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= 0101.0004.p (762 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... 196 5e-51 gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 161 2e-40 gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate tran... 134 3e-32 gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate tran... 79 1e-15 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 196 bits (498), Expect = 5e-51, Method: Compositional matrix adjust. Identities = 164/491 (33%), Positives = 261/491 (53%), Gaps = 33/491 (6%) Query: 3 FGAASVLGRSRH------VGIDSLRGVFPKTWLPYVLRLCDWIIAFVSLSLAYTTWLLLE 56 GAA L R H VG S RG K W + + ++ + L + W E Sbjct: 74 LGAAVALRRGTHMRTTVLVGFMSERG---KAWAEALAIIAPCVMLLI---LMHPMW---E 124 Query: 57 ISND----QTTPSGLPQTIFVLPVLIGSLLLSVFAMTHALKKFGRHALVSGLIGA----A 108 + D QT G P T+ V +G+ L+ + +L + R LV L+G A Sbjct: 125 YAEDEMFVQTPALGWPNTVRAAAVAVGAALM----IALSLLRISRQKLVD-LVGVLALLA 179 Query: 109 VVGGVLALQTFWPDHALRPMHVLLAGFLFCL--VAGVPIAFALTFGALMFFLLEPTLSVM 166 VV G + L W V+ G + + + G+PIAF + F L T + Sbjct: 180 VVAGAMYLGAAWLQAIGNWNLVVFFGLVLAVSVLLGIPIAFCFGLATVAFMLTVTTSPLA 239 Query: 167 VFAQQVAAGSDHFVMLAVPFFILAGMVMECNGMSSRLIELLLRMFGRLRGGLNLIMVTAM 226 V A + G ++LAVP FIL G ++E GM+ +++ L + G +RGGLN +++ AM Sbjct: 240 VVAGRFDEGMSSLILLAVPLFILLGHLVEMTGMAKAMVDFLASLLGHVRGGLNYVLLGAM 299 Query: 227 AFFSGVSGSKLADVAAVGGILMPAVRQTRQNPNEAAGLLAASAIMAETIPPCINMIILGF 286 SG+SG+K AD+AAV +L+P +++ + E LLAAS MAETIPP + +I +G Sbjct: 300 LLVSGISGAKTADMAAVAPVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGS 359 Query: 287 VANLSIGGLFLAGILPALAMAIALCIMAYYTGRKVDVSVVFIKPRPMGKLIGGALVGLIM 346 VA +SI LF GI+P + +A+ L I+A + ++ + R + + + AL L++ Sbjct: 360 VAGVSIAALFTGGIMPGIVLAVLLAILARWRSAEIMEGIQRAPGRVVLRTLIIALPALLL 419 Query: 347 IVMIGKGVASGIATSTEISSFAVIYAIVVGWLAFRELNRKVLVKLFVDAASMSGMVLFIV 406 ++I V G+AT+TE+S+ + Y++V G L +R+ + K L + VD A++SG +LFI+ Sbjct: 420 PILIRTAVVEGVATATEVSTIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFII 479 Query: 407 AAASSVAYALTVEQIPHALAELMVSLAHDYGSWMFILISVLALILFGAVLEGAXLALILF 466 A+ +++ALT HALAE M S+ G + F+L+S+ A I+ G+VLEG A++LF Sbjct: 480 GTATGMSWALTQSGFSHALAEAMTSVPG--GKYGFLLVSIAAFIVLGSVLEGIP-AMVLF 536 Query: 467 GAVLADHFRAV 477 +L +A+ Sbjct: 537 APLLFPVAKAI 547 >gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate transport system dctQ-M fusion permease large permease [Herbaspirillum seropedicae SmR1] Length = 627 Score = 161 bits (408), Expect = 2e-40, Method: Compositional matrix adjust. Identities = 137/427 (32%), Positives = 233/427 (54%), Gaps = 21/427 (4%) Query: 78 IGSLLLSVFAMTHALKKFGRHALVSGLIGAAVVGGVLALQTFWP------DHALRPMHVL 131 +G++L+ + A++ L+S L AV+GG L L P ++ L VL Sbjct: 154 VGAILMLLAAVSRMAAMTTMRLLLSALAVVAVIGGALWLAK--PMLLGMGNYNLIVFFVL 211 Query: 132 LAGFLFCLVAGVPIAFALTFGALMFFLLEPTLSVMVFAQQVAAGSDHFVMLAVPFFILAG 191 L G C+ G+PIAFA + + L T +M+ ++ G ++L+VP F+L G Sbjct: 212 LIGV--CVAGGIPIAFAFGTATMAYLALATTAPLMIVVSRMDEGMSSLILLSVPLFVLLG 269 Query: 192 MVMECNGMSSRLIELLLRMFGRLRGGLNLIMVTAMAFFSGVSGSKLADVAAVGGILMPAV 251 ++E +G++ LI+ + + G +RGGL +++ AM SG+SGSK AD+AA+ L P + Sbjct: 270 SLLEMSGLAKTLIDFMAALLGHVRGGLQYVLLGAMFLVSGISGSKAADMAAIAPALFPEM 329 Query: 252 RQTRQNPNEAAGLLAASAIMAETIPPCINMIILGFVANLSIGGLFLAGILPALAMAIALC 311 ++ P E LL++S M ETIPP + +I +G V ++SI LF+ G++PA IA+ Sbjct: 330 KKRGSKPEELVALLSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPAAIATIAIA 389 Query: 312 IMAYYTGRKVDVSVVFIKPRPMG---KLIGGALVGLIMIVMIGKGVASGIATSTEISSFA 368 ++ + R+ + V K P+ K + A+ L + ++I V G+AT+TE+++ Sbjct: 390 VVCWMRARREPMPDV--KRAPLSLIVKALIAAIPALALPMLIRVAVIEGVATATEVATIG 447 Query: 369 VIYAIVVGW---LAFRELNRKVLVKLFVDAASMSGMVLFIVAAASSVAYALTVEQIPHAL 425 V Y +VVG L R L+ K L + +++A++SG +L I+ A+++A+ALT L Sbjct: 448 VAYTVVVGLIMHLFMRHLSFKRLYPMLIESAALSGAILLIIGMATAMAWALTQSGFSAKL 507 Query: 426 AELMVSLAHDYGSWMFILISVLALILFGAVLEGAXLALILFGAVLADHFRAVADADCSAA 485 LM + G F+LI+++ I+ G++LEG A++LFG +L R++ D A Sbjct: 508 VALMQGVPG--GGVGFLLITIVIFIVLGSLLEGIP-AIVLFGPLLFPVARSLGVHDVHYA 564 Query: 486 WVQSAAL 492 V A+ Sbjct: 565 MVVILAM 571 >gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 426 Score = 134 bits (337), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 97/297 (32%), Positives = 160/297 (53%), Gaps = 17/297 (5%) Query: 139 LVAGVPIAFALTFGALMFFLLEPTLSVMVFAQQVAAGSDHFVMLAVPFFILAGMVMECNG 198 ++ G+PI+ +L L F + + A ++ G + F ++A+PFFILAG + G Sbjct: 14 MLTGMPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIPFFILAGNFLTHGG 73 Query: 199 MSSRLIELLLRMFGRLRGGLNLIMVTAMAFFSGVSGSKLADVAAVGGILMPAVRQTRQNP 258 ++ R+I M G GGL L V A A F+ VSGS A V A+G I++PA+ + + P Sbjct: 74 VARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGSIILPAMVK-QGFP 132 Query: 259 NE-AAGLLAASAIMAETIPPCINMIILGFVANLSIGGLFLAGILPALAMAIALCIMAYYT 317 N AG++ S + IPP I M++ N S+G LF+AG++P L +A L + ++ Sbjct: 133 NRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLLLAFLLGVTTWFL 192 Query: 318 GRKVDVSVVFIKPRPMGKLIGGALV--------GLIMIVMIGKGVASGIATSTEISSFAV 369 RK + PR + K GL +IV++ G+ +G+ T TE ++ A Sbjct: 193 ARKNN------YPR-LKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFTPTEAAAMAA 245 Query: 370 IYAIVVGWLAFRELNRKVLVKLFVDAASMSGMVLFIVAAASSVAYALTVEQIPHALA 426 +YA + +++L K + K+ +D+ASMS M+L+I+ A ++ +T E IP A+A Sbjct: 246 VYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIPQAMA 302 >gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 449 Score = 79.3 bits (194), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 60/186 (32%), Positives = 94/186 (50%), Gaps = 5/186 (2%) Query: 138 CLVAGVPIAFAL---TFGALMFFLLEPTLSVMVFAQQVAAGSDHFVMLAVPFFILAGMVM 194 + +G+PIAFAL G + FF+ E +L + Q V +L++P FIL G + Sbjct: 17 VMCSGMPIAFALGVVATGFMYFFMPESSLDTI--TQNVYEEIASITLLSIPLFILKGAAI 74 Query: 195 ECNGMSSRLIELLLRMFGRLRGGLNLIMVTAMAFFSGVSGSKLADVAAVGGILMPAVRQT 254 + L + ++ GGL + V A A F+ ++GS A +A+G +P +R+ Sbjct: 75 GKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPEMRRR 134 Query: 255 RQNPNEAAGLLAASAIMAETIPPCINMIILGFVANLSIGGLFLAGILPALAMAIALCIMA 314 +P AAG++AA + +PP I MI+ A S+G LFLAGI P + + + A Sbjct: 135 GYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVLLFAGYA 194 Query: 315 YYTGRK 320 Y RK Sbjct: 195 VYRARK 200 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 0.140 0.427 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: 2,182,583 Number of extensions: 85630 Number of successful extensions: 442 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 433 Number of HSP's successfully gapped: 4 Length of query: 762 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 669 Effective length of database: 1,179,515 Effective search space: 789095535 Effective search space used: 789095535 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: 134 (56.2 bits)