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= 0025.0126.p (344 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312847|ref|YP_003776939.1| branched-chain amino acid ABC t... 254 8e-69 gi|300311772|ref|YP_003775864.1| branched-chain amino acid ABC t... 57 3e-09 >gi|300312847|ref|YP_003776939.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 383 Score = 254 bits (649), Expect = 8e-69, Method: Compositional matrix adjust. Identities = 148/337 (43%), Positives = 199/337 (59%), Gaps = 17/337 (5%) Query: 17 LIGAKVYFDKINRQGGVHGRRIELLTRDDQYTASLAAYNTRQLIGQDRVFALFGFVGWPT 76 L+GA+ YF +N +GGVHGRR+ LL+ DD Y A NT+QLI +D+VFALFG+ G T Sbjct: 55 LVGAQSYFAMVNAKGGVHGRRVRLLSLDDGYEPERTAANTQQLIWRDKVFALFGYSGTAT 114 Query: 77 SQAGLQIASRARVPFFAPFTGG-ALHTSFDRYLFSIRASYVDEHAYFLRNMNGLGIRKLA 135 + A L A VP FAP +G AL F+R +F +RASY E + LR + G G RK+A Sbjct: 115 TLAALPAIREANVPLFAPVSGALALREPFNRLIFHVRASYAQETDFLLRQLQGTGRRKVA 174 Query: 136 LVYQQDQYGVSIKQDIENRAR--------REAIELTSISINHAGVNLTPLIDKTLAAQVD 187 + YQ D+ G S+ + + RA A+E S ++ A L L + D Sbjct: 175 VFYQNDELGKSMLEQLRLRALVYGLTLVGTAAVERNSDAVEGAAQAL-------LKVKPD 227 Query: 188 VVMLVNADYQINARIVHGLRSRGFLGQFFAVSFVGTKQLASELGDMAHGILVTQVVPLPW 247 VV+ V Y+ A ++ +R G+LG F SFVG+ L++ L + G + QVVP P Sbjct: 228 VVIQV-VSYRPAAALIARMRQAGYLGGFSHYSFVGSLSLSARLKECGIGAEIAQVVPFPN 286 Query: 248 RISMPLVAEYRKSMAEAGYEEFTVTSLEGYIAARVLVEGFRRTGRNLTRERLIRALEGIN 307 + +PLV EYRK++A+ SLEGYIAAR LVEG RR GR LTRE LIRALE I+ Sbjct: 287 KARLPLVYEYRKAVAQHPGAVDNFLSLEGYIAARTLVEGLRRAGRALTREGLIRALETIS 346 Query: 308 ARNYDGGGYVVNFSPTNHLGSMYVDIATMTKDARFMN 344 NYDGGG+ +FS T+H GS +VD+ + RF+N Sbjct: 347 PANYDGGGFSQHFSRTDHSGSDFVDLTAIGSGGRFIN 383 >gi|300311772|ref|YP_003775864.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 404 Score = 56.6 bits (135), Expect = 3e-09, Method: Compositional matrix adjust. Identities = 86/312 (27%), Positives = 131/312 (41%), Gaps = 43/312 (13%) Query: 19 GAKVYFDKINRQGGVHGRRIELLTRDDQYTASLAAYNTRQLIGQDRVFALFGFVGWPTSQ 78 G ++ D+IN GGV G+++E++ RDD + +L+ ++RV LFG T Sbjct: 53 GWEMALDEINASGGVLGKKLEVIARDDNGNPGDSVRVAEELMARERVALLFGGFLSNTGL 112 Query: 79 AGLQIASRARVPFFA--PFTGGALHTSFDRYLFSIRASYVDEHAYFLRNMNGLGIRKLAL 136 A A + RV F A P T + + ++Y + +R S A ++ L ++ A+ Sbjct: 113 ALTDYAKQHRVFFLAAEPLTDKIVWQNGNKYTYRLRPSTSMLVASVVKEAVKLKKKRWAI 172 Query: 137 VYQQDQYGVS--------IKQ---DIENRARREAIELTSISINHAGVNLTPLIDKTLAAQ 185 VY +YG S +KQ D+E A +A L I AG L D A+ Sbjct: 173 VYPNYEYGQSAVASFKTLMKQAQPDVEFVA-EQAPPLGKID---AGAVTQALAD----AK 224 Query: 186 VDVVM--LVNADYQINARIVHGLRSRGFLGQFFAVSFV-GTKQLASEL-GDMAHGILVTQ 241 D + L AD + V +RG Q VS + G + L G+ +VT Sbjct: 225 PDAIFNALFAADL---GKFVREGNTRGLFEQVDVVSLLTGEPEYLDPLKGEAPQNWIVTG 281 Query: 242 VVPLPW-RISMP----LVAEYRKSMAEAGYEEFTVT-SLEGYIAARVLVEGFRRTGRNLT 295 PW I P V YRK + ++ SL GY A + G R+ G + Sbjct: 282 ---YPWYAIHTPEHKKFVEAYRKK-----FNDYPRNGSLVGYSALMSIAAGLRKAG-STD 332 Query: 296 RERLIRALEGIN 307 +RL A G+ Sbjct: 333 ADRLAAAFSGLK 344 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 0.324 0.138 0.398 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: 1,010,615 Number of extensions: 40995 Number of successful extensions: 166 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 166 Number of HSP's successfully gapped: 3 Length of query: 344 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 258 Effective length of database: 1,212,660 Effective search space: 312866280 Effective search space used: 312866280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 131 (55.1 bits)