + +I+ G L +++ P++ P G++ + F I++ + M +GL Sbjct: 331 SKWLLLAVILGMVIVLGFFLPPVSIILMTAPIILPPLKAAGFDLIWFGIVMTVVMEMGLI 390 Query: 299 SPPFGLGMYATCAIA-QVRLQDVVKPYLKYLAILLVTLVVIIVWPDLSLWLPR 350 PP GL ++ IA + L DV+K + +LA++ + ++++ ++P ++ LP Sbjct: 391 HPPVGLNLFVIKNIAPDIALGDVIKGTIPFLALMFLAVLLLCMFPGIATLLPD 443 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 0.330 0.143 0.419 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: 883,072 Number of extensions: 32228 Number of successful extensions: 234 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 225 Number of HSP's successfully gapped: 5 Length of query: 355 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 269 Effective length of database: 1,212,660 Effective search space: 326205540 Effective search space used: 326205540 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 (21.8 bits) S2: 131 (55.1 bits)