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= 0003.0003.p (283 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313087|ref|YP_003777179.1| sn-glycerol-3-phosphate ABC tra... 484 e-138 gi|300311927|ref|YP_003776019.1| glycerol-3-phosphate ABC transp... 171 6e-44 gi|300309612|ref|YP_003773704.1| sugar ABC transporter permease ... 117 1e-27 gi|300312389|ref|YP_003776481.1| sugar ABC transporter permease ... 107 9e-25 gi|300313834|ref|YP_003777926.1| sugar ABC transporter permease ... 91 8e-20 >gi|300313087|ref|YP_003777179.1| sn-glycerol-3-phosphate ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 283 Score = 484 bits (1247), Expect = e-138, Method: Compositional matrix adjust. Identities = 244/283 (86%), Positives = 266/283 (93%) Query: 1 MIERRPILDAVSHLVLIIGAIIVIFPLYVAFIASTQTAEQSAMSPLSLLPGTELVANYKT 60 MIERRPILD +SH+VL++G +IV FPLYVAF+ASTQ+AEQSA+SPLSL PG E + NY T Sbjct: 1 MIERRPILDFLSHVVLVLGVLIVFFPLYVAFVASTQSAEQSALSPLSLAPGGEFMNNYST 60 Query: 61 VLTQGASGNVSSPPVSRMLWISLVTALVIAIGKISISMLSAFAMVYFRFRGRNLFFWMIF 120 VL +GA+G V++PPV MLW+SL TAL+IAIGKISISMLSAFA+VYFRF GR LFFWMIF Sbjct: 61 VLFKGAAGQVTAPPVLHMLWVSLATALIIAIGKISISMLSAFAIVYFRFPGRGLFFWMIF 120 Query: 121 VTLMLPVEVRITPTYQVVSDFGMLNTYAGLTVPLIASATATFLFRQFFLTVPDELAEAAR 180 VTLMLPVEVRITPTYQVVSD GMLN+YAGL+VPLIASATATFLFRQFFLTVPDELAEAAR Sbjct: 121 VTLMLPVEVRITPTYQVVSDLGMLNSYAGLSVPLIASATATFLFRQFFLTVPDELAEAAR 180 Query: 181 IDGAGPLRFLKDVLWPLSRTNVIALFVIMFIYGWNQYLWPLMIATEQTMYPIGIGIKTLI 240 IDGAGPLRFLKDVLWPLSRTNVIALFVIMFIYGWNQYLWPL+IAT+ +MYPIGIGIKTLI Sbjct: 181 IDGAGPLRFLKDVLWPLSRTNVIALFVIMFIYGWNQYLWPLIIATDTSMYPIGIGIKTLI 240 Query: 241 SGGDSAVEWNMVMATMILAMLPPGLVVVVMQKWFVKGLVDSEK 283 SGGDSAVEWN+VMATMILAMLPPGLVVVVMQKWFVKGLVDSEK Sbjct: 241 SGGDSAVEWNLVMATMILAMLPPGLVVVVMQKWFVKGLVDSEK 283 >gi|300311927|ref|YP_003776019.1| glycerol-3-phosphate ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 298 Score = 171 bits (433), Expect = 6e-44, Method: Compositional matrix adjust. Identities = 120/306 (39%), Positives = 180/306 (58%), Gaps = 31/306 (10%) Query: 1 MIERRPILDAVSHLVLIIGAIIVIFPLYVAFIASTQTAEQSAMSPLSLLPGTELVANYKT 60 M+ER P + A+++ VL +G ++ + PLY+ +++ T++ + L PGT L+ N + Sbjct: 1 MVERHPRMTALAYCVLGLGLLLALGPLYLILCSASVTSQAWISQGMPLTPGTALLENLRE 60 Query: 61 VLTQGASGNVSSPPVSRMLWISLVTALVIAIGKISISMLSAFAMVYFRFRGRNLFFWMIF 120 V + R L+ SL+ A ++ GK+ +S ++AFA+ YFR R R L ++F Sbjct: 61 V--------AQRIDLWRYLFNSLLVASLVVSGKLLLSSVTAFAVSYFRPRCRGLILVLLF 112 Query: 121 VTLMLPVEVRITPTYQVVSDF----------------------GMLNTYAGLTVPLIASA 158 L+LP+EVRI PTY SD ++NTYAGL++PL+ASA Sbjct: 113 SALLLPLEVRIVPTYAAASDLLEPLRSLLQALDLSGQQAVPSISLVNTYAGLSLPLVASA 172 Query: 159 TATFLFRQFFLTVPDELAEAARIDGAGPLRFLKDVLWPLSRTNVIALFVIMFIYGWNQYL 218 T TFLF QF+ T+P EL EAARIDGAGP RF D+L PLS+TN AL I+FI W Y+ Sbjct: 173 TGTFLFLQFYRTIPPELVEAARIDGAGPWRFYVDILLPLSKTNFAALGAIVFISTWKDYM 232 Query: 219 WPLMIATEQTMYPIGIGIKTLISGGDSAV-EWNMVMATMILAMLPPGLVVVVMQKWFVKG 277 WPL+I + + M I + + + + + +WN++MA + A+ P + VV Q+WFVKG Sbjct: 233 WPLVITSHEQMRTITLAMASFLPVESGQMPQWNLLMAAALAAIAVPAVFVVAAQRWFVKG 292 Query: 278 LVDSEK 283 +V +EK Sbjct: 293 IVGTEK 298 >gi|300309612|ref|YP_003773704.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 283 Score = 117 bits (292), Expect = 1e-27, Method: Compositional matrix adjust. Identities = 83/281 (29%), Positives = 135/281 (48%), Gaps = 14/281 (4%) Query: 2 IER-RPILDAVSHLVLIIGAIIVIFPLYVAFIASTQTAEQSAMSPLSLLPGT-ELVANYK 59 IE+ +PI A+ L + +I + P+ A + S ++ ++ P ++ NY+ Sbjct: 6 IEKWKPINRALYRASLPVALLIWLLPMLAALVTSIRSNDELMAGNYWGWPQDFAMLENYR 65 Query: 60 TVLTQGASGNVSSPPVSRMLWISLVTALVIAIGKISISMLSAFAMVYFRFRGRNLFFWMI 119 LT + P+ W S + + IG IS++ ++ FA+ ++FRG + F Sbjct: 66 EALT--------ASPMLHYFWNSCLITIPSVIGAISLAAMAGFALSTYQFRGNTVLFATF 117 Query: 120 FVTLMLPVEVRITPTYQVVSDFGMLNTYAGLTVPLIASAT--ATFLFRQFFLTVPDELAE 177 +P ++ + P + G+ NT G+ + IA T T R F +P E+ E Sbjct: 118 VACNFVPQQILMIPVRDLSLSLGLFNTITGMMLFHIAMQTGFCTLFLRNFIKQLPFEMIE 177 Query: 178 AARIDGAGPLRFLKDVLWPLSRTNVIALFVIMFIYGWNQYLWPLMIATEQTMYPIGIGIK 237 AARI+GA ++ PL R + AL V++F + WN Y W L++ + PI +G+ Sbjct: 178 AARIEGASEWTVFYRIVLPLIRPALAALAVLVFTFVWNDYFWALVLTQGDDVAPITVGVA 237 Query: 238 TLISGGDSAVEWNMVMATMILAMLPPGLVVVVMQKWFVKGL 278 L G WN+V A ILA LP ++ VMQK FV GL Sbjct: 238 AL--RGQWTTAWNLVSAGSILAALPSVILFFVMQKQFVAGL 276 >gi|300312389|ref|YP_003776481.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 276 Score = 107 bits (268), Expect = 9e-25, Method: Compositional matrix adjust. Identities = 63/211 (29%), Positives = 112/211 (53%), Gaps = 1/211 (0%) Query: 71 SSPPVSRMLWISLVTALVIAIGKISISMLSAFAMVYFRFRGRNLFFWMIFVTLMLPVEVR 130 + P R + + +I ++ ++ L+A+A F FRG N+ F ++ + LM+ ++ Sbjct: 64 QAAPFPRYFLNTFLLVTMILAAQLVLATLAAYAFARFTFRGSNVMFMLVLLQLMVMPDIL 123 Query: 131 ITPTYQVVSDFGMLNTYAGLTVPLIASATATFLFRQFFLTVPDELAEAARIDGAGPLRFL 190 I YQ ++ G+ +T + +P ASA FL RQ F TVP EL EAA ++GA + L Sbjct: 124 IVENYQTMNLLGLRDTILSIGLPYFASAFGIFLLRQTFKTVPRELDEAATVEGASAWQIL 183 Query: 191 KDVLWPLSRTNVIALFVIMFIYGWNQYLWPLMIATEQTMYPIGIGIKTLISGGDSAVEWN 250 V PL+R IA ++ WN +LWPL++ P+ +G++ + S D V+W+ Sbjct: 184 MQVYVPLARPIYIAFGLVSVSTHWNNFLWPLIVTNSVESRPLTVGLQ-VFSSTDQGVDWS 242 Query: 251 MVMATMILAMLPPGLVVVVMQKWFVKGLVDS 281 ++ A ++ P L ++ Q+ FV+ + + Sbjct: 243 IITAATLMTSAPLLLAFLLFQRQFVQSFMRA 273 >gi|300313834|ref|YP_003777926.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 300 Score = 91.3 bits (225), Expect = 8e-20, Method: Compositional matrix adjust. Identities = 73/277 (26%), Positives = 128/277 (46%), Gaps = 23/277 (8%) Query: 13 HLVLIIGAIIVIFPLYVAFIASTQTAEQSAMSPLSLLPGTELV--ANYKTVLTQGAS--- 67 H VL + A+I +FP+ + I S +T P++L P E + A ++ VL Sbjct: 36 HTVLCLYAVIALFPIALILINSVKTRNAIFEGPMAL-PTAETLTFAGFQKVLAGTHFLLY 94 Query: 68 -GNVSSPPVSRMLWISLVTALVIAIGKISISMLSAFAMVYFRFRGRNLFFWMIFVTLMLP 126 GN + V+ + I L A+ +A+A+ +RF G + I + +M+P Sbjct: 95 FGNSLAVTVAALFLIVLFGAM------------AAWALTEYRFFGNRALNFFIAIGIMIP 142 Query: 127 VEVRITPTYQVVSDFGMLNTYAGLTVPLIASAT--ATFLFRQFFLTVPDELAEAARIDGA 184 + + Q+V ++NT L + A A + +F +P EL +AAR DG Sbjct: 143 IRLGTVSILQLVVALDLINTRTALVLVYTAQGLPLAVMILSEFMRQIPGELKDAARCDGV 202 Query: 185 GPLRFLKDVLWPLSRTNVIALFVIMFIYGWNQYLWPLMIATEQTMYPIGIGIKTLISGGD 244 G L V+ PL R + + V I WN +PL++A + + +G++ I G Sbjct: 203 GELSIFFRVILPLLRPAIATVAVFTMIPAWNDLWFPLILAPGEDTRTVTLGVQQFI--GQ 260 Query: 245 SAVEWNMVMATMILAMLPPGLVVVVMQKWFVKGLVDS 281 A +WN V+A + +A++P L+ + + ++GL Sbjct: 261 YATDWNSVLAALSMAVIPVLLLYMAFSRQLIRGLTSG 297 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 0.328 0.140 0.421 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: 820,192 Number of extensions: 31051 Number of successful extensions: 156 Number of sequences better than 1.0e-08: 9 Number of HSP's gapped: 141 Number of HSP's successfully gapped: 9 Length of query: 283 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 199 Effective length of database: 1,222,130 Effective search space: 243203870 Effective search space used: 243203870 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 130 (54.7 bits)