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= 0034.0137.p (303 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... 581 e-167 gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 338 4e-94 gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate tran... 110 2e-25 gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate tran... 96 3e-21 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 581 bits (1497), Expect = e-167, Method: Compositional matrix adjust. Identities = 301/303 (99%), Positives = 303/303 (100%) Query: 1 VAPVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMP 60 VAPVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMP Sbjct: 316 VAPVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMP 375 Query: 61 GIVLAVLLAILARWRSAEILEGIQRAPGRVVLRTLIIALPALLLPILIRTAVVEGVATAT 120 GIVLAVLLAILARWRSAEI+EGIQRAPGRVVLRTLIIALPALLLPILIRTAVVEGVATAT Sbjct: 376 GIVLAVLLAILARWRSAEIMEGIQRAPGRVVLRTLIIALPALLLPILIRTAVVEGVATAT 435 Query: 121 EVSTIGIAYSVVAGLLVYRQFDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQSGFS 180 EVSTIGIAYSVVAGLLVYR+FDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQSGFS Sbjct: 436 EVSTIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQSGFS 495 Query: 181 HALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHEVHYA 240 HALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHEVHYA Sbjct: 496 HALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHEVHYA 555 Query: 241 MVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVPWFSI 300 MVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVPWFSI Sbjct: 556 MVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVPWFSI 615 Query: 301 GFL 303 GFL Sbjct: 616 GFL 618 >gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate transport system dctQ-M fusion permease large permease [Herbaspirillum seropedicae SmR1] Length = 627 Score = 338 bits (867), Expect = 4e-94, Method: Compositional matrix adjust. Identities = 192/303 (63%), Positives = 243/303 (80%), Gaps = 4/303 (1%) Query: 5 LLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMPGIVL 64 L PEMK+RG+ EL++LL++SGAM ETIPPSLVLITIG+V VSI ALF GG+MP + Sbjct: 325 LFPEMKKRGSKPEELVALLSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPAAIA 384 Query: 65 AVLLAILARWRSA-EILEGIQRAPGRVVLRTLIIALPALLLPILIRTAVVEGVATATEVS 123 + +A++ R+ E + ++RAP ++++ LI A+PAL LP+LIR AV+EGVATATEV+ Sbjct: 385 TIAIAVVCWMRARREPMPDVKRAPLSLIVKALIAAIPALALPMLIRVAVIEGVATATEVA 444 Query: 124 TIGIAYSVVAGLLVY---RQFDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQSGFS 180 TIG+AY+VV GL+++ R +KRLYPML+++AALSGAIL IIG AT M+WALTQSGFS Sbjct: 445 TIGVAYTVVVGLIMHLFMRHLSFKRLYPMLIESAALSGAILLIIGMATAMAWALTQSGFS 504 Query: 181 HALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHEVHYA 240 L M VPGG GFLL++I FIVLGS+LEGIPA+VLF PLLFPVA+++GVH+VHYA Sbjct: 505 AKLVALMQGVPGGGVGFLLITIVIFIVLGSLLEGIPAIVLFGPLLFPVARSLGVHDVHYA 564 Query: 241 MVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVPWFSI 300 MV+IL+MG+GLFAPPFG+G+YAAC IG+V PD R+W YL ALVV LL+VAFVPW SI Sbjct: 565 MVVILAMGIGLFAPPFGVGFYAACAIGKVSPDGVFNRVWGYLAALVVALLVVAFVPWISI 624 Query: 301 GFL 303 GFL Sbjct: 625 GFL 627 >gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 426 Score = 110 bits (274), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 87/304 (28%), Positives = 155/304 (50%), Gaps = 7/304 (2%) Query: 1 VAPVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMP 60 + ++LP M ++G ++ SGA+ IPPS+V++ S+ LF G++P Sbjct: 118 IGSIILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVP 177 Query: 61 GIVLAVLLAI----LARWRSAEILEGIQRAPGRVVLRTLIIALPALLLPILIRTAVVEGV 116 G++LA LL + LAR + L+ A R + L L +++ + GV Sbjct: 178 GLLLAFLLGVTTWFLARKNNYPRLKKATWAERAAAFRK---SGWGLFLIVIVMGGIYTGV 234 Query: 117 ATATEVSTIGIAYSVVAGLLVYRQFDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQ 176 T TE + + Y+ + VY+ K++ +L+D+A++S +L+II A S+ +T Sbjct: 235 FTPTEAAAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTS 294 Query: 177 SGFSHALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHE 236 A+A +T G FLLV ++ G+V+E +++ AP+LFPVA +G+ Sbjct: 295 ENIPQAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDP 354 Query: 237 VHYAMVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVP 296 VH+ ++I+++M VG+ PP GL Y A I ++ + P+L ++ L +V + P Sbjct: 355 VHFGILIVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGFLALVTYWP 414 Query: 297 WFSI 300 S+ Sbjct: 415 ALSL 418 >gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 449 Score = 96.3 bits (238), Expect = 3e-21, Method: Compositional matrix adjust. Identities = 88/311 (28%), Positives = 152/311 (48%), Gaps = 23/311 (7%) Query: 6 LPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMPGIVLA 65 +PEM+RRG G ++AA G + +PPS+ +I A S+ LF GI PG++L Sbjct: 128 IPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLV 187 Query: 66 VLLAILARWRSAE---ILEGIQRAPGRVV-------------LRTLIIALPALLLPILIR 109 +L A A +R+ + + + A G + L LP L+L I + Sbjct: 188 LLFAGYAVYRARKEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVM 247 Query: 110 TAVVEGVATATEVSTIGIAYSVVAGLLVYRQFDWKRLYPMLVDTAALSGAILFIIGTATG 169 A+ G+AT +E + +G ++V +VYR + + + P L T SG +L IIG + Sbjct: 248 VALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLLIIGMSLL 307 Query: 170 MSWALTQSGFSHALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVA 229 S+ ++ S + A+ + + K+ L V + IVLG L + +++ AP++ P Sbjct: 308 YSYVMSYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTAPIILPPL 367 Query: 230 KAIGVHEVHYAMVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVA----VKRIWPYLGAL 285 KA G + + +V+ + M +GL PP GL + I + PD+A +K P+L + Sbjct: 368 KAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLF---VIKNIAPDIALGDVIKGTIPFLALM 424 Query: 286 VVGLLIVAFVP 296 + +L++ P Sbjct: 425 FLAVLLLCMFP 435 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 0.327 0.143 0.426 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: 828,768 Number of extensions: 32153 Number of successful extensions: 205 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 200 Number of HSP's successfully gapped: 4 Length of query: 303 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 218 Effective length of database: 1,217,395 Effective search space: 265392110 Effective search space used: 265392110 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 (21.7 bits) S2: 130 (54.7 bits)