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= 0008.0010.p (359 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... 541 e-155 gi|300311113|ref|YP_003775205.1| branched-chain amino acid ABC t... 70 3e-13 gi|300312236|ref|YP_003776328.1| amino acid ABC transporter peri... 67 2e-12 gi|300312761|ref|YP_003776853.1| branched-chain amino acid ABC t... 67 3e-12 gi|300310681|ref|YP_003774773.1| amino acid ABC transporter peri... 66 4e-12 >gi|300312847|ref|YP_003776939.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 383 Score = 541 bits (1394), Expect = e-155, Method: Compositional matrix adjust. Identities = 273/371 (73%), Positives = 307/371 (82%), Gaps = 12/371 (3%) Query: 1 LGVACGLHAA-QAAENGVSPQEIVLGQSAPFTGPAAEVGRDFQEGARSYFAQVNARGGVH 59 LG+A L A AAE+GVS E+VLGQSAPF+GPA+++GRDF GA+SYFA VNA+GGVH Sbjct: 13 LGLAMSLLAVGAAAEDGVSATEVVLGQSAPFSGPASDLGRDFLVGAQSYFAMVNAKGGVH 72 Query: 60 GRRVRLLSLDDGYQPERTLANTQQLIWRDKVFALFGFSGTPTVLAALPAIREAGIPLIAP 119 GRRVRLLSLDDGY+PERT ANTQQLIWRDKVFALFG+SGT T LAALPAIREA +PL AP Sbjct: 73 GRRVRLLSLDDGYEPERTAANTQQLIWRDKVFALFGYSGTATTLAALPAIREANVPLFAP 132 Query: 120 HTGAAALREPFN-----------XKAGFLLRQLQGTGRKRVAVFYQNDELGKGLLDNLSQ 168 +GA ALREPFN + FLLRQLQGTGR++VAVFYQNDELGK +L+ L Sbjct: 133 VSGALALREPFNRLIFHVRASYAQETDFLLRQLQGTGRRKVAVFYQNDELGKSMLEQLRL 192 Query: 169 RAAQYGLTLVGSMPIERNSDAVGPAAEQFMKMRPDVVIQAVSYEPAAALITRMRAAGYLG 228 RA YGLTLVG+ +ERNSDAV AA+ +K++PDVVIQ VSY PAAALI RMR AGYLG Sbjct: 193 RALVYGLTLVGTAAVERNSDAVEGAAQALLKVKPDVVIQVVSYRPAAALIARMRQAGYLG 252 Query: 229 GFSHYSFVGSLSLAARLKQTGVGTEITQVVPFPNKARLPIVYEYQKALESSPGARCNFIG 288 GFSHYSFVGSLSL+ARLK+ G+G EI QVVPFPNKARLP+VYEY+KA+ PGA NF+ Sbjct: 253 GFSHYSFVGSLSLSARLKECGIGAEIAQVVPFPNKARLPLVYEYRKAVAQHPGAVDNFLS 312 Query: 289 LEGYIAARVLVEGLRRAGXQLTRAGLIRALESITPANYDGGGFSLQFGRTDHSGSDFVDL 348 LEGYIAAR LVEGLRRAG LTR GLIRALE+I+PANYDGGGFS F RTDHSGSDFVDL Sbjct: 313 LEGYIAARTLVEGLRRAGRALTREGLIRALETISPANYDGGGFSQHFSRTDHSGSDFVDL 372 Query: 349 TAIGTGGRFIN 359 TAIG+GGRFIN Sbjct: 373 TAIGSGGRFIN 383 >gi|300311113|ref|YP_003775205.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 383 Score = 69.7 bits (169), Expect = 3e-13, Method: Compositional matrix adjust. Identities = 45/138 (32%), Positives = 72/138 (52%), Gaps = 3/138 (2%) Query: 3 VACGLHAAQAAENGVSPQEIVLGQSAPFTGPAAEVGRDFQEGARSYFAQVNARGGVHGRR 62 VA L + P I +G S P+TG +A +G ++G + A++NA GG+ GR+ Sbjct: 9 VAAALMSLALTSQAADP--IKIGVSGPYTGGSAPMGVSMRDGVKLAVAEINAAGGLLGRQ 66 Query: 63 VRLLSLDDGYQPERTLANTQQLIWRDKVFALFGFSGTPTVLAALPAIREAGIPLIAP-HT 121 ++L+ DD + ER + Q+LI ++KV A GF T LA+ +EA IP+I T Sbjct: 67 IQLIERDDEAKNERGVQIAQELINKEKVVATVGFINTGVALASQRFYQEAKIPVINNVAT 126 Query: 122 GAAALREPFNXKAGFLLR 139 G ++ K ++ R Sbjct: 127 GTVITKQFEKEKDNYVFR 144 >gi|300312236|ref|YP_003776328.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 385 Score = 67.0 bits (162), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 89/365 (24%), Positives = 152/365 (41%), Gaps = 36/365 (9%) Query: 21 EIVLGQSAPFTGPAAEVGRDFQEGARSYFAQVNARGGVHGRRVRLLSLDDGYQPERTLAN 80 +I LG + TGPAA+ G + G ++NA+GGV+G ++ L+ D+ + E + Sbjct: 27 DIKLGVAEALTGPAAKYGVAIKNGFTLASEEINAKGGVNGDKLALVIEDEQGKKEEAINV 86 Query: 81 TQQLIWRDKVFALFGFSGTPTVLAALPAIREA------------GIPLIAPHTGAAALRE 128 ++LI++DKV A+FG + + + AA P A GI + P T ++ E Sbjct: 87 FKKLIFQDKVLAVFGPTLSNSAFAADPIANAAKVVVFGTSNTADGITAMGPFTFRNSVME 146 Query: 129 ----PFNXKAGFLLRQLQGTGRKRVAVFYQNDELGKGLLDNLSQRAAQYGLTLVGSMPIE 184 P KA ++ G K+VAV Y ND+ ++ + ++ V + Sbjct: 147 ADVLPVTVKAA-----VKHFGIKKVAVIYGNDDAFTKSGYDVFKATLEHQKIPVTTTEAY 201 Query: 185 RNSDAVGPAAEQFMKMR---PDVVIQAVSYEPAAALITRMRAAGYLGGFSHYSFVGSLSL 241 D A Q K++ PD ++ + E AA +I + RA G F + + S L Sbjct: 202 AKGDVDFKA--QLTKIKAGNPDAIVCSCLAEEAANIILQTRALGMKQPFIGGNGLNSPKL 259 Query: 242 AARLKQTGVGTEITQVVPFPNKARLPIVYEYQKALESSPGARCNFIGLEGYIAARVLVEG 301 K G T + P+ + + P + A ++ GA + + Y A ++ + Sbjct: 260 FEIAKDAGDNTLMGS--PWSAENQTPANKAFITAYKAKFGADPDQFAAQAYDAMYIVADA 317 Query: 302 LRRAGXQLTRAGLIRALESITPA-NYDGGGFSLQF-------GRTDHSGSDFVDLTAIGT 353 L+ A AL + PA DG F G+ +D + I Sbjct: 318 LKNVKLSGNLAKDRDALRAALPAVKIDGATGKFAFRAAPAVAGKQVGFDADQEAIVNIAK 377 Query: 354 GGRFI 358 GG+F+ Sbjct: 378 GGKFV 382 >gi|300312761|ref|YP_003776853.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 66.6 bits (161), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 62/221 (28%), Positives = 104/221 (47%), Gaps = 21/221 (9%) Query: 1 LGVACGLHAAQAAENGVSPQEIV-LGQSAPFTGPAAEVGRDFQEGARSYFAQVNARG-GV 58 L A GL A AA + QE+V + P +GP A +G+D + GAR ++NA+G + Sbjct: 10 LTAAIGLAFAGAAYS----QEVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNAKGFTI 65 Query: 59 HGRRVR--LLSLDDGYQPERTLANTQQLIWRDKVFALFGFSGTPTVLAALPAIREAGIPL 116 G++V+ L+ DD P++ A +L+ + KV A+ G + T + A +AGIP Sbjct: 66 GGKKVKFELVGEDDASDPKQATAVATKLVDQ-KVAAVIGHLNSGTTIPASKIYSDAGIPQ 124 Query: 117 IAPH-TGAAALREPF---------NXKAGFLLRQ--LQGTGRKRVAVFYQNDELGKGLLD 164 ++P T ++ F + + G L + +Q G K++AV G+G+ D Sbjct: 125 VSPSATNPKYTQQGFKTAFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQGVAD 184 Query: 165 NLSQRAAQYGLTLVGSMPIERNSDAVGPAAEQFMKMRPDVV 205 ++ A G T+VG+ + +PDVV Sbjct: 185 EFAKGAKAAGGTIVGTQYTNDKATDFNAILTSLKGKKPDVV 225 >gi|300310681|ref|YP_003774773.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 385 Score = 66.2 bits (160), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 77/312 (24%), Positives = 131/312 (41%), Gaps = 35/312 (11%) Query: 62 RVRLLSLDDGYQPERTLANTQQLIWRDKVFALFGFSGTPTVLAALPAIREAGIPLIAPHT 121 +V +SLDD P +++ ++LI V A+ G SG+P + + + EAG+PL+AP Sbjct: 61 KVEYISLDDASDPTKSVTEIKKLIAEHNVDAIIGPSGSPNAMGVISFVAEAGVPLLAP-V 119 Query: 122 GAAALREPFNXKAGF--------------LLRQLQGTGRKRVAVFYQNDELGKGLLDNLS 167 G AA+ P + + L+ Q+ T K ND G+ S Sbjct: 120 GTAAVVLPMTEQKKWVFKTTQNDDLIAKALVDQMVKTKVKTAGFIAVNDPFGENWARVFS 179 Query: 168 QRAAQYGLTLVGSMPIERNSDAVGPAAEQFMKMRPDVVIQAVSYEPAAALI---TRMRAA 224 AA+ + +V + +R +V + + + PD V+ A P AA + T + Sbjct: 180 DLAAKNNIKIVANERYQRTDTSVTAQSLKIVAANPDAVLVAA---PGAATVLPQTTLFDQ 236 Query: 225 GYLGGF--SH-YSFVGSLSLAA-RLKQTGVGTEITQVVP-FPN-----KARLPIVYEYQK 274 GY G +H + L L +++ T + + V+P P+ K + Y+K Sbjct: 237 GYKGKIYQTHGAALPAFLQLGKNKVEGTILAASLMLVLPEIPDSNPSKKVATDYIEAYKK 296 Query: 275 ALESSPGARCNFIGLEGYIAARVLVEGLRRA--GXQLTRAGLIRALESITPANYDGGGFS 332 + P + G + + + R+A G + RA L ALE+ G ++ Sbjct: 297 MYNAVPATFGANVYDAGLLLEKAIPVAARKAKPGSKEFRAALRDALENTKEVVGTQGVYN 356 Query: 333 LQFGRTDHSGSD 344 + TDHSG D Sbjct: 357 M--SATDHSGFD 366 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 0.320 0.137 0.399 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: 1,169,957 Number of extensions: 50329 Number of successful extensions: 185 Number of sequences better than 1.0e-08: 9 Number of HSP's gapped: 178 Number of HSP's successfully gapped: 9 Length of query: 359 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 273 Effective length of database: 1,212,660 Effective search space: 331056180 Effective search space used: 331056180 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)