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= 0001.4517.p (386 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311947|ref|YP_003776039.1| branched-chain amino acid ABC t... 234 6e-63 gi|300313995|ref|YP_003778087.1| urea ABC transporter periplasmi... 223 2e-59 gi|300310957|ref|YP_003775049.1| branched-chain amino acid ABC t... 77 2e-15 gi|300311772|ref|YP_003775864.1| branched-chain amino acid ABC t... 77 3e-15 gi|300312955|ref|YP_003777047.1| amino acid ABC transporter peri... 64 3e-11 >gi|300311947|ref|YP_003776039.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 418 Score = 234 bits (598), Expect = 6e-63, Method: Compositional matrix adjust. Identities = 131/360 (36%), Positives = 206/360 (57%), Gaps = 8/360 (2%) Query: 19 IGVLFSRSGATGVTESEHFFGTALAIEEINQLGGVLGRPLIPVAYDPKGDITEYRKLVTR 78 +G L S +G ++E+ LAI++IN +GG+LGR + + D D + + + Sbjct: 58 VGQLHSATGTMAISETGSIQAERLAIDQINAMGGILGRKIKIIQEDGASDWPTFAEKAKK 117 Query: 79 MLLEDEINVVFGCSRSSSRKAVLPVIERNNALLWYCSFYEGFEYSPNVIYTGAVPNQNSV 138 +L D + VFGC S+SRKAVLPV E++N LL+Y +FYEG E S NV YTG Q + Sbjct: 118 LLENDRVAAVFGCWTSASRKAVLPVFEKDNGLLYYPTFYEGLEQSKNVFYTGQEATQQVL 177 Query: 139 QLAAYLMQNKRTR-FFLVGTDYIYPRESNRLMRDMVEQ-HGGEVLDEIYLPLEAGRAELE 196 ++ + K+ + FFLVG+DYI+PR SN++ R +E G V+ E Y PL G + Sbjct: 178 AGLNWVAKEKKAKTFFLVGSDYIWPRTSNKIARKHIENVLKGSVVGEEYYPL--GNTQFG 235 Query: 197 EILTEIRAAQPDVVFSTLVGQSARQFYQLYPGFGFDPKVTPIASLSMAEEEVRLIGPEIC 256 ++ +I+ +PDV+F+ +VG S FY+ G K + ++S+ E+E+ IG E Sbjct: 236 SLINKIKLKKPDVIFADVVGGSNVAFYKQLKAAGVTAKTQNLLTISVTEDEMLGIGGENV 295 Query: 257 AGHITAATYFGSLDNASNRHFVELWRKRFN-DRPTSTWSEMAYTQIHLFARALQRAGSLD 315 G + YF SLDNA+N+ FV ++ +F + ++ AY L+ A+++AGS D Sbjct: 296 EGFFASMKYFQSLDNANNKKFVAEFKAKFGANSVIGDVTQAAYLGPWLWKAAVEKAGSFD 355 Query: 316 RRKLVEATHAVSFDS-PEGRISVDAENNHCALTPRIGICRSDGQFDIAWEASEPVKPDPY 374 K+V A+ + + PEG + V EN+H RIG + DGQF + +E SE ++P+P+ Sbjct: 356 VDKVVAASPGIELKTAPEGYVKVH-ENHHLWSKTRIGEAQKDGQFKVVYE-SELIEPNPF 413 >gi|300313995|ref|YP_003778087.1| urea ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 417 Score = 223 bits (567), Expect = 2e-59, Method: Compositional matrix adjust. Identities = 124/377 (32%), Positives = 205/377 (54%), Gaps = 19/377 (5%) Query: 15 DGWRIGVLFSRSGATGVTESEHFFGTALAIEEINQLGGVLGRPLIPVAYDPKGDITEYRK 74 D ++G+L S SG ++E+ + I+EIN GGV+G+ L PV DP + + + Sbjct: 30 DTIKVGILHSLSGTMAISETSLKDVALMTIDEINAAGGVMGKKLEPVVVDPASNWPLFAE 89 Query: 75 LVTRMLLEDEINVVFGCSRSSSRKAVLPVIERNNALLWYCSFYEGFEYSPNVIYTGAVPN 134 +++ +D+++VVFGC S SRK+VLPV + N+LL+Y YEG E NV YTGA PN Sbjct: 90 KARQLISQDKVSVVFGCWTSVSRKSVLPVFKELNSLLFYPVQYEGEELEKNVFYTGAAPN 149 Query: 135 QNSVQLAAYLMQNK---RTRFFLVGTDYIYPRESNRLMRDMVEQHG--GEVLDEIYLPLE 189 Q ++ YLM + RF L+GTDY+YPR +N+++R + G +DE+Y P Sbjct: 150 QQAIPAVEYLMSKEGGGAKRFVLLGTDYVYPRTTNKILRAFLHSKGVKDSDIDEVYTPF- 208 Query: 190 AGRAELEEILTEIR---AAQPDVVFSTLVGQSARQFYQLYPGFGFDPKVTPIASLSMAEE 246 G ++ + I+ I+ A V ST+ G S FY+ G P+ + S+ EE Sbjct: 209 -GHSDYQTIVANIKKFSAGGKTAVISTINGDSNVPFYKELGNAGLKATDVPVVAFSVGEE 267 Query: 247 EVRLIGPEICAGHITAATYFGSLDNASNRHFVELWRK--RFNDRP------TSTWSEMAY 298 E+R + + GH+ A YF S+ N N F++ W++ + + P T+ E Y Sbjct: 268 ELRGVDTKPLVGHLAAWNYFESVKNPVNTAFIKKWKEYAKAKNLPNADTVVTNDPMEATY 327 Query: 299 TQIHLFARALQRAGSLDRRKLVEATHAVSFDSPEG-RISVDAENNHCALTPRIGICRSDG 357 IH++A+A+++A S D K++ A ++ +P G + +D N+H IG ++DG Sbjct: 328 VGIHMWAQAVEKAKSTDTDKVIAAMGGQTYKAPSGYTLEMDKTNHHLHKPVMIGEIKADG 387 Query: 358 QFDIAWEASEPVKPDPY 374 QF++ ++ ++ P+ Sbjct: 388 QFNVVYKTKTTIRAQPW 404 >gi|300310957|ref|YP_003775049.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 413 Score = 77.0 bits (188), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 87/365 (23%), Positives = 159/365 (43%), Gaps = 29/365 (7%) Query: 10 PPRREDGWRIGVLFSRSGATGVTESEHFFGTALAIEEINQLGGVLGRPLIPVAYDPKGDI 69 P + RIG + SR + ++ + G ALA+E+IN GGV GRPL V + GD Sbjct: 31 PSHAAEAIRIGEINSRHRLSTAGQA-YRNGLALALEQINAAGGVGGRPLQLVVREDDGDA 89 Query: 70 TEYRKLVTRMLLEDEINVVFGCSRSSSRKAVLPVIERNNALLWYC-SFYEGFEYSPNVIY 128 + + ++ +D + V+ G S AV R +L + + Y Sbjct: 90 DQAARNARALISQDHVEVLTGSMLSDVALAVSREAARGRTVLVVGDALSDAITLDKGNRY 149 Query: 129 TGAVPNQNSVQLAAYLMQNKRT---RFFLVGTDYIYPRESNRLMRDMVEQHGGEV--LDE 183 T V +Q A Q R R+ +V +Y Y + + + +++Q +V + + Sbjct: 150 TFRVRPSTYMQAAMLAEQAARLPGRRWAVVAPNYEYGQSAVASFKLLLKQARPDVEFVSD 209 Query: 184 IYLPLEAGRAELEEILTEIRAAQPDVVFSTLVGQSARQFY------QLYPGFGFDPKVTP 237 + L G+ + +++ IR ++PD +F+ G+ ++F QL+ G Sbjct: 210 QWPAL--GKIKADDVARAIRQSRPDGIFNATFGEDLQKFVQAGNRQQLFEG--------- 258 Query: 238 IASLSMAEEEVRLIGP---EICAGHITAATYFGSLDNASNRHFVELWRKRFNDRPTSTWS 294 + +SMA + P E + + + ++ F+E + KRF++RP + + Sbjct: 259 VRVVSMASAGAPSLDPSQSEAIRDWLAIGYPWDQVSLPEHQRFLEAYLKRFSERPQLS-A 317 Query: 295 EMAYTQIHLFARALQRAGSLDRRKLVEATHAVSFDSPEGRISVDAENNHCALTPRIG-IC 353 YT + A L+++ D LVEA + F SP G +S A + +L +G + Sbjct: 318 VFGYTTMMAIAAGLKKSEGGDGEVLVEAMRGLQFGSPLGPVSFRALDQQASLGAFVGLVS 377 Query: 354 RSDGQ 358 + DG+ Sbjct: 378 QKDGR 382 >gi|300311772|ref|YP_003775864.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 404 Score = 76.6 bits (187), Expect = 3e-15, Method: Compositional matrix adjust. Identities = 77/358 (21%), Positives = 157/358 (43%), Gaps = 24/358 (6%) Query: 7 GDKPPRREDGWRIGVLFSRSGATGVTESEHFFGTALAIEEINQLGGVLGRPLIPVAYDPK 66 G R +D RIG + S E + G +A++EIN GGVLG+ L +A D Sbjct: 22 GSVAARAQDTIRIGEINSYKAQPAFLEP-YRRGWEMALDEINASGGVLGKKLEVIARDDN 80 Query: 67 GDITEYRKLVTRMLLEDEINVVFGCSRSSSRKAVLPVIERN-----------NALLWYCS 115 G+ + ++ ++ + + ++FG S++ A+ +++ + ++W Sbjct: 81 GNPGDSVRVAEELMARERVALLFGGFLSNTGLALTDYAKQHRVFFLAAEPLTDKIVWQNG 140 Query: 116 FYEGFEYSPNVIYTGAVPNQNSVQLAAYLMQNKRTRFFLVGTDYIYPRESNRLMRDMVEQ 175 + P+ A + +V+L K+ R+ +V +Y Y + + + +++Q Sbjct: 141 NKYTYRLRPSTSMLVASVVKEAVKL-------KKKRWAIVYPNYEYGQSAVASFKTLMKQ 193 Query: 176 HGGEV--LDEIYLPLEAGRAELEEILTEIRAAQPDVVFSTLVGQSARQFYQLYPGFGFDP 233 +V + E PL G+ + + + A+PD +F+ L +F + G Sbjct: 194 AQPDVEFVAEQAPPL--GKIDAGAVTQALADAKPDAIFNALFAADLGKFVREGNTRGLFE 251 Query: 234 KVTPIASLSMAEEEVRLIGPEICAGHITAATYFGSLDNASNRHFVELWRKRFNDRPTSTW 293 +V ++ L+ E + + E I + ++ ++ FVE +RK+FND P + Sbjct: 252 QVDVVSLLTGEPEYLDPLKGEAPQNWIVTGYPWYAIHTPEHKKFVEAYRKKFNDYPRNG- 310 Query: 294 SEMAYTQIHLFARALQRAGSLDRRKLVEATHAVSFDSPEGRISVDAENNHCALTPRIG 351 S + Y+ + A L++AGS D +L A + ++P I +++ L +G Sbjct: 311 SLVGYSALMSIAAGLRKAGSTDADRLAAAFSGLKVETPVASIVYRPQDHQSTLGAFVG 368 >gi|300312955|ref|YP_003777047.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 392 Score = 63.5 bits (153), Expect = 3e-11, Method: Compositional matrix adjust. Identities = 76/344 (22%), Positives = 150/344 (43%), Gaps = 25/344 (7%) Query: 1 MTIHPSGDKPPRREDGWRIGVLFSRSG---ATGVTESEHFFGTALAIEEI-NQLGGVLGR 56 M + P + D ++G L + SG A GV E E F LA++ + N+LGGV Sbjct: 13 MAMAVGASLPAQAADVVKVGFLTTLSGPASAPGVDEREGFM---LALKTLGNKLGGV--- 66 Query: 57 PLIPVAYDPKGDITEYRKLVTRMLLEDEINVVFGCSRSSSRKAVLPVIERNNALLWYCSF 116 P + D + ++ R++ ++++++ G S+ AV P + ++ + Sbjct: 67 PAEVIVVDDQFSPDAAKQGADRLIKREKVDILSGFVYSNILLAVAPAAFASKTVVVSANA 126 Query: 117 ----YEGFEYSPNVIYTGAVPNQNSVQLAAYLMQNKR-TRFFLVGTDYIYPRESNRLMRD 171 G +P ++ + N + + A LM +K R ++ +Y ++++ + Sbjct: 127 GPAQLAGAGCNP-YFFSASYQNDAAHEAAGKLMADKGYQRVAIIAPNYPAGKDASAGFKR 185 Query: 172 MVEQHGGEVLDEIYLPLEAGRAELEEILTEIRAAQPDVVFSTLVGQSARQFYQLYPGFGF 231 +++ + E++ L G+ + + ++RAA D ++ L G F + Y G Sbjct: 186 FLKK---DPAVELFPKL--GQLDFATEIAQLRAANIDALYFFLPGGMGVNFVKQYAAAGM 240 Query: 232 DPKVTPIASLSMAEEEVRLIGPEICAGHITAATYFGSLDNASNRHFVELWRKRFNDRPTS 291 DPK+ + A++++ L ++ AG + L N NR FV + K + +P S Sbjct: 241 DPKIVRVMPAYDADQQM-LSNGDLIAGVANTGQWSSDLPNEQNRAFVAAYLKEYGRQP-S 298 Query: 292 TWSEMAYTQIHLFARALQRAGSL--DRRKLVEATHAVSFDSPEG 333 ++ AY L A++ G +R L+ A +F S G Sbjct: 299 MFASQAYDAAMLIDSAVKAVGGKVENREALIAAIKTANFKSVRG 342 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 0.321 0.137 0.417 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: 1,280,936 Number of extensions: 53194 Number of successful extensions: 167 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 157 Number of HSP's successfully gapped: 6 Length of query: 386 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 299 Effective length of database: 1,207,925 Effective search space: 361169575 Effective search space used: 361169575 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: 131 (55.1 bits)