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= 0001.1335.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|300310826|ref|YP_003774918.1| amino-acid ABC transporter peri... 454 e-129 gi|300313169|ref|YP_003777261.1| amino acid transport periplasmi... 193 9e-51 gi|300313535|ref|YP_003777627.1| amino acid ABC transporter/sign... 157 9e-40 gi|300313886|ref|YP_003777978.1| amino acid ABC transporter peri... 138 5e-34 gi|300311590|ref|YP_003775682.1| amino acid ABC transporter/sign... 120 9e-29 >gi|300310826|ref|YP_003774918.1| amino-acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 267 Score = 454 bits (1167), Expect = e-129, Method: Compositional matrix adjust. Identities = 260/267 (97%), Positives = 263/267 (98%) Query: 2 MSIKKVFNAKFLALTLAAACAVATAASASAQSIAELTKKGKITIGVVSGTPPFGSVDAKG 61 MSIKK+FNAKFLALTLAAACAVAT ASASAQSIA+LTKKGKITIGVVSGTPPFGSVDAKG Sbjct: 1 MSIKKIFNAKFLALTLAAACAVATTASASAQSIADLTKKGKITIGVVSGTPPFGSVDAKG 60 Query: 62 VPIGYDVDVANLIGKYLGLPVEIVPLVPPARIPALESGKVDMLAATLAPTPERAKSVLFT 121 PIGYDVDVANLIGKYLGLPVEIVPLVPPARIPALESGKVDMLAATLAPTPERAKSVLFT Sbjct: 61 TPIGYDVDVANLIGKYLGLPVEIVPLVPPARIPALESGKVDMLAATLAPTPERAKSVLFT 120 Query: 122 IPYSGFELSIVGPVGSHYKKLDDLVKKKVGVSRGSTNDTALTRLAPAGTVLVRFEDDSTV 181 IPYSGFELSIV PVGS+YKKLDDLVKKKVGVSRGSTNDTALTRLAP GTVLVRFEDDSTV Sbjct: 121 IPYSGFELSIVAPVGSNYKKLDDLVKKKVGVSRGSTNDTALTRLAPPGTVLVRFEDDSTV 180 Query: 182 TQALLSNQVDAISIPNTMANEIVKSRGQGKIEVKFPYSVQPNSMTVRKGSYELQQWLNNF 241 TQALLSNQVDAISIPNTMANEIVKSRGQGKIEVKFPYSVQPNSMTVRKGSYELQQWLNNF Sbjct: 181 TQALLSNQVDAISIPNTMANEIVKSRGQGKIEVKFPYSVQPNSMTVRKGSYELQQWLNNF 240 Query: 242 IYYVKLNGELDAISRKWAGPLPNLPVF 268 IYYVKLNGELDAISRKWAGPLPNLPVF Sbjct: 241 IYYVKLNGELDAISRKWAGPLPNLPVF 267 >gi|300313169|ref|YP_003777261.1| amino acid transport periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 268 Score = 193 bits (491), Expect = 9e-51, Method: Compositional matrix adjust. Identities = 107/262 (40%), Positives = 154/262 (58%), Gaps = 4/262 (1%) Query: 8 FNAKFLALTLAAACAVATAASASAQSIAELTKKGKITIGVVSGTPPFGSVDAKGVPIGYD 67 F K A+ L AC A + + I + K+ + + G PPFG +AK P G D Sbjct: 7 FTRKAAAVVLGLACFAQAAHADALADI---KARKKVLVAIDLGAPPFGMTNAKLEPQGSD 63 Query: 68 VDVANLIGKYLGLPVEIVPLVPPARIPALESGKVDMLAATLAPTPERAKSVLFTIPYSGF 127 V+ A L+ K LG+ +EIV + P RIP L +GK DM+ ++ + TPER K V FT PY Sbjct: 64 VETARLLAKDLGVELEIVQVTGPNRIPFLMTGKADMVISSFSITPERQKVVAFTQPYGAS 123 Query: 128 ELSIVGPVGSHYKKLDDLVKKKVGVSRGSTNDTALTRLAPAGTVLVRFEDDSTVTQALLS 187 + + P G + K L+DLV K+V V RG+ D+ LT +AP GT +VRF+DD+TVT A++S Sbjct: 124 QFVVAAPKGENIKSLNDLVGKRVAVVRGNMQDSLLTPIAPKGTNIVRFDDDATVTAAIIS 183 Query: 188 NQVDAISIPNTMANEIVKSRGQGKIEVKFPYSVQPNSMTVRKGSYELQQWLNNFIYYVKL 247 QVDA+ PN++A+ I K +E KF P ++ +RKG L++WLN +I Sbjct: 184 GQVDALCTPNSLASAIAKQNPSKNLETKFAIKDIPYAIGLRKGEPALEKWLNEWISANLK 243 Query: 248 NGELDAISRKWAG-PLPNLPVF 268 NG+L I ++W G P+P+L F Sbjct: 244 NGKLPGIYQQWVGSPMPDLAQF 265 >gi|300313535|ref|YP_003777627.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 157 bits (397), Expect = 9e-40, Method: Compositional matrix adjust. Identities = 91/252 (36%), Positives = 138/252 (54%), Gaps = 1/252 (0%) Query: 13 LALTLAAACAVATAASASAQSIAELTKKGKITIGVVSGTPPFGSVDAKGVPIGYDVDVAN 72 L L L A + +A+ A A ++ ++ K G + + V + PPFGSVDA P G D+DVA Sbjct: 6 LLLGLMAGAMMFSASVARADALDDIQKHGTLRVAVPADFPPFGSVDADLKPQGLDIDVAT 65 Query: 73 LIGKYLGLPVEIVPLVPPARIPALESGKVDMLAATLAPTPERAKSVLFTIPYSGFELSIV 132 LI K LG+ VE++P+ RIP L + KVD++ +++ ER K + F+ Y+ F + Sbjct: 66 LIAKKLGVKVELIPVSSANRIPYLTTKKVDLVISSMGKNAEREKVIDFSAAYAPFFNGVF 125 Query: 133 GPVGSHYKKLDDLVKKKVGVSRGSTNDTALTRLAPAGTVLVRFEDDSTVTQALLSNQVDA 192 GP K DL K + V+RGS D LT++ PA + R+ED+++ + LS QV Sbjct: 126 GPADLSVKSAADLAGKTIAVTRGSVEDLELTKIVPASATVKRYEDNNSTISSFLSGQVQL 185 Query: 193 ISIPNTMANEIVKSRGQGKIEVKFPYSVQPNSMTVRKGSYELQQWLNNFIYYVKLNGELD 252 ++ N +A I+ K E KF P + + KG +LQ ++ + K +G L Sbjct: 186 VATGNVVAAAIIARNPPKKPETKFLIKDSPCFIGLNKGEKKLQDKVDAILAESKKDGSLS 245 Query: 253 AISRKWAG-PLP 263 AIS+KW G PLP Sbjct: 246 AISQKWLGMPLP 257 >gi|300313886|ref|YP_003777978.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 267 Score = 138 bits (347), Expect = 5e-34, Method: Compositional matrix adjust. Identities = 78/236 (33%), Positives = 132/236 (55%), Gaps = 1/236 (0%) Query: 25 TAASASAQSIAELTKKGKITIGVVSGTPPFGSVDAKGVPIGYDVDVANLIGKYLGLPVEI 84 TA +A A + ++ K GKI I S TP FG D K G DV+ A L+ + LG+ +++ Sbjct: 22 TAHAALADQLDDIKKAGKIRIATTSSTPLFGYSDEKLQLAGSDVEAARLLAQDLGVQLDL 81 Query: 85 VPLVPPARIPALESGKVDMLAATLAPTPERAKSVLFTIPYSGFELSIVGPVGSHYKKLDD 144 +P+ AR+P L++ + D++ +L+ TPER K + F+ PY+ L I P K D Sbjct: 82 IPVANAARVPTLQANRADIVVGSLSITPERLKVIDFSTPYAVISLIIGAPKSMVIKDYAD 141 Query: 145 LVKKKVGVSRGSTNDTALTRLAPAGTVLVRFEDDSTVTQALLSNQVDAISIPNTMANEIV 204 L K++GV+R + NDT T+ A G ++R+EDD+T+ ++++ QVD S + E+ Sbjct: 142 LNGKRIGVTRATPNDTLTTQNA-KGAEIMRYEDDATLITSMVTGQVDVFSSTPSNLQEMQ 200 Query: 205 KSRGQGKIEVKFPYSVQPNSMTVRKGSYELQQWLNNFIYYVKLNGELDAISRKWAG 260 K +E+KF + + K L++W++ ++ NG+L+AI +K+ G Sbjct: 201 KKAPGKNLEMKFEQKAFDLGIAINKNQPRLKEWIDGWVKTNMKNGKLNAIYKKYHG 256 >gi|300311590|ref|YP_003775682.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 267 Score = 120 bits (302), Expect = 9e-29, Method: Compositional matrix adjust. Identities = 75/236 (31%), Positives = 122/236 (51%), Gaps = 1/236 (0%) Query: 29 ASAQSIAELTKKGKITIGVVSGTPPFGSVDAKGVPIGYDVDVANLIGKYLGLPVEIVPLV 88 A A ++A++ K G + IGV PFGSV+ G D+DVA LI + +G+ +++VP+ Sbjct: 24 ARADALADIQKNGVVRIGVPQDFAPFGSVNTDLQLQGLDIDVARLIAQKMGVKLQLVPVA 83 Query: 89 PPARIPALESGKVDMLAATLAPTPERAKSVLFTIPYSGFELSIVGPVGSHYKKLDDLVKK 148 RI L++ K D++ +TL ER K + F+ PY+ + S+ G DL K Sbjct: 84 SANRIAYLQTHKADLVISTLGRNAEREKVIDFSQPYAPYNNSVFGVASVKVSGPADLADK 143 Query: 149 KVGVSRGSTNDTALTRLAPAGTVLVRFEDDSTVTQALLSNQVDAISIPNTMANEIVKSRG 208 VGV+RG+ D LT AP + R+ED++ + A +S QV + + +A + + Sbjct: 144 TVGVARGTFQDLQLTDTAPKSATIKRYEDNNAMISAYVSGQVQLVGTGDFVAYALAEKAP 203 Query: 209 QGKIEVKFPYSVQPNSMTVRKGSYELQQWLNNFIYYVKLNGELDAISRKWAG-PLP 263 K +K+ ++ + KG L +N + K +GEL+ I +KW PLP Sbjct: 204 NNKPVLKYIIQESACNVGLNKGEPALLAKVNEALTAAKKSGELNGIVQKWLNVPLP 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 0.316 0.133 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: 730,711 Number of extensions: 29175 Number of successful extensions: 137 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 (21.6 bits) S2: 130 (54.7 bits)