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= 0001.4512.p (387 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... 202 3e-53 gi|300313995|ref|YP_003778087.1| urea ABC transporter periplasmi... 158 8e-40 gi|300312236|ref|YP_003776328.1| amino acid ABC transporter peri... 101 1e-22 gi|300311113|ref|YP_003775205.1| branched-chain amino acid ABC t... 90 3e-19 gi|300311772|ref|YP_003775864.1| branched-chain amino acid ABC t... 80 3e-16 >gi|300311947|ref|YP_003776039.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 418 Score = 202 bits (515), Expect = 3e-53, Method: Compositional matrix adjust. Identities = 126/357 (35%), Positives = 193/357 (54%), Gaps = 8/357 (2%) Query: 29 IRIGVAVGLSGANSVVAPAVVQSSQLAVDEINAAGGILGRKLELDIVDDASGAVGAQKAF 88 + +G +G ++ +Q+ +LA+D+INA GGILGRK+++ D AS + Sbjct: 56 VTVGQLHSATGTMAISETGSIQAERLAIDQINAMGGILGRKIKIIQEDGASDWPTFAEKA 115 Query: 89 DTLVFQKKVNAVIAMETSAARNAALPVISRGKLPYIYTSFYEGRSCNKWMYVNGWVPEQQ 148 L+ +V AV TSA+R A LPV + Y +FYEG +K ++ G QQ Sbjct: 116 KKLLENDRVAAVFGCWTSASRKAVLPVFEKDNGLLYYPTFYEGLEQSKNVFYTGQEATQQ 175 Query: 149 VAPVVDYFTKSKHAKTFFLVGSDYAFGRGMLEFTKKYIEQK-GGKVIGEEYLPIDGSDWT 207 V +++ K K AKTFFLVGSDY + R + +K+IE G V+GEEY P+ + + Sbjct: 176 VLAGLNWVAKEKKAKTFFLVGSDYIWPRTSNKIARKHIENVLKGSVVGEEYYPLGNTQFG 235 Query: 208 TVVSKIRSSKPDALISATAGGAPNVSLAKQLKGAGLTLPYGNLAVDEGTAQTM----GDA 263 ++++KI+ KPD + + GG+ NV+ KQLK AG+T NL T M G+ Sbjct: 236 SLINKIKLKKPDVIFADVVGGS-NVAFYKQLKAAGVTAKTQNLLTISVTEDEMLGIGGEN 294 Query: 264 ADGLYMSASYLTGIDTPENKKFMEALKKKFGADMKTPNELSEPQYEAFYLFKAAVEKAGS 323 +G + S Y +D NKKF+ K KFGA+ ++++ Y +L+KAAVEKAGS Sbjct: 295 VEGFFASMKYFQSLDNANNKKFVAEFKAKFGAN-SVIGDVTQAAYLGPWLWKAAVEKAGS 353 Query: 324 TDNDKVIKALGEVSF-NGPRGLVAMNKSRHTPLSMRLGQVQHDGTIKILETFASVDP 379 D DKV+ A + P G V ++++ H R+G+ Q DG K++ ++P Sbjct: 354 FDVDKVVAASPGIELKTAPEGYVKVHENHHLWSKTRIGEAQKDGQFKVVYESELIEP 410 >gi|300313995|ref|YP_003778087.1| urea ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 417 Score = 158 bits (399), Expect = 8e-40, Method: Compositional matrix adjust. Identities = 125/402 (31%), Positives = 199/402 (49%), Gaps = 30/402 (7%) Query: 11 GAFVLFAAMTV-QAQAADPIRIGVAVGLSGANSVVAPAVVQSSQLAVDEINAAGGILGRK 69 GAF L A+ + A AAD I++G+ LSG ++ ++ + + +DEINAAGG++G+K Sbjct: 13 GAFALAASSWLPSAFAADTIKVGILHSLSGTMAISETSLKDVALMTIDEINAAGGVMGKK 72 Query: 70 LELDIVDDASG-AVGAQKAFDTLVFQKKVNAVIAMETSAARNAALPVISRGKLPYIYTSF 128 LE +VD AS + A+KA L+ Q KV+ V TS +R + LPV Y Sbjct: 73 LEPVVVDPASNWPLFAEKA-RQLISQDKVSVVFGCWTSVSRKSVLPVFKELNSLLFYPVQ 131 Query: 129 YEGRSCNKWMYVNGWVPEQQVAPVVDYFTKSK--HAKTFFLVGSDYAFGRGMLEFTKKYI 186 YEG K ++ G P QQ P V+Y + AK F L+G+DY + R + + ++ Sbjct: 132 YEGEELEKNVFYTGAAPNQQAIPAVEYLMSKEGGGAKRFVLLGTDYVYPRTTNKILRAFL 191 Query: 187 EQKGGK--VIGEEYLPIDGSDWTTVVSKIR--SSKPDALISATAGGAPNVSLAKQLKGAG 242 KG K I E Y P SD+ T+V+ I+ S+ + +T G NV K+L AG Sbjct: 192 HSKGVKDSDIDEVYTPFGHSDYQTIVANIKKFSAGGKTAVISTINGDSNVPFYKELGNAG 251 Query: 243 LT---LPYGNLAVDEGTAQTMGDAADGLYMSA-SYLTGIDTPENKKFMEALKKKF----- 293 L +P +V E + + +++A +Y + P N F++ K+ Sbjct: 252 LKATDVPVVAFSVGEEELRGVDTKPLVGHLAAWNYFESVKNPVNTAFIKKWKEYAKAKNL 311 Query: 294 -GADMKTPNELSEPQYEAFYLFKAAVEKAGSTDNDKVIKALGEVSFNGPRGL-VAMNKS- 350 AD N+ E Y +++ AVEKA STD DKVI A+G ++ P G + M+K+ Sbjct: 312 PNADTVVTNDPMEATYVGIHMWAQAVEKAKSTDTDKVIAAMGGQTYKAPSGYTLEMDKTN 371 Query: 351 RHTPLSMRLGQVQHDGTIKIL---------ETFASVDPGNQC 383 H + +G+++ DG ++ + ++ PGN+ Sbjct: 372 HHLHKPVMIGEIKADGQFNVVYKTKTTIRAQPWSPYIPGNES 413 >gi|300312236|ref|YP_003776328.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 385 Score = 101 bits (251), Expect = 1e-22, Method: Compositional matrix adjust. Identities = 106/355 (29%), Positives = 156/355 (43%), Gaps = 22/355 (6%) Query: 3 RFTFALRHGAFVLFAAMTVQAQAADPIRIGVAVGLSGANSVVAPAVVQSSQLAVDEINAA 62 +F L+ +L A QA A I++GVA L+G + A+ LA +EINA Sbjct: 2 QFNTMLKTIPALLIGATLSQAALAADIKLGVAEALTGPAAKYGVAIKNGFTLASEEINAK 61 Query: 63 GGILGRKLELDIVDDASGAVGAQKAFDTLVFQKKVNAVIAMETSAARNAALPVISRGKLP 122 GG+ G KL L I D+ A F L+FQ KV AV S + AA P+ + K+ Sbjct: 62 GGVNGDKLALVIEDEQGKKEEAINVFKKLIFQDKVLAVFGPTLSNSAFAADPIANAAKVV 121 Query: 123 YIYTS-FYEGRSCNKWMYVNGWVPEQQVAPV-----VDYFTKSKHAKTFFLVGSDYAFGR 176 TS +G + V E V PV V +F K A + G+D AF + Sbjct: 122 VFGTSNTADGITAMGPFTFRNSVMEADVLPVTVKAAVKHFGIKKVAVIY---GNDDAFTK 178 Query: 177 GMLEFTKKYIEQKGGKVIGEEYLPIDGSDWTTVVSKIRSSKPDALI-SATAGGAPNVSLA 235 + K +E + V E D+ ++KI++ PDA++ S A A N+ L Sbjct: 179 SGYDVFKATLEHQKIPVTTTEAYAKGDVDFKAQLTKIKAGNPDAIVCSCLAEEAANIIL- 237 Query: 236 KQLKGAGLTLPY--GNLAVDEGTAQTMGDAADGLYMSASYLTGIDTPENKKFMEALKKKF 293 Q + G+ P+ GN + DA D M + + TP NK F+ A K KF Sbjct: 238 -QTRALGMKQPFIGGNGLNSPKLFEIAKDAGDNTLMGSPWSAENQTPANKAFITAYKAKF 296 Query: 294 GADMKTPNELSEPQYEAFYLFKAAVEKAG-----STDNDKVIKALGEVSFNGPRG 343 GAD P++ + Y+A Y+ A++ + D D + AL V +G G Sbjct: 297 GAD---PDQFAAQAYDAMYIVADALKNVKLSGNLAKDRDALRAALPAVKIDGATG 348 >gi|300311113|ref|YP_003775205.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 383 Score = 89.7 bits (221), Expect = 3e-19, Method: Compositional matrix adjust. Identities = 99/337 (29%), Positives = 163/337 (48%), Gaps = 20/337 (5%) Query: 12 AFVLFAAMTV--QAQAADPIRIGVAVGLSGANSVVAPAVVQSSQLAVDEINAAGGILGRK 69 AFV A M++ +QAADPI+IGV+ +G ++ + ++ +LAV EINAAGG+LGR+ Sbjct: 7 AFVAAALMSLALTSQAADPIKIGVSGPYTGGSAPMGVSMRDGVKLAVAEINAAGGLLGRQ 66 Query: 70 LELDIVDD-ASGAVGAQKAFDTLVFQKKVNAVIAMETSAA-------RNAALPVISRGKL 121 ++L DD A G Q A + + +K V V + T A + A +PVI+ Sbjct: 67 IQLIERDDEAKNERGVQIAQELINKEKVVATVGFINTGVALASQRFYQEAKIPVINNVAT 126 Query: 122 PYIYTSFYEGRSCNKWMYVNGWVPEQQVAPVVDY-FTKSKHAKTFFLVGSDYAFGRGMLE 180 + T +E N +++ + Q + D K K K L S G + Sbjct: 127 GTVITKQFEKEKDN-YVFRTSAADKIQAKMIADEAVDKQKFTKVAILADSTNYGQLGRED 185 Query: 181 FTKKYIEQKGGKVIGEEYLPIDGSDWTTVVSKIRSSKPDALISATAGGAPNVS-LAKQLK 239 K ++K V E+Y I D T + K + A++ T G P ++ +A ++ Sbjct: 186 LEKVLADKKVTPVAVEKY-NIKDVDMTAQLLKSKQGGAQAVL--TYGIGPELAQIANGME 242 Query: 240 GAGLTLP-YGNLAVDEGT-AQTMGDAADGLYMSASYLTGIDTPENKKFMEALKKKFGADM 297 +P G+ + G G +G M +++ +TP+ K F+EA +K + D Sbjct: 243 KLNWHVPIIGSWPLSMGNFIDNSGKNGNGARMPQTFIQDGNTPKRKAFIEAYQKAYKVD- 301 Query: 298 KTPNELSEPQ-YEAFYLFKAAVEKAGSTDNDKVIKAL 333 + P+ +S Q Y++ L AA+++AG+TD DKV AL Sbjct: 302 RMPSAVSAAQGYDSILLLAAAIKQAGTTDGDKVRAAL 338 >gi|300311772|ref|YP_003775864.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 404 Score = 79.7 bits (195), Expect = 3e-16, Method: Compositional matrix adjust. Identities = 96/368 (26%), Positives = 156/368 (42%), Gaps = 25/368 (6%) Query: 1 MNRFTF--ALRHGAFVLFAAM-TVQAQAADPIRIGVAVGLSGANSVVAPAVVQSSQLAVD 57 MN+F F LR M +V A+A D IRIG + + P + ++A+D Sbjct: 1 MNQFNFQRGLRWALAAALLTMGSVAARAQDTIRIGEINSYKAQPAFLEP-YRRGWEMALD 59 Query: 58 EINAAGGILGRKLELDIVDDASGAVGAQKAFDTLVFQKKVNAVIAMETSAARNAALPVIS 117 EINA+GG+LG+KLE+ DD + + + L+ +++V + S N L + Sbjct: 60 EINASGGVLGKKLEVIARDDNGNPGDSVRVAEELMARERVALLFGGFLS---NTGLALTD 116 Query: 118 RGKLPYIY-------TSFYEGRSCNKWMYVNGWVPEQQVAPVVDYFTKSKHAKTFFLVGS 170 K ++ T ++ NK+ Y VA VV K K K + +V Sbjct: 117 YAKQHRVFFLAAEPLTDKIVWQNGNKYTYRLRPSTSMLVASVVKEAVKLKK-KRWAIVYP 175 Query: 171 DYAFGRGMLEFTKKYIEQKGGKV--IGEEYLPIDGSDWTTVVSKIRSSKPDALISATAGG 228 +Y +G+ + K ++Q V + E+ P+ D V + +KPDA+ +A Sbjct: 176 NYEYGQSAVASFKTLMKQAQPDVEFVAEQAPPLGKIDAGAVTQALADAKPDAIFNALF-A 234 Query: 229 APNVSLAKQLKGAGLTLPYGNLAVDEGTAQTM----GDAADGLYMSASYLTGIDTPENKK 284 A ++ GL +++ G + + G+A ++ I TPE+KK Sbjct: 235 ADLGKFVREGNTRGLFEQVDVVSLLTGEPEYLDPLKGEAPQNWIVTGYPWYAIHTPEHKK 294 Query: 285 FMEALKKKFGADMKTPNELSEPQYEAFYLFKAAVEKAGSTDNDKVIKALGEVSFNGPRGL 344 F+EA +KKF P S Y A A + KAGSTD D++ A + P Sbjct: 295 FVEAYRKKFN---DYPRNGSLVGYSALMSIAAGLRKAGSTDADRLAAAFSGLKVETPVAS 351 Query: 345 VAMNKSRH 352 + H Sbjct: 352 IVYRPQDH 359 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 0.316 0.132 0.378 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: 1,171,863 Number of extensions: 47219 Number of successful extensions: 227 Number of sequences better than 1.0e-08: 17 Number of HSP's gapped: 203 Number of HSP's successfully gapped: 17 Length of query: 387 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 300 Effective length of database: 1,207,925 Effective search space: 362377500 Effective search space used: 362377500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 131 (55.1 bits)