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= 0025.0004.p (324 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313309|ref|YP_003777401.1| sugar ABC transporter permease ... 587 e-169 gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galacto... 79 6e-16 gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease ... 74 2e-14 gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease ... 65 8e-12 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 62 5e-11 >gi|300313309|ref|YP_003777401.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 331 Score = 587 bits (1514), Expect = e-169, Method: Compositional matrix adjust. Identities = 307/328 (93%), Positives = 314/328 (95%), Gaps = 5/328 (1%) Query: 2 TTLARTPVRARHGLLSRHEIQTLLLPMATLAVVLAPIFWINPNTMSYFGLGLLLNLAVPM 61 T+ A + R G+LSRHEIQTLLLPMATLAVVLAPIFWINPNTMSYFGLGLLLNLAVPM Sbjct: 4 TSAATVTAQRRMGVLSRHEIQTLLLPMATLAVVLAPIFWINPNTMSYFGLGLLLNLAVPM 63 Query: 62 ILASMAQLCIIAVNDLDLSIGAFISLVSCIAVTWLPERPLLGVAALIACVLLYAAIGALV 121 ILASMAQLCIIAVNDLDLSIGAFISLVSCIAVTWLPERP+LGVAAL+ACVLLYAAIGALV Sbjct: 64 ILASMAQLCIIAVNDLDLSIGAFISLVSCIAVTWLPERPVLGVAALVACVLLYAAIGALV 123 Query: 122 ELFDLPSIVVTLGLSFVWGG-----WALILLPMPGGATPQWIQDVMNLAIPVVPTPIVYA 176 ELFDLPSIVVTLGLSFVWGG WALILLPMPGGATPQWIQDVMNLAIPV+PTPIVYA Sbjct: 124 ELFDLPSIVVTLGLSFVWGGFVWGGWALILLPMPGGATPQWIQDVMNLAIPVIPTPIVYA 183 Query: 177 VVIALCGHWFLMRSSLGVRLRGAGGNPKAIVRSGGSVVRAKALMYGLAGVLGILSALTLV 236 V+IALC HWFLMRSS GVRLRGAGGNPKAIVRSGGSVVRAKALMYGLAGVLGILSALTLV Sbjct: 184 VLIALCAHWFLMRSSTGVRLRGAGGNPKAIVRSGGSVVRAKALMYGLAGVLGILSALTLV 243 Query: 237 GITTSADANIAQRYTLISIAAVILGGGSFIGGKVSPIGATLGAITLGIAASFLSFLNIAP 296 GITTSADANIAQRYTLISIAAVILGGGSFIGGKVSPIGATLGAITLGIAASFLSFLNIAP Sbjct: 244 GITTSADANIAQRYTLISIAAVILGGGSFIGGKVSPIGATLGAITLGIAASFLSFLNIAP 303 Query: 297 KWQIGLQGAILIIVLSMRILLSARGERQ 324 KWQIGLQGAILIIVLSMRILLSARGERQ Sbjct: 304 KWQIGLQGAILIIVLSMRILLSARGERQ 331 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 79.0 bits (193), Expect = 6e-16, Method: Compositional matrix adjust. Identities = 77/248 (31%), Positives = 120/248 (48%), Gaps = 9/248 (3%) Query: 71 IIAVNDLDLSIGAFISLVSCIAVTWLPERPLLGVAALIACVLLYAAIG----ALVELFDL 126 +I +DLS+GA ++L I+ + L AL+ V L IG ALV + Sbjct: 76 VILTGGIDLSVGAAMALAGTISAGLIVNSGLPAPLALLCGVGLATCIGLLNGALVAWGRM 135 Query: 127 PSIVVTLGLSFVWGGWALIL---LPMPGGATPQWIQDVMNLAIPVVPTPIVYAVVIALCG 183 P+I+VTL V G LI P+ G P WI I +VP P++ +++ Sbjct: 136 PAIIVTLATMGVARGVGLIYSGGYPISG--LPGWISWFGVGRIGMVPVPVILMLIVYALA 193 Query: 184 HWFLMRSSLGVRLRGAGGNPKAIVRSGGSVVRAKALMYGLAGVLGILSALTLVGITTSAD 243 L R++ G + GGN A SG R K +Y ++G L+A+ L G S Sbjct: 194 WLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGLAAIILTGRLMSGQ 253 Query: 244 ANIAQRYTLISIAAVILGGGSFIGGKVSPIGATLGAITLGIAASFLSFLNIAPKWQIGLQ 303 N + L +IAAV+LGG + GG+ +G +GA+ LGI + L+ + I P Q ++ Sbjct: 254 PNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIIR 313 Query: 304 GAILIIVL 311 G I+++ + Sbjct: 314 GVIILLAI 321 >gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 352 Score = 73.9 bits (180), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 90/302 (29%), Positives = 142/302 (47%), Gaps = 30/302 (9%) Query: 36 APIFWINPNTMSYFGLGLLLNLAVPMILASMAQLCIIAVNDLDLSIGAFISLVSCIAVTW 95 AP+F ++ +M LL + A+ ++LA +AQ+ +I +DLS+ + ++L ++ Sbjct: 46 APVF-LSAQSMD----NLLTDSAITIMLA-LAQMLVILTRGIDLSVASNLALSGMMSALL 99 Query: 96 LPERPLLGVAALIACVLLYAAI-----GALVELFDLPSIVVTLGLSFVWGGWALILLPMP 150 P L V I +L + G L+ +LP IVVTLG V+ G +L Sbjct: 100 AMHFPALPVGVFILMAVLIGLMLGLLNGWLIGYLELPPIVVTLGSMSVYRGMVFVL---S 156 Query: 151 GGATPQWIQD----VMNLAIPVVP----TPIVYAVVIALCGHWFLMRSSLGVRLRGAGGN 202 GGA W+ +A P+ T +V+ +A+ WFL R + R A GN Sbjct: 157 GGA---WVSSRNMPADFIAFPLARLGGLTHLVWLGALAVVAIWFLARHTRFGRDLYAIGN 213 Query: 203 PKAIVRSGGSVVRAKAL-MYGLAGVLGILSALTLVGITTSADANIAQRYTLISIAAVILG 261 A G R + L YGL+G + L+ V A IA + L IAA ++G Sbjct: 214 DPAAAAYVGIASRGRLLWTYGLSGAMAGLAGYLWVARYAVAYTEIAYGFELTVIAACVIG 273 Query: 262 GGSFIGGKVSPIGATLGAITLGIAASFLSFLNIAPKWQIGLQGAILIIVLSMRILLSARG 321 G S GG GA LGA+ L + + L + I+P WQ L G +++ ++L+ARG Sbjct: 274 GVSIAGGVGQVSGAVLGALFLSVINNALPIMRISPFWQSALTGLVILCA----VVLNARG 329 Query: 322 ER 323 ++ Sbjct: 330 KQ 331 >gi|300313726|ref|YP_003777818.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 342 Score = 65.1 bits (157), Expect = 8e-12, Method: Compositional matrix adjust. Identities = 92/297 (30%), Positives = 136/297 (45%), Gaps = 21/297 (7%) Query: 34 VLAPIFWINPNTM--SYFGLGLLLNLAVPMILASMAQLCIIAVNDLDLSIGAFISLVS-C 90 +L P F+ +P + S F +A+PM L +I ++D+S+ A I+L S Sbjct: 52 LLLPHFF-DPYNLADSTFNFSEKAMIALPMAL-------LIICREIDISVSAIIALASVA 103 Query: 91 IAVTWLPERPLLG-----VAALIACVLLYAAIGALVELFDLPSIVVTLG-LSFVWGGWAL 144 + + P LG +A AC LL GALV LPSIVVT+G +S G ++ Sbjct: 104 MGLANQAGVPPLGLLLVAIATGTACGLLN---GALVTRLGLPSIVVTIGSMSLFRGLASV 160 Query: 145 ILLPMPGGATPQWIQD-VMNLAIPVVPTPIVYAVVIALCGHWFLMRSSLGVRLRGAGGNP 203 +L P+ + D V+P P V ++ A+ L + G RL G NP Sbjct: 161 VLGDQAFTQYPEVLGDWGQGYFFDVLPRPFVVWLLAAVVFAVLLHVTRWGRRLYAIGNNP 220 Query: 204 KAIVRSGGSVVRAKALMYGLAGVLGILSALTLVGITTSADANIAQRYTLISIAAVILGGG 263 A SG +V R + ++ L G + L+A L G S NIA + L I VILGG Sbjct: 221 VAARFSGVAVDRYRLALFVLTGAMAGLAAFFLTGRIGSTRPNIAMGWELEIITVVILGGV 280 Query: 264 SFIGGKVSPIGATLGAITLGIAASFLSFLNIAPKWQIGLQGAILIIVLSMRILLSAR 320 S GG S G L + +G+ L+ NI + GA+L+ +++ LL R Sbjct: 281 SIAGGTGSIGGVMLSVLVMGMLTYGLALANIPGIIMTIVVGALLLATIAIPRLLRGR 337 >gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 62.4 bits (150), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 81/284 (28%), Positives = 137/284 (48%), Gaps = 36/284 (12%) Query: 43 PNTMSYFGLGLLLNLAVPMILASMAQLCIIAVNDLDLSIGAFISLVSCIAVT-WLPERPL 101 NTM+ +L +A+ ++LA+ I+ +DLS+G+ +++ + + + L P Sbjct: 64 ENTMN-----ILRQVAINLVLAAGMTFVILTAG-IDLSVGSVLAVSAVLGMQVSLGAAPG 117 Query: 102 LGVAALIACVLLYAAI-GALVELFDLPSIVVTLGLSFVWGGWALILLPMPGGATPQWIQD 160 + I L+ + GA+V L ++ + VVTLG + G A +L G T Sbjct: 118 WAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLL---ADGTT------ 168 Query: 161 VMNLAIPV-----------VPTPIVYAVVIALCGHWFLMRSSLGVRLRGAGGNPKAIVRS 209 V+N IP VP I AV + L L ++ LG+ + GGN +A + Sbjct: 169 VLNNDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLT 228 Query: 210 GGSVVRAKALMYGLAGVL----GILSALTLVGITTSADANIAQRYTLISIAAVILGGGSF 265 G V +Y ++G+ G +SA L G A+ N Y L +IAAV+LGG S Sbjct: 229 GIRVGLVLLFVYSISGLFSGLAGAMSASRLYG----ANGNWGSGYELDAIAAVVLGGTSL 284 Query: 266 IGGKVSPIGATLGAITLGIAASFLSFLNIAPKWQIGLQGAILII 309 +GG S G +GA+ +G+ + L+ L ++ WQ +GA++++ Sbjct: 285 MGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVL 328 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 0.327 0.142 0.428 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: 1,081,560 Number of extensions: 49677 Number of successful extensions: 325 Number of sequences better than 1.0e-08: 15 Number of HSP's gapped: 304 Number of HSP's successfully gapped: 15 Length of query: 324 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 239 Effective length of database: 1,217,395 Effective search space: 290957405 Effective search space used: 290957405 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 (21.7 bits) S2: 131 (55.1 bits)