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= 0003.0159.p (268 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313169|ref|YP_003777261.1| amino acid transport periplasmi... 508 e-145 gi|300309582|ref|YP_003773674.1| amino acid ABC transporter/sign... 219 1e-58 gi|300313886|ref|YP_003777978.1| amino acid ABC transporter peri... 207 1e-54 gi|300313535|ref|YP_003777627.1| amino acid ABC transporter/sign... 189 3e-49 gi|300311590|ref|YP_003775682.1| amino acid ABC transporter/sign... 184 5e-48 >gi|300313169|ref|YP_003777261.1| amino acid transport periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 268 Score = 508 bits (1309), Expect = e-145, Method: Compositional matrix adjust. Identities = 260/268 (97%), Positives = 265/268 (98%) Query: 1 MKKLFNFTRKAAAVVLGLACFAQAAHADALADIKARKKVLIAIDLGAPPFGMTNAKLEPQ 60 MKKL +FTRKAAAVVLGLACFAQAAHADALADIKARKKVL+AIDLGAPPFGMTNAKLEPQ Sbjct: 1 MKKLLSFTRKAAAVVLGLACFAQAAHADALADIKARKKVLVAIDLGAPPFGMTNAKLEPQ 60 Query: 61 GSDVETARLLAKDMGVELEIVQVTGPNRIPFLMTGKADMVISSFSITPERQKVVAFTQPY 120 GSDVETARLLAKD+GVELEIVQVTGPNRIPFLMTGKADMVISSFSITPERQKVVAFTQPY Sbjct: 61 GSDVETARLLAKDLGVELEIVQVTGPNRIPFLMTGKADMVISSFSITPERQKVVAFTQPY 120 Query: 121 GASQFVVAAPKGENIKGLNDLVGKRVAVVRGNMQDSLLTPLAPKGTNIVRFDDDATVTAA 180 GASQFVVAAPKGENIK LNDLVGKRVAVVRGNMQDSLLTP+APKGTNIVRFDDDATVTAA Sbjct: 121 GASQFVVAAPKGENIKSLNDLVGKRVAVVRGNMQDSLLTPIAPKGTNIVRFDDDATVTAA 180 Query: 181 IISGQVDALCTPNSLASAIAKQNPSKNLETKFAIKDIPYAIGLRKGEPALEKWLNEWITA 240 IISGQVDALCTPNSLASAIAKQNPSKNLETKFAIKDIPYAIGLRKGEPALEKWLNEWI+A Sbjct: 181 IISGQVDALCTPNSLASAIAKQNPSKNLETKFAIKDIPYAIGLRKGEPALEKWLNEWISA 240 Query: 241 NLKNGKLPGIYQQWVGSPMPDLAQFAPK 268 NLKNGKLPGIYQQWVGSPMPDLAQFA K Sbjct: 241 NLKNGKLPGIYQQWVGSPMPDLAQFAAK 268 >gi|300309582|ref|YP_003773674.1| amino acid ABC transporter/signal transduction system periplasmic binding protein [Herbaspirillum seropedicae SmR1] Length = 269 Score = 219 bits (559), Expect = 1e-58, Method: Compositional matrix adjust. Identities = 111/235 (47%), Positives = 150/235 (63%) Query: 26 HADALADIKARKKVLIAIDLGAPPFGMTNAKLEPQGSDVETARLLAKDMGVELEIVQVTG 85 AD L I A KK+ +AIDL PP+ M + KL GSDVETA+ +AKD G+ELE+V T Sbjct: 27 QADQLDTILAAKKLRVAIDLAVPPYSMKDDKLRLIGSDVETAQRMAKDFGLELEVVPTTL 86 Query: 86 PNRIPFLMTGKADMVISSFSITPERQKVVAFTQPYGASQFVVAAPKGENIKGLNDLVGKR 145 NR+P+L T KAD+VIS+FSITPER KV+ F+ PY VV AP+ I DL GK+ Sbjct: 87 TNRVPYLQTNKADIVISAFSITPERAKVIDFSVPYAPILVVVGAPRSMKITSPADLAGKK 146 Query: 146 VAVVRGNMQDSLLTPLAPKGTNIVRFDDDATVTAAIISGQVDALCTPNSLASAIAKQNPS 205 + RG D LT +AP I RFDDDAT A++SGQ D T L + ++NPS Sbjct: 147 IIATRGTTNDQELTKIAPSSATITRFDDDATSMTAMVSGQADIWATSPMLLKVVNQKNPS 206 Query: 206 KNLETKFAIKDIPYAIGLRKGEPALEKWLNEWITANLKNGKLPGIYQQWVGSPMP 260 +++E+K +K A+GLRKGEP L++ ++ WI NL NG+L IY+++ + +P Sbjct: 207 RDIESKLTLKANLLAVGLRKGEPRLKEKIDGWIRTNLSNGELNTIYKKYHEAELP 261 >gi|300313886|ref|YP_003777978.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 267 Score = 207 bits (526), Expect = 1e-54, Method: Compositional matrix adjust. Identities = 109/251 (43%), Positives = 153/251 (60%), Gaps = 3/251 (1%) Query: 14 VVLGLACFAQAAHADALADIKARKKVLIAIDLGAPPFGMTNAKLEPQGSDVETARLLAKD 73 +VLGL A AA AD L DIK K+ IA P FG ++ KL+ GSDVE ARLLA+D Sbjct: 17 LVLGLT--AHAALADQLDDIKKAGKIRIATTSSTPLFGYSDEKLQLAGSDVEAARLLAQD 74 Query: 74 MGVELEIVQVTGPNRIPFLMTGKADMVISSFSITPERQKVVAFTQPYGASQFVVAAPKGE 133 +GV+L+++ V R+P L +AD+V+ S SITPER KV+ F+ PY ++ APK Sbjct: 75 LGVQLDLIPVANAARVPTLQANRADIVVGSLSITPERLKVIDFSTPYAVISLIIGAPKSM 134 Query: 134 NIKGLNDLVGKRVAVVRGNMQDSLLTPLAPKGTNIVRFDDDATVTAAIISGQVDALCTPN 193 IK DL GKR+ V R D+L T A KG I+R++DDAT+ ++++GQVD + Sbjct: 135 VIKDYADLNGKRIGVTRATPNDTLTTQNA-KGAEIMRYEDDATLITSMVTGQVDVFSSTP 193 Query: 194 SLASAIAKQNPSKNLETKFAIKDIPYAIGLRKGEPALEKWLNEWITANLKNGKLPGIYQQ 253 S + K+ P KNLE KF K I + K +P L++W++ W+ N+KNGKL IY++ Sbjct: 194 SNLQEMQKKAPGKNLEMKFEQKAFDLGIAINKNQPRLKEWIDGWVKTNMKNGKLNAIYKK 253 Query: 254 WVGSPMPDLAQ 264 + G +P Q Sbjct: 254 YHGRDLPAAVQ 264 >gi|300313535|ref|YP_003777627.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 189 bits (479), Expect = 3e-49, Method: Compositional matrix adjust. Identities = 98/239 (41%), Positives = 146/239 (61%) Query: 22 AQAAHADALADIKARKKVLIAIDLGAPPFGMTNAKLEPQGSDVETARLLAKDMGVELEIV 81 A A ADAL DI+ + +A+ PPFG +A L+PQG D++ A L+AK +GV++E++ Sbjct: 19 ASVARADALDDIQKHGTLRVAVPADFPPFGSVDADLKPQGLDIDVATLIAKKLGVKVELI 78 Query: 82 QVTGPNRIPFLMTGKADMVISSFSITPERQKVVAFTQPYGASQFVVAAPKGENIKGLNDL 141 V+ NRIP+L T K D+VISS ER+KV+ F+ Y V P ++K DL Sbjct: 79 PVSSANRIPYLTTKKVDLVISSMGKNAEREKVIDFSAAYAPFFNGVFGPADLSVKSAADL 138 Query: 142 VGKRVAVVRGNMQDSLLTPLAPKGTNIVRFDDDATVTAAIISGQVDALCTPNSLASAIAK 201 GK +AV RG+++D LT + P + R++D+ + ++ +SGQV + T N +A+AI Sbjct: 139 AGKTIAVTRGSVEDLELTKIVPASATVKRYEDNNSTISSFLSGQVQLVATGNVVAAAIIA 198 Query: 202 QNPSKNLETKFAIKDIPYAIGLRKGEPALEKWLNEWITANLKNGKLPGIYQQWVGSPMP 260 +NP K ETKF IKD P IGL KGE L+ ++ + + K+G L I Q+W+G P+P Sbjct: 199 RNPPKKPETKFLIKDSPCFIGLNKGEKKLQDKVDAILAESKKDGSLSAISQKWLGMPLP 257 >gi|300311590|ref|YP_003775682.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 267 Score = 184 bits (468), Expect = 5e-48, Method: Compositional matrix adjust. Identities = 110/252 (43%), Positives = 152/252 (60%), Gaps = 7/252 (2%) Query: 13 AVVLGLACFAQA-AHADALADIKARKKVLIAIDLGAPPFGMTNAKLEPQGSDVETARLLA 71 AVVLGLA A ADALADI+ V I + PFG N L+ QG D++ ARL+A Sbjct: 11 AVVLGLAAMQGGLARADALADIQKNGVVRIGVPQDFAPFGSVNTDLQLQGLDIDVARLIA 70 Query: 72 KDMGVELEIVQVTGPNRIPFLMTGKADMVISSFSITPERQKVVAFTQPYG---ASQFVVA 128 + MGV+L++V V NRI +L T KAD+VIS+ ER+KV+ F+QPY S F VA Sbjct: 71 QKMGVKLQLVPVASANRIAYLQTHKADLVISTLGRNAEREKVIDFSQPYAPYNNSVFGVA 130 Query: 129 APKGENIKGLNDLVGKRVAVVRGNMQDSLLTPLAPKGTNIVRFDDDATVTAAIISGQVDA 188 + K + G DL K V V RG QD LT APK I R++D+ + +A +SGQV Sbjct: 131 SVK---VSGPADLADKTVGVARGTFQDLQLTDTAPKSATIKRYEDNNAMISAYVSGQVQL 187 Query: 189 LCTPNSLASAIAKQNPSKNLETKFAIKDIPYAIGLRKGEPALEKWLNEWITANLKNGKLP 248 + T + +A A+A++ P+ K+ I++ +GL KGEPAL +NE +TA K+G+L Sbjct: 188 VGTGDFVAYALAEKAPNNKPVLKYIIQESACNVGLNKGEPALLAKVNEALTAAKKSGELN 247 Query: 249 GIYQQWVGSPMP 260 GI Q+W+ P+P Sbjct: 248 GIVQKWLNVPLP 259 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 0.318 0.134 0.386 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: 797,032 Number of extensions: 32032 Number of successful extensions: 138 Number of sequences better than 1.0e-08: 16 Number of HSP's gapped: 128 Number of HSP's successfully gapped: 16 Length of query: 268 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 184 Effective length of database: 1,222,130 Effective search space: 224871920 Effective search space used: 224871920 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 (21.7 bits) S2: 130 (54.7 bits)