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= 0001.0038.p (403 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310372|ref|YP_003774464.1| sugar ABC transporter permease ... 748 0.0 gi|300313778|ref|YP_003777870.1| D-xylose ABC transporter permea... 200 2e-52 gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galacto... 125 6e-30 gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ... 122 4e-29 gi|300311740|ref|YP_003775832.1| sugar ABC transporter permease ... 117 2e-27 >gi|300310372|ref|YP_003774464.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 405 Score = 748 bits (1931), Expect = 0.0, Method: Compositional matrix adjust. Identities = 390/405 (96%), Positives = 394/405 (97%), Gaps = 2/405 (0%) Query: 1 MESIDMSKKPAVASGAV--EKKDYGSFLKNNMREYGMLMSLVAIMAFFQIMTDGTLMRPL 58 MESIDMSKKPA A+ EKKDYGSFLKNNMREYGMLMSLVAIMAFFQIMTDGTLMRPL Sbjct: 1 MESIDMSKKPAAAAAGGAAEKKDYGSFLKNNMREYGMLMSLVAIMAFFQIMTDGTLMRPL 60 Query: 59 NLTNLVLQNSYIVIMALGMLMVIVAGHIDLSVGSVVGLIGALAAVLMVDYGWGFVPASIV 118 NLTNLVLQNSYIVIMALGMLMVIVAGHIDLSVGSVVGLIGALAAVLMVDYGWGFVPASIV Sbjct: 61 NLTNLVLQNSYIVIMALGMLMVIVAGHIDLSVGSVVGLIGALAAVLMVDYGWGFVPASIV 120 Query: 119 CLIAGALIGAAQGYWIAYFKIPSFIVTLAGMLVFKGMALALLQGQSLGPFPQTFQMLSSG 178 CLIAG LIGAAQGYWIAYFKIPSFIVTLAGMLVFKGMALALLQGQSLGPFPQTFQMLSSG Sbjct: 121 CLIAGGLIGAAQGYWIAYFKIPSFIVTLAGMLVFKGMALALLQGQSLGPFPQTFQMLSSG 180 Query: 179 FIPELTDNTTFRTTSLIVGIIAAVVLILVKLHGRRKQTKHGMEDEPAMFFLLKNGVFAIA 238 FIPELT NTTFRTTSLIVG+IAAVVLILVKLHGRRKQTKHGMEDEP +FFLLKNGVFA A Sbjct: 181 FIPELTGNTTFRTTSLIVGVIAAVVLILVKLHGRRKQTKHGMEDEPVLFFLLKNGVFAAA 240 Query: 239 IIAFSYLLSTYRGMPNVLIIMFALMVLYTFITSRTTLGRRVYAVGGNEKAAKLSGIKTER 298 IIAFSYLLSTYRGMPNVLIIMFALMVLYTFITSRTTLGRRVYAVGGNEKAAKLSGIKTER Sbjct: 241 IIAFSYLLSTYRGMPNVLIIMFALMVLYTFITSRTTLGRRVYAVGGNEKAAKLSGIKTER 300 Query: 299 VSFFTFVNMGVLAALAGLIFAARLNTATPKAGLGFELDVIAACFIGGASASGGVGKVMGA 358 VSFFTFVNMGVLAALAGLIFAARLNTATPKAGLGFELDVIAACFIGGASASGGVGKVMGA Sbjct: 301 VSFFTFVNMGVLAALAGLIFAARLNTATPKAGLGFELDVIAACFIGGASASGGVGKVMGA 360 Query: 359 VIGAFIMGVMNNGMSIMGIGIDYQQMIKGLVLLMAVCFDVYNKNK 403 VIGAF+MGVMNNGMSIMGIGIDYQQMIKG VLLMAVCFDVYNKNK Sbjct: 361 VIGAFVMGVMNNGMSIMGIGIDYQQMIKGFVLLMAVCFDVYNKNK 405 >gi|300313778|ref|YP_003777870.1| D-xylose ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 385 Score = 200 bits (508), Expect = 2e-52, Method: Compositional matrix adjust. Identities = 141/358 (39%), Positives = 215/358 (60%), Gaps = 8/358 (2%) Query: 45 FFQIMTDGTLMRPLNLTNLVLQNSYIVIMALGMLMVIVAGHIDLSVGSVVGLIGALAAVL 104 FF MTDG + P NL+NL+ Q S I+A GM++VI+AG IDLSVGS++GL+G LAA+L Sbjct: 34 FFSFMTDGGFVTPRNLSNLLRQMSVTGILACGMVLVIIAGEIDLSVGSLLGLLGGLAALL 93 Query: 105 MVDYGWGFVPASIVCLIAGALIGAAQGYWIAYFKIPSFIVTLAGMLVFKGMALALLQGQS 164 V + ++ L G +G GY AY IPSFIV L GML F+G+ L + G + Sbjct: 94 DVSHHLPLALNLVLALGFGLALGLLNGYLTAYLGIPSFIVGLGGMLAFRGILLGITGGLT 153 Query: 165 LGPFPQTFQMLSSGFIPELTDNTTFRTTSLIVGIIAAVVLILVKLHGRRKQTKHGMEDEP 224 + P L G++P + +GI V+ + + R +++HG+ Sbjct: 154 IAPVSDNMVYLGQGYLPP--------QMGVALGIALFVLAVALTWMSRVNRSRHGLPLAA 205 Query: 225 AMFFLLKNGVFAIAIIAFSYLLSTYRGMPNVLIIMFALMVLYTFITSRTTLGRRVYAVGG 284 LK V ++AF L++Y G+P ++++ AL+ L+++++++T GRR+Y+VG Sbjct: 206 LWRDALKVVVIGAVLLAFVRTLNSYDGIPVPVLLLLALLGLFSYVSTQTVFGRRIYSVGS 265 Query: 285 NEKAAKLSGIKTERVSFFTFVNMGVLAALAGLIFAARLNTATPKAGLGFELDVIAACFIG 344 N +A +LSG+ + V + F MGV+ ALAGL+ ARL +P AG ELD IAACFIG Sbjct: 266 NMEATRLSGVNVQAVKLWVFGIMGVMCALAGLVNTARLAAGSPSAGNMGELDAIAACFIG 325 Query: 345 GASASGGVGKVMGAVIGAFIMGVMNNGMSIMGIGIDYQQMIKGLVLLMAVCFDVYNKN 402 G S GG G + GA+IGA +M ++NGMS++ +G +Q ++KG +L++AV DV ++ Sbjct: 326 GTSMRGGSGTIYGALIGALVMASLDNGMSMLDVGTYWQMIVKGSILVLAVWVDVSTRS 383 >gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galactoside ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 328 Score = 125 bits (314), Expect = 6e-30, Method: Compositional matrix adjust. Identities = 62/143 (43%), Positives = 95/143 (66%) Query: 252 MPNVLIIMFALMVLYTFITSRTTLGRRVYAVGGNEKAAKLSGIKTERVSFFTFVNMGVLA 311 +P +I+M + L + RT GR VYA+GGNE AA+LSG+KT R+ + G + Sbjct: 179 VPVPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTS 238 Query: 312 ALAGLIFAARLNTATPKAGLGFELDVIAACFIGGASASGGVGKVMGAVIGAFIMGVMNNG 371 LA +I RL + P AG+GFELD IAA +GG + +GG G V+G +IGA ++G++NNG Sbjct: 239 GLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNG 298 Query: 372 MSIMGIGIDYQQMIKGLVLLMAV 394 +++MGI Q +I+G+++L+A+ Sbjct: 299 LNLMGINPYLQDIIRGVIILLAI 321 Score = 55.1 bits (131), Expect = 9e-09, Method: Compositional matrix adjust. Identities = 45/125 (36%), Positives = 67/125 (53%), Gaps = 6/125 (4%) Query: 59 NLTNLVLQNSYIVIMALGMLMVIVAGHIDLSVGSVVGLIGALAAVLMVDYGWGFVPASIV 118 N N++ Q S + I+A+GM VI+ G IDLSVG+ + L G ++A L+V+ G +PA + Sbjct: 55 NWFNVLRQVSIVGILAVGMSFVILTGGIDLSVGAAMALAGTISAGLIVNSG---LPAPLA 111 Query: 119 CLIAGAL---IGAAQGYWIAYFKIPSFIVTLAGMLVFKGMALALLQGQSLGPFPQTFQML 175 L L IG G +A+ ++P+ IVTLA M V +G+ L G + P Sbjct: 112 LLCGVGLATCIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWISWF 171 Query: 176 SSGFI 180 G I Sbjct: 172 GVGRI 176 >gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 344 Score = 122 bits (307), Expect = 4e-29, Method: Compositional matrix adjust. Identities = 106/346 (30%), Positives = 169/346 (48%), Gaps = 72/346 (20%) Query: 59 NLTNLVLQNSYIVIMALGMLMVIVAGHIDLSVGSVVGLIGALAAVLMVDYGWGFVPASIV 118 N N++ Q + +++A GM VI+ IDLSVGSV+ A++AVL + Sbjct: 65 NTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVL----AVSAVLGMQVS--------- 111 Query: 119 CLIAGALIGAAQGYWIAYFKIPSFIVTLAGMLVFKGMALALLQGQSLGPFPQTFQMLS-S 177 +GAA G+ IP FI F G+ + ++ G + +L+ + Sbjct: 112 -------LGAAPGW-----AIPMFI--------FSGLVMGMVNGAMV-------ALLNIN 144 Query: 178 GFIPELTDNTTFRTTSLIVGIIAAVVLILVKLHGRRKQTKHGMEDEPAMFFLLKNGVFAI 237 F+ L T FR + ++ V+ D P+ F + NG F Sbjct: 145 AFVVTLGTMTAFRGAAYLLADGTTVL----------------NNDIPS-FEWIGNGDF-- 185 Query: 238 AIIAFSYLLSTYRGMPNVLIIMFALMVLYTFITSRTTLGRRVYAVGGNEKAAKLSGIKTE 297 +P ++ + A+++L I +T LG +YA+GGN +AA+L+GI+ Sbjct: 186 ------------LHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVG 233 Query: 298 RVSFFTFVNMGVLAALAGLIFAARLNTATPKAGLGFELDVIAACFIGGASASGGVGKVMG 357 V F + G+ + LAG + A+RL A G G+ELD IAA +GG S GGVG + G Sbjct: 234 LVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWG 293 Query: 358 AVIGAFIMGVMNNGMSIMGIGIDYQQMIKGLVLLMAVCFDVYNKNK 403 V+GA I+GVMNNG++I+G+ +Q + KG V+++AV D + + Sbjct: 294 TVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQKD 339 >gi|300311740|ref|YP_003775832.1| sugar ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 379 Score = 117 bits (293), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 102/374 (27%), Positives = 177/374 (47%), Gaps = 38/374 (10%) Query: 32 EYGMLMSLVAIMAFFQIMTDGTLMRPLN-LTNLVLQNSYIVIMALGMLMVIVAGHIDLSV 90 E+ L ++ + F + + M L+ + N + +Y+ I+A+ ++++ G DLS+ Sbjct: 37 EFASLAGVILVFLVFGLTAGDSGMFNLDGVVNWMQVAAYLGIIAVAACLLMIGGEFDLSI 96 Query: 91 GSVVGLIGALAAVLMVDYGWGFVPASIVCLIAGALIGAAQGYWIAYFKIPSFIVTLAGML 150 GS++GL G + A+ V +GW F A + A +G GY + ++PSFIVTLA + Sbjct: 97 GSMIGLAGMMVAIPTVYFGWPFWLAVLFAFAASMGLGWLNGYLVMKTRLPSFIVTLAFLF 156 Query: 151 VFKGMALALLQGQSLGPFPQTFQMLSSGFIPELTDNTTFRTTSLIVGIIAAVVLILVKLH 210 + +G+ LAL + F +++ G+ H Sbjct: 157 ILRGLTLAL--------------------------SILFANRTIVSGVGERAA------H 184 Query: 211 GRRKQTKHGMEDEPAMF-FLLKNGVFAIAIIAFSYLLSTYRGMPNVLIIMFALMVLYTFI 269 Q +F +L ++G IA +A L T G+P V++ + + +F+ Sbjct: 185 DWLGQLLFSGNVGAGLFSWLARHG--WIATVADGTPLVT--GIPKVILWWAVVALAASFV 240 Query: 270 TSRTTLGRRVYAVGGNEKAAKLSGIKTERVSFFTFVNMGVLAALAGLIFAARLNTATPKA 329 +RT LG ++AVGG+ AAK G+ +V FV A L ++ +A Sbjct: 241 LARTRLGNWIFAVGGDAVAAKNMGVPVRKVKIGLFVFTAFCACLFAVLQVGDFGSAAADR 300 Query: 330 GLGFELDVIAACFIGGASASGGVGKVMGAVIGAFIMGVMNNGMSIMGIGIDYQQMIKGLV 389 GL E + I A IGGA +GG G V+GA GA I GV+ G++ + D+ ++ G++ Sbjct: 301 GLQKEFEAIIAAVIGGALLTGGYGSVIGACFGALIFGVVQIGITYTNLSSDWFRVFLGVM 360 Query: 390 LLMAVCFDVYNKNK 403 LL+AV F+ + + + Sbjct: 361 LLVAVLFNNFVRRR 374 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 0.141 0.406 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: 1,016,711 Number of extensions: 35601 Number of successful extensions: 256 Number of sequences better than 1.0e-08: 21 Number of HSP's gapped: 255 Number of HSP's successfully gapped: 30 Length of query: 403 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 316 Effective length of database: 1,207,925 Effective search space: 381704300 Effective search space used: 381704300 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: 132 (55.5 bits)