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= 0001.2439.p (320 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 329 2e-91 gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel A... 200 1e-52 gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 181 5e-47 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 132 3e-32 gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herba... 123 2e-29 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 329 bits (843), Expect = 2e-91, Method: Compositional matrix adjust. Identities = 163/316 (51%), Positives = 242/316 (76%) Query: 4 RRALQSVLVIFVMSILAFVGINLVGNPIHLLVAPDAPLEEIQRASHALGLDLPMYQQYLR 63 R +Q+++V+ +M+++ F G++++GNP+ +L+ D + R LGLD P+++QYL Sbjct: 7 RSVVQALMVVLLMTVIVFFGLHMIGNPVDILIGQDVDQVDRLRIIQELGLDQPVWRQYLA 66 Query: 64 FVSNALHGDLGNSFVFNQPAIGLILERMPATFELAVAALLLSAVIGIPLGMWSGLRPGSR 123 F++ ALHG+LGNSFV+N PAI LI +R+PAT ELA AALLL+ V+G+PLG+++G++P Sbjct: 67 FLNGALHGNLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVPLGLFAGMKPDHP 126 Query: 124 VHKLAMGFSVLGVTVPVFWLGLILILVFSVNLGWLPSGGRGPTTSLLGVQVSFLSWEGLK 183 +L M S+ G ++P FW+GL+LI+ FSV LGWLPSGGRG T L GVQ S+L+ +G + Sbjct: 127 FSRLVMTTSIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWLTADGWR 186 Query: 184 YIVLPACTLALHNIALVMRMTEAGTREVAVQEYVKFARAKGVGAVRLMMRHIAPNVMIPI 243 +++LPA L+L I+LV+R+T A REV ++VKFARAKG+ R+++ ++ N +IP+ Sbjct: 187 HMILPAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLRNTLIPL 246 Query: 244 VTVMGIEFGHLIAFSLITETIFAWPGMGKLIIDSVLQLDRPVVVAYLMVVLLLYVVINFV 303 VTV+G+EFG IAF+++TE+IFAWPG GKLI+DS+ LDRPV+VAYLMV++ ++V IN V Sbjct: 247 VTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMFVTINLV 306 Query: 304 VDVLYLILDPRLRTKS 319 VDVLY +LDPR+R ++ Sbjct: 307 VDVLYKLLDPRVRVEA 322 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 200 bits (508), Expect = 1e-52, Method: Compositional matrix adjust. Identities = 103/317 (32%), Positives = 185/317 (58%), Gaps = 16/317 (5%) Query: 2 LLRRALQSVLVIFVMSILAFVGINLVGNPIHLLVAPDAPLEEIQRASHALGLDLPMYQQY 61 +LRR ++ V +S+++F +++ G+ + P+A +++ GLD PM QY Sbjct: 5 ILRRLAIALCVAVTVSVVSFTLLHMSGDLAVSIAGPEATAAQVESVRTQFGLDRPMATQY 64 Query: 62 LRFVSNALHGDLGNSFVFNQPAIGLILERMPATFELAVAALLLSAVIGIPLGMWSGLRPG 121 L ++ A+ D G SF F P + +I ER+P TF+L +ALLL+ + IPLG+ + + Sbjct: 65 LDWLGRAVQLDFGKSFYFQGPVMEMIAERLPITFKLGGSALLLAVLTAIPLGVLAAIYRD 124 Query: 122 SRVHKLAMGFSVLGVTVPVFWLGLILILVFSVNLGWLPSGGRGPTTSLLGVQVSFLSWEG 181 + + + A+ +V+G +P FW GL LIL+F+V L WLP G E Sbjct: 125 TWLDRAALLIAVVGQAMPSFWFGLTLILIFAVTLHWLPVAGN----------------ES 168 Query: 182 LKYIVLPACTLALHNIALVMRMTEAGTREVAVQEYVKFARAKGVGAVRLMMRHIAPNVMI 241 ++ +LPA L + + +MR+T +G EV +Y++ ARAKG+ R++ +H N +I Sbjct: 169 WQHFILPAVALGYYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVI 228 Query: 242 PIVTVMGIEFGHLIAFSLITETIFAWPGMGKLIIDSVLQLDRPVVVAYLMVVLLLYVVIN 301 P+V + +E G ++ S++ E++++ G+G+L D++ + D PVV A ++++ + Y+ + Sbjct: 229 PVVALAAVELGFMLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLT 288 Query: 302 FVVDVLYLILDPRLRTK 318 F+ DV+ +LDPR+RT+ Sbjct: 289 FLADVINALLDPRIRTR 305 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 181 bits (460), Expect = 5e-47, Method: Compositional matrix adjust. Identities = 104/293 (35%), Positives = 168/293 (57%), Gaps = 16/293 (5%) Query: 26 LVGNPIHLLVAPDAPLEEIQRASHALGLDLPMYQQYLRFVSNALHGDLGNSFVFNQPAIG 85 L G+P L P+A + + LGLD P+ +Q++ F NA GD G+S +P Sbjct: 30 LPGDPARLAAGPEADDKTVALVRADLGLDKPLPEQFVNFFLNAARGDFGHSIRTKRPVSE 89 Query: 86 LILERMPATFELAVAALLLSAVIGIPLGMWSGLRPGSRVHKLAMGFSVLGVTVPVFWLGL 145 I R T L V A++ + + G+ +G+ S + +L M +V G++ P F LG+ Sbjct: 90 EISARFWPTLWLTVVAMVWAVLFGLIIGISSAVWRNQWPDRLGMTLAVSGISFPAFSLGI 149 Query: 146 ILILVFSVNLGWLPSGGRGPTTSLLGVQVSFLSWEGLKYIVLPACTLALHNIALVMRMTE 205 +L+ VFSV LGWLP+ G +W L YI LP+ TL A++ R T Sbjct: 150 LLVQVFSVKLGWLPTVGDD-------------TW--LHYI-LPSITLGAAVAAVMARFTR 193 Query: 206 AGTREVAVQEYVKFARAKGVGAVRLMMRHIAPNVMIPIVTVMGIEFGHLIAFSLITETIF 265 + E+ +++V+ ARAKG+ ++++H N +IP+VT+MG++FG L+ S++ E +F Sbjct: 194 SSFIEILQEDFVRTARAKGLTETVVVIKHCLRNALIPVVTMMGLQFGFLLGGSILVEVVF 253 Query: 266 AWPGMGKLIIDSVLQLDRPVVVAYLMVVLLLYVVINFVVDVLYLILDPRLRTK 318 WPGMG+L++D+V D PV+ A +++ L ++ IN VVDVLY +++P +R K Sbjct: 254 NWPGMGRLLVDAVEMRDYPVIQAEILLFSLEFIFINLVVDVLYAVINPSIRFK 306 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 132 bits (333), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 84/267 (31%), Positives = 138/267 (51%), Gaps = 8/267 (2%) Query: 52 GLDLPMYQQYLRFVSNALHGDLGNSFVFNQPAIGLILERMPATFELAVAALLLSAVIGIP 111 GLDLP +Y ++ N L G+ G S V N P +I R+PA+ LA L+S + + Sbjct: 60 GLDLPAPLRYAHWLGNLLSGNPGMSLVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALF 119 Query: 112 LGMWSGLRPGSRVHKLAMGFSVLGVTVPVFWLGLILILVFSVNLGWLPSGGRGPTTSLLG 171 LG++S + GS + +V V+VP F + + +++F+V L WL + + LG Sbjct: 120 LGIFSAMYRGSFFDRAVNVSAVSMVSVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLG 179 Query: 172 VQVSFLSWEGLKYIVLPACTLALHNIALVMRMTEAGTREVAVQEYVKFARAKGVGAVRLM 231 + K +P TL +A + RMT A + Y + A KGV R++ Sbjct: 180 AFI--------KAYAMPVLTLCCVIVAQMTRMTRAAVIDQLRSSYAEMALLKGVKRTRIV 231 Query: 232 MRHIAPNVMIPIVTVMGIEFGHLIAFSLITETIFAWPGMGKLIIDSVLQLDRPVVVAYLM 291 +RH PN + PI + + +L+ +I E+IF +PG+ L+ID+V D P+V A M Sbjct: 232 LRHALPNAIGPIANAVALSLSYLLGGVIIVESIFNYPGIATLMIDAVTTRDMPLVQACSM 291 Query: 292 VVLLLYVVINFVVDVLYLILDPRLRTK 318 + Y+++ DVL ++ +PRL+T+ Sbjct: 292 IFCAGYLLLVLTADVLAIVSNPRLKTR 318 >gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 356 Score = 123 bits (309), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 83/285 (29%), Positives = 145/285 (50%), Gaps = 12/285 (4%) Query: 42 EEIQRASHALGLDLPMYQQYLRFVSNALHGDLGNSFVFNQPAIGLILERMPATFELAVAA 101 + I G D P +++ + L DLG SF + L+ ++P + + + Sbjct: 74 QRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVKSKLPVSISIGLWT 133 Query: 102 LLLSAVIGIPLGMWSGLRPGSRVHKLAMGFSVLGVTVPVFWLGLILILVFSVN--LGWLP 159 LLS +I +PLG+ +R G+R G ++G ++P F LG+ L+++F+ + W P Sbjct: 134 FLLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLLVLFAGGSFVQWFP 193 Query: 160 ----SGGRGPTTSLLGVQVSFLSWEGLKYIVLPACTLALHNIALVMRMTEAGTREVAVQE 215 + + SL+G +L W +I LP + + A++ +T E ++ Sbjct: 194 LRGLTSDNWESLSLMGKITDYL-W----HITLPVTASVIGSFAVITMLTRNTFLEEIRKQ 248 Query: 216 YVKFARAKGVGAVRLMMRHIAPNVMIPIVTVMGIEF-GHLIAFSLITETIFAWPGMGKLI 274 YV ARAKG+ R++ +H+ N +IP+VT F A SL+ ET+F+ GMG L Sbjct: 249 YVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFSLDGMGLLA 308 Query: 275 IDSVLQLDRPVVVAYLMVVLLLYVVINFVVDVLYLILDPRLRTKS 319 +S ++ D PVV+ L + L+ +V+ V D+ Y+ DPR++ +S Sbjct: 309 YESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQFES 353 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 0.329 0.144 0.430 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: 954,972 Number of extensions: 40244 Number of successful extensions: 200 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 196 Number of HSP's successfully gapped: 6 Length of query: 320 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 235 Effective length of database: 1,217,395 Effective search space: 286087825 Effective search space used: 286087825 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)