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= 0001.3900.p (383 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313298|ref|YP_003777390.1| branched-chain amino acid ABC t... 742 0.0 gi|300313408|ref|YP_003777500.1| branched-chain amino acid ABC t... 320 1e-88 gi|300310681|ref|YP_003774773.1| amino acid ABC transporter peri... 286 2e-78 gi|300312236|ref|YP_003776328.1| amino acid ABC transporter peri... 78 9e-16 gi|300312847|ref|YP_003776939.1| branched-chain amino acid ABC t... 65 8e-12 >gi|300313298|ref|YP_003777390.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 381 Score = 742 bits (1915), Expect = 0.0, Method: Compositional matrix adjust. Identities = 362/381 (95%), Positives = 374/381 (98%) Query: 3 IKMKLAIKAGVLASMLACAGMAHAELTIGVVMSLTGPGSGLGIPAKNGFSLWPDTIGGEK 62 +K KLAIKAGVLA+MLACAG+AHAELTIGVVMSLTGPGSGLGIPAKNGF+LWP+TI GEK Sbjct: 1 MKTKLAIKAGVLAAMLACAGIAHAELTIGVVMSLTGPGSGLGIPAKNGFALWPETIAGEK 60 Query: 63 VKLIILDDATDPTQASKNARRLVAEDKVDLIIGSAAVPPTLAIADVALETQTVQLAISPI 122 VK+IILDDATDPTQASKNARRLVAEDKVDLIIGSAAVPPTLAIADVALETQTVQLAISPI Sbjct: 61 VKMIILDDATDPTQASKNARRLVAEDKVDLIIGSAAVPPTLAIADVALETQTVQLAISPI 120 Query: 123 ETAEGKDAWTFRLPQSTAVMAGGVVEQMKKMGVKTIGFLGYSDSYGENWLKEMQRLATAA 182 ETAEGKDAWTFRLPQSTAVMAGGVV QMKK+GVKTIGFLGYSDSYGENWLKE+QRLATAA Sbjct: 121 ETAEGKDAWTFRLPQSTAVMAGGVVNQMKKLGVKTIGFLGYSDSYGENWLKEVQRLATAA 180 Query: 183 GMKMGTVERFSRADTSVTAQALRVVSSNPDAVLVVASGSGAAMPHKALIERGYKGKIFQT 242 GMKMGTVERFSRADTSVTAQALRVVSSNPDAVLVVASGSGAAMPHKALIERGYKGKIFQT Sbjct: 181 GMKMGTVERFSRADTSVTAQALRVVSSNPDAVLVVASGSGAAMPHKALIERGYKGKIFQT 240 Query: 243 HSAASRDLIRLGGKDVEGSYVISGPAVVPEALPDSNPSKKLALDFVTRYEKQFGAGSRNL 302 HSAASRDLIRLGGKDVEG+YVISGPAVVPEALPDSN SKKLA+DFVTRYEKQFGAGSRNL Sbjct: 241 HSAASRDLIRLGGKDVEGAYVISGPAVVPEALPDSNASKKLAMDFVTRYEKQFGAGSRNL 300 Query: 303 FAAHTYDAQLVLQKVVPEALKKAKPGTPAFRTALKEALETAGPIQISQGTLRYSAKDHFG 362 FAAHTYDAQLVLQKVVPEALKKAKPGTPAFR ALKEALET+GPIQI+QGTL YS KDHFG Sbjct: 301 FAAHTYDAQLVLQKVVPEALKKAKPGTPAFRAALKEALETSGPIQITQGTLNYSPKDHFG 360 Query: 363 LGDDARIMLTIQNGNWKAVNP 383 LGDDARIMLTIQNGNWKAVNP Sbjct: 361 LGDDARIMLTIQNGNWKAVNP 381 >gi|300313408|ref|YP_003777500.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 381 Score = 320 bits (819), Expect = 1e-88, Method: Compositional matrix adjust. Identities = 154/359 (42%), Positives = 235/359 (65%), Gaps = 4/359 (1%) Query: 25 HAELTIGVVMSLTGPGSGLGIPAKNGFSLWPDTIGGEKVKLIILDDATDPTQASKNARRL 84 A++ +GV +S TGP + LGIP KN +L P TI G KV IILDDA+D TQA KNARR Sbjct: 20 RADINVGVTVSTTGPAASLGIPEKNTIALLPTTIAGHKVNYIILDDASDTTQAVKNARRF 79 Query: 85 VAEDKVDLIIGSAAVPPTLAIADVALETQTVQLAISP----IETAEGKDAWTFRLPQSTA 140 V+E+ VD+I+GS+ P ++++ +VA + QT ++++ +E + K W F+ PQ+ Sbjct: 80 VSENNVDVIVGSSVSPNSISMIEVAADAQTPMISLAAAARIVEPMDAKKKWVFKTPQNDI 139 Query: 141 VMAGGVVEQMKKMGVKTIGFLGYSDSYGENWLKEMQRLATAAGMKMGTVERFSRADTSVT 200 +M+ + M G + I F+GYS++YGE W +E ++ A +++ ERF+ D+S T Sbjct: 140 MMSLAIARDMVARGYQRIAFIGYSNAYGEGWYEEFKKAAGLKKLELVANERFAPTDSSTT 199 Query: 201 AQALRVVSSNPDAVLVVASGSGAAMPHKALIERGYKGKIFQTHSAASRDLIRLGGKDVEG 260 AQAL++V++ PDA+L+ ASG+ A +P +AL ERG+KG+I+QTH A+ D +R+GGK ++G Sbjct: 200 AQALKLVAAKPDAILIAASGTPAVVPQRALKERGFKGQIYQTHGVANADFLRVGGKMLDG 259 Query: 261 SYVISGPAVVPEALPDSNPSKKLALDFVTRYEKQFGAGSRNLFAAHTYDAQLVLQKVVPE 320 + + +GP +V LP SNP +K+ALD+ T+YE G S +LF + +DA ++L+ +P Sbjct: 260 TLLPAGPVLVAAQLPASNPIRKVALDYTTKYEAVHGKDSVSLFGGYAWDAGVLLRWAIPV 319 Query: 321 ALKKAKPGTPAFRTALKEALETAGPIQISQGTLRYSAKDHFGLGDDARIMLTIQNGNWK 379 ALK AKPGTP FR AL++ LE + G S+ DH GL A +M+ I +G W+ Sbjct: 320 ALKGAKPGTPEFRAALRDVLEATKEVTGVHGVYTMSSTDHLGLDQRAAVMVKIVDGAWQ 378 >gi|300310681|ref|YP_003774773.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 385 Score = 286 bits (732), Expect = 2e-78, Method: Compositional matrix adjust. Identities = 160/380 (42%), Positives = 226/380 (59%), Gaps = 10/380 (2%) Query: 6 KLAIKAGVLASMLACAGM-AHAELTIGVVMSLTGPGSGLGIPAKNGFSLWPDTIGGEKVK 64 K I A VL M + A A A++ +GVV S TGP S +GIP KN L P IG KV+ Sbjct: 4 KRLIAAVVLLGMSSLAMHPALAQVKVGVVTSSTGPVSLVGIPQKNTVPLLPTKIGDLKVE 63 Query: 65 LIILDDATDPTQASKNARRLVAEDKVDLIIGSAAVPPTLAIADVALETQTVQLAISPIET 124 I LDDA+DPT++ ++L+AE VD IIG + P + + E LA P+ T Sbjct: 64 YISLDDASDPTKSVTEIKKLIAEHNVDAIIGPSGSPNAMGVISFVAEAGVPLLA--PVGT 121 Query: 125 A------EGKDAWTFRLPQSTAVMAGGVVEQMKKMGVKTIGFLGYSDSYGENWLKEMQRL 178 A + W F+ Q+ ++A +V+QM K VKT GF+ +D +GENW + L Sbjct: 122 AAVVLPMTEQKKWVFKTTQNDDLIAKALVDQMVKTKVKTAGFIAVNDPFGENWARVFSDL 181 Query: 179 ATAAGMKMGTVERFSRADTSVTAQALRVVSSNPDAVLVVASGSGAAMPHKALIERGYKGK 238 A +K+ ER+ R DTSVTAQ+L++V++NPDAVLV A G+ +P L ++GYKGK Sbjct: 182 AAKNNIKIVANERYQRTDTSVTAQSLKIVAANPDAVLVAAPGAATVLPQTTLFDQGYKGK 241 Query: 239 IFQTHSAASRDLIRLGGKDVEGSYVISGPAVVPEALPDSNPSKKLALDFVTRYEKQFGAG 298 I+QTH AA ++LG VEG+ + + +V +PDSNPSKK+A D++ Y+K + A Sbjct: 242 IYQTHGAALPAFLQLGKNKVEGTILAASLMLVLPEIPDSNPSKKVATDYIEAYKKMYNAV 301 Query: 299 SRNLFAAHTYDAQLVLQKVVPEALKKAKPGTPAFRTALKEALETAGPIQISQGTLRYSAK 358 F A+ YDA L+L+K +P A +KAKPG+ FR AL++ALE + +QG SA Sbjct: 302 PAT-FGANVYDAGLLLEKAIPVAARKAKPGSKEFRAALRDALENTKEVVGTQGVYNMSAT 360 Query: 359 DHFGLGDDARIMLTIQNGNW 378 DH G D R ++T++ GNW Sbjct: 361 DHSGFDDRGRELITVKGGNW 380 >gi|300312236|ref|YP_003776328.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 385 Score = 78.2 bits (191), Expect = 9e-16, Method: Compositional matrix adjust. Identities = 90/332 (27%), Positives = 151/332 (45%), Gaps = 33/332 (9%) Query: 9 IKAGVLASMLACAGMAHAELTIGVVMSLTGPGSGLGIPAKNGFSLWPDTI------GGEK 62 I A ++ + L+ A +A A++ +GV +LTGP + G+ KNGF+L + I G+K Sbjct: 10 IPALLIGATLSQAALA-ADIKLGVAEALTGPAAKYGVAIKNGFTLASEEINAKGGVNGDK 68 Query: 63 VKLIILDDATDPTQASKNARRLVAEDKVDLIIGSAAVPPTLAIADVALETQTVQLAISPI 122 + L+I D+ +A ++L+ +DKV + G A +A + V S Sbjct: 69 LALVIEDEQGKKEEAINVFKKLIFQDKVLAVFGPTLSNSAFAADPIANAAKVVVFGTS-- 126 Query: 123 ETAEGKDA---WTFRLPQSTA-VMAGGVVEQMKKMGVKTIGFL-GYSDSYGENWLKEMQR 177 TA+G A +TFR A V+ V +K G+K + + G D++ ++ + Sbjct: 127 NTADGITAMGPFTFRNSVMEADVLPVTVKAAVKHFGIKKVAVIYGNDDAFTKSGYDVFKA 186 Query: 178 LATAAGMKMGTVERFSRADTSVTAQALRVVSSNPDAVLVVASGSGAA---MPHKALIERG 234 + + T E +++ D AQ ++ + NPDA++ AA + +AL G Sbjct: 187 TLEHQKIPVTTTEAYAKGDVDFKAQLTKIKAGNPDAIVCSCLAEEAANIILQTRAL---G 243 Query: 235 YKGKIFQTHSAASRDLIRLGGKDVEGSYVISGPAVVPEALPDSNPSKKLALDFVTRYEKQ 294 K + S L + KD G + G P + + P+ K F+T Y+ + Sbjct: 244 MKQPFIGGNGLNSPKLFEI-AKDA-GDNTLMGS---PWSAENQTPANKA---FITAYKAK 295 Query: 295 FGAGSRNLFAAHTYDAQLVLQKVVPEALKKAK 326 FGA + FAA YDA +V +ALK K Sbjct: 296 FGA-DPDQFAAQAYDAMY----IVADALKNVK 322 >gi|300312847|ref|YP_003776939.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 383 Score = 65.5 bits (158), Expect = 8e-12, Method: Compositional matrix adjust. Identities = 94/376 (25%), Positives = 154/376 (40%), Gaps = 48/376 (12%) Query: 12 GVLASMLACA-----GMAHAELTIGVVMSLTGPGSGLG----IPAKNGFSLWPDTIG--G 60 G+ S+LA G++ E+ +G +GP S LG + A++ F++ G G Sbjct: 14 GLAMSLLAVGAAAEDGVSATEVVLGQSAPFSGPASDLGRDFLVGAQSYFAMVNAKGGVHG 73 Query: 61 EKVKLIILDDATDPTQASKNARRLVAEDKVDLIIGSAAVPPTLAIADVALETQTVQLAIS 120 +V+L+ LDD +P + + N ++L+ DKV + G + TLA A A+ V L + Sbjct: 74 RRVRLLSLDDGYEPERTAANTQQLIWRDKVFALFGYSGTATTLA-ALPAIREANVPL-FA 131 Query: 121 PIETA----EGKDAWTFRLPQSTAVMAGGVVEQMKKMGVKTIGFLGYSDSYGENWLKEMQ 176 P+ A E + F + S A ++ Q++ G + + +D G++ L++++ Sbjct: 132 PVSGALALREPFNRLIFHVRASYAQETDFLLRQLQGTGRRKVAVFYQNDELGKSMLEQLR 191 Query: 177 RLATAAGMKMGTVERFSRADTSVTAQALRVVSSNPDAVLVVASGSGAAMPHKALIER--- 233 A G+ + R +V A ++ PD V+ V S P ALI R Sbjct: 192 LRALVYGLTLVGTAAVERNSDAVEGAAQALLKVKPDVVIQVVS----YRPAAALIARMRQ 247 Query: 234 -GYKGKIFQTHSAASRDL-IRLGGKDVEGSYVISGPAVVPEALPDSNPSKKLALDFVTRY 291 GY G S L RL + A + + +P N ++ L V Y Sbjct: 248 AGYLGGFSHYSFVGSLSLSARLKECGI--------GAEIAQVVPFPNKAR---LPLVYEY 296 Query: 292 EK---QFGAGSRNLFAAHTYDAQLVLQKVVPEALKKAKPGTPAFRTALKEALETAGPIQI 348 K Q N + Y + + + E L++A G R L ALET P Sbjct: 297 RKAVAQHPGAVDNFLSLEGY----IAARTLVEGLRRA--GRALTREGLIRALETISPANY 350 Query: 349 SQGTL--RYSAKDHFG 362 G +S DH G Sbjct: 351 DGGGFSQHFSRTDHSG 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 0.316 0.131 0.371 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: 1,165,809 Number of extensions: 47363 Number of successful extensions: 222 Number of sequences better than 1.0e-08: 13 Number of HSP's gapped: 220 Number of HSP's successfully gapped: 13 Length of query: 383 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 296 Effective length of database: 1,207,925 Effective search space: 357545800 Effective search space used: 357545800 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)