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= 0001.3457.p (393 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... 590 e-170 gi|300313298|ref|YP_003777390.1| branched-chain amino acid ABC t... 70 2e-13 gi|300311113|ref|YP_003775205.1| branched-chain amino acid ABC t... 70 4e-13 gi|300312761|ref|YP_003776853.1| branched-chain amino acid ABC t... 67 2e-12 gi|300312236|ref|YP_003776328.1| amino acid ABC transporter peri... 64 2e-11 >gi|300312847|ref|YP_003776939.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 383 Score = 590 bits (1520), Expect = e-170, Method: Compositional matrix adjust. Identities = 292/393 (74%), Positives = 332/393 (84%), Gaps = 10/393 (2%) Query: 1 MGWSWSKARYWCGRLVMVFTLATCLVAAGSTVATAAENGVTPTEIVLGQSAPFTGPAAEI 60 MGW+W C RL LA L+A G+ AAE+GV+ TE+VLGQSAPF+GPA+++ Sbjct: 1 MGWNW------CHRLRGCLGLAMSLLAVGA----AAEDGVSATEVVLGQSAPFSGPASDL 50 Query: 61 GRDFQEGARSYFSQVNAKGGIHGRRVRLLSLDDRYEPERTLANTQQLIWRDKVFALFGYS 120 GRDF GA+SYF+ VNAKGG+HGRRVRLLSLDD YEPERT ANTQQLIWRDKVFALFGYS Sbjct: 51 GRDFLVGAQSYFAMVNAKGGVHGRRVRLLSLDDGYEPERTAANTQQLIWRDKVFALFGYS 110 Query: 121 GTPTVLAALPAMREAGIPLIAPHSGASSLREPFNRLIFHVRASYQQETDFLLRQLQGTGR 180 GT T LAALPA+REA +PL AP SGA +LREPFNRLIFHVRASY QETDFLLRQLQGTGR Sbjct: 111 GTATTLAALPAIREANVPLFAPVSGALALREPFNRLIFHVRASYAQETDFLLRQLQGTGR 170 Query: 181 LRVAVFYQNDELGKELLDNLRLRALVYGLTVVGSVAIERNSDAVTTAAEQFMKMQPDVVI 240 +VAVFYQNDELGK +L+ LRLRALVYGLT+VG+ A+ERNSDAV AA+ +K++PDVVI Sbjct: 171 RKVAVFYQNDELGKSMLEQLRLRALVYGLTLVGTAAVERNSDAVEGAAQALLKVKPDVVI 230 Query: 241 QVVPYLPAAALITRMRAAGYLGGFSNYSFVGSHSLATRLKDGGVGTEITQVVPFPNKARL 300 QVV Y PAAALI RMR AGYLGGFS+YSFVGS SL+ RLK+ G+G EI QVVPFPNKARL Sbjct: 231 QVVSYRPAAALIARMRQAGYLGGFSHYSFVGSLSLSARLKECGIGAEIAQVVPFPNKARL 290 Query: 301 PIVYEYQKAMARSSRACCNFIGLEGYIAARVLVEALRRAGPQLSREGLIRALESITPANY 360 P+VYEY+KA+A+ A NF+ LEGYIAAR LVE LRRAG L+REGLIRALE+I+PANY Sbjct: 291 PLVYEYRKAVAQHPGAVDNFLSLEGYIAARTLVEGLRRAGRALTREGLIRALETISPANY 350 Query: 361 DGGGFSLHFSRTDHTGSDFVDLTAIGTAGRFIN 393 DGGGFS HFSRTDH+GSDFVDLTAIG+ GRFIN Sbjct: 351 DGGGFSQHFSRTDHSGSDFVDLTAIGSGGRFIN 383 >gi|300313298|ref|YP_003777390.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 381 Score = 70.5 bits (171), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 95/378 (25%), Positives = 154/378 (40%), Gaps = 51/378 (13%) Query: 26 VAAGSTVATAAENGVTPTEIVLGQSAPFTGPAAEIGRDFQEGARSYFSQVNAKGGIHGRR 85 + AG A A G+ E+ +G TGP + +G + G + I G + Sbjct: 7 IKAGVLAAMLACAGIAHAELTIGVVMSLTGPGSGLGIPAKNGFALWPET------IAGEK 60 Query: 86 VRLLSLDDRYEPERTLANTQQLIWRDKVFALFGYSGTPTVLA-ALPAMREAGIPL-IAPH 143 V+++ LDD +P + N ++L+ DKV + G + P LA A A+ + L I+P Sbjct: 61 VKMIILDDATDPTQASKNARRLVAEDKVDLIIGSAAVPPTLAIADVALETQTVQLAISPI 120 Query: 144 SGASSLREPFNRLIFHVRASYQQETDFLLRQLQGTGRLRVAVFYQNDELGKELLDNLRLR 203 A E + F + S ++ Q++ G + +D G+ L ++ Sbjct: 121 ETA----EGKDAWTFRLPQSTAVMAGGVVNQMKKLGVKTIGFLGYSDSYGENWLKEVQRL 176 Query: 204 ALVYGLTVVGSVAIERNSDAVTTAAEQFMKMQPDVVIQVVP----YLPAAALITRMRAAG 259 A G+ + R +VT A + + PD V+ V +P ALI R G Sbjct: 177 ATAAGMKMGTVERFSRADTSVTAQALRVVSSNPDAVLVVASGSGAAMPHKALIER----G 232 Query: 260 YLGGFSNYSFVGSHSLATR--LKDGGVGTE----------ITQVVPFPNKAR---LPIVY 304 Y G +HS A+R ++ GG E + + +P N ++ + V Sbjct: 233 YKG-----KIFQTHSAASRDLIRLGGKDVEGAYVISGPAVVPEALPDSNASKKLAMDFVT 287 Query: 305 EYQKAMARSSRACCNFIGLEGYIA----ARVLVEALRRAGPQLS--REGLIRALESITPA 358 Y+K SR N Y A +V+ EAL++A P R L ALE+ P Sbjct: 288 RYEKQFGAGSR---NLFAAHTYDAQLVLQKVVPEALKKAKPGTPAFRAALKEALETSGPI 344 Query: 359 NYDGGGFSLHFSRTDHTG 376 G +L++S DH G Sbjct: 345 QITQG--TLNYSPKDHFG 360 >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 = 4e-13, Method: Compositional matrix adjust. Identities = 36/111 (32%), Positives = 65/111 (58%) Query: 45 IVLGQSAPFTGPAAEIGRDFQEGARSYFSQVNAKGGIHGRRVRLLSLDDRYEPERTLANT 104 I +G S P+TG +A +G ++G + +++NA GG+ GR+++L+ DD + ER + Sbjct: 26 IKIGVSGPYTGGSAPMGVSMRDGVKLAVAEINAAGGLLGRQIQLIERDDEAKNERGVQIA 85 Query: 105 QQLIWRDKVFALFGYSGTPTVLAALPAMREAGIPLIAPHSGASSLREPFNR 155 Q+LI ++KV A G+ T LA+ +EA IP+I + + + + F + Sbjct: 86 QELINKEKVVATVGFINTGVALASQRFYQEAKIPVINNVATGTVITKQFEK 136 >gi|300312761|ref|YP_003776853.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 55/201 (27%), Positives = 94/201 (46%), Gaps = 6/201 (2%) Query: 44 EIV-LGQSAPFTGPAAEIGRDFQEGARSYFSQVNAKG-GIHGRRVR--LLSLDDRYEPER 99 E+V + P +GP A +G+D + GAR ++NAKG I G++V+ L+ DD +P++ Sbjct: 26 EVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNAKGFTIGGKKVKFELVGEDDASDPKQ 85 Query: 100 TLANTQQLIWRDKVFALFGYSGTPTVLAALPAMREAGIPLIAPHSGASSLREPFNRLIFH 159 A +L+ + KV A+ G+ + T + A +AGIP ++P + + + F Sbjct: 86 ATAVATKLVDQ-KVAAVIGHLNSGTTIPASKIYSDAGIPQVSPSATNPKYTQQGFKTAFR 144 Query: 160 VRASYQQETDFLLR-QLQGTGRLRVAVFYQNDELGKELLDNLRLRALVYGLTVVGSVAIE 218 V A+ Q L + +Q G ++AV G+ + D A G T+VG+ Sbjct: 145 VVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQGVADEFAKGAKAAGGTIVGTQYTN 204 Query: 219 RNSDAVTTAAEQFMKMQPDVV 239 + +PDVV Sbjct: 205 DKATDFNAILTSLKGKKPDVV 225 >gi|300312236|ref|YP_003776328.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 385 Score = 63.5 bits (153), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 80/329 (24%), Positives = 139/329 (42%), Gaps = 21/329 (6%) Query: 17 MVFTLATCLVAAGSTVATAAENGVTPTEIVLGQSAPFTGPAAEIGRDFQEGARSYFSQVN 76 M+ T+ L+ G+T++ AA +I LG + TGPAA+ G + G ++N Sbjct: 6 MLKTIPALLI--GATLSQAA----LAADIKLGVAEALTGPAAKYGVAIKNGFTLASEEIN 59 Query: 77 AKGGIHGRRVRLLSLDDRYEPERTLANTQQLIWRDKVFALFGYSGTPTVLAALPAMREAG 136 AKGG++G ++ L+ D++ + E + ++LI++DKV A+FG + + + AA P A Sbjct: 60 AKGGVNGDKLALVIEDEQGKKEEAINVFKKLIFQDKVLAVFGPTLSNSAFAADPIANAAK 119 Query: 137 IPLIAPHSGASSLRE--PFNRLIFHVRASYQQETDFLLRQLQGT----GRLRVAVFYQND 190 + + + A + PF R S E D L ++ G +VAV Y ND Sbjct: 120 VVVFGTSNTADGITAMGPFT-----FRNSV-MEADVLPVTVKAAVKHFGIKKVAVIYGND 173 Query: 191 E-LGKELLDNLRLRALVYGLTVVGSVAIERNSDAVTTAAEQFMKMQPDVVIQVVPYLPAA 249 + K D + + V + A + + PD ++ AA Sbjct: 174 DAFTKSGYDVFKATLEHQKIPVTTTEAYAKGDVDFKAQLTKIKAGNPDAIVCSCLAEEAA 233 Query: 250 ALITRMRAAGYLGGFSNYSFVGSHSLATRLKDGGVGTEITQVVPFPNKARLPIVYEYQKA 309 +I + RA G F + + S L KD G T + P+ + + P + A Sbjct: 234 NIILQTRALGMKQPFIGGNGLNSPKLFEIAKDAGDNTLMGS--PWSAENQTPANKAFITA 291 Query: 310 MARSSRACCNFIGLEGYIAARVLVEALRR 338 A + + Y A ++ +AL+ Sbjct: 292 YKAKFGADPDQFAAQAYDAMYIVADALKN 320 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 0.322 0.136 0.403 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: 1,153,797 Number of extensions: 45916 Number of successful extensions: 181 Number of sequences better than 1.0e-08: 10 Number of HSP's gapped: 181 Number of HSP's successfully gapped: 10 Length of query: 393 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 306 Effective length of database: 1,207,925 Effective search space: 369625050 Effective search space used: 369625050 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 (21.9 bits) S2: 131 (55.1 bits)