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= 0029.0041.p (312 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel A... 208 6e-55 gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 194 7e-51 gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 179 2e-46 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 173 2e-44 gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herba... 147 1e-36 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 208 bits (529), Expect = 6e-55, Method: Compositional matrix adjust. Identities = 115/308 (37%), Positives = 184/308 (59%), Gaps = 9/308 (2%) Query: 4 LIKRILLVIPTLLLVSMVIFSLLAILPGDPVTAILGLEATPEAAAALRLQLGLDDPLYVQ 63 +++R+ + + + VS+V F+LL + GD +I G EAT ++R Q GLD P+ Q Sbjct: 5 ILRRLAIALCVAVTVSVVSFTLLH-MSGDLAVSIAGPEATAAQVESVRTQFGLDRPMATQ 63 Query: 64 YARWLWNVLHGDLGRSFIDRTPVIDVLMQRLPVTIELAVGSFAVGILIAVPAGILSAVRP 123 Y WL + D G+SF + PV++++ +RLP+T +L + + +L A+P G+L+A+ Sbjct: 64 YLDWLGRAVQLDFGKSFYFQGPVMEMIAERLPITFKLGGSALLLAVLTAIPLGVLAAIYR 123 Query: 124 RGIANYFTTLVALFGMSVPHFWLGMMFIILFAVKLGWLPASGYVPFTEDWRGNLAAMCMP 183 + L+A+ G ++P FW G+ I++FAV L WLP +G E W+ +P Sbjct: 124 DTWLDRAALLIAVVGQAMPSFWFGLTLILIFAVTLHWLPVAG----NESWQ----HFILP 175 Query: 184 VLATGLRESAILMRMVRSSLLEVLNEDYIRTAFSKGLRDWQVVIGHALRNALIPVVTASG 243 +A G +MR+ RS +LEVL DYIRTA +KGL +VV HALRNA+IPVV + Sbjct: 176 AVALGYYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVIPVVALAA 235 Query: 244 LMVSVLLGGLVITESIFAIPGMGKMIVDAIFQRDYVMVQGGVLAAALMVVIVNLAVDVLY 303 + + +LGG V+ ES++++ G+G++ DAI + DY +VQ VL A+ + + DV+ Sbjct: 236 VELGFMLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVIN 295 Query: 304 TVIDPRIE 311 ++DPRI Sbjct: 296 ALLDPRIR 303 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 194 bits (493), Expect = 7e-51, Method: Compositional matrix adjust. Identities = 114/284 (40%), Positives = 161/284 (56%), Gaps = 8/284 (2%) Query: 28 ILPGDPVTAILGLEATPEAAAALRLQLGLDDPLYVQYARWLWNVLHGDLGRSFIDRTPVI 87 +LPGDP G EA + A +R LGLD PL Q+ + N GD G S + PV Sbjct: 29 LLPGDPARLAAGPEADDKTVALVRADLGLDKPLPEQFVNFFLNAARGDFGHSIRTKRPVS 88 Query: 88 DVLMQRLPVTIELAVGSFAVGILIAVPAGILSAVRPRGIANYFTTLVALFGMSVPHFWLG 147 + + R T+ L V + +L + GI SAV + +A+ G+S P F LG Sbjct: 89 EEISARFWPTLWLTVVAMVWAVLFGLIIGISSAVWRNQWPDRLGMTLAVSGISFPAFSLG 148 Query: 148 MMFIILFAVKLGWLPASGYVPFTEDWRGNLAAMCMPVLATGLRESAILMRMVRSSLLEVL 207 ++ + +F+VKLGWLP G + W +P + G +A++ R RSS +E+L Sbjct: 149 ILLVQVFSVKLGWLPTVG----DDTW----LHYILPSITLGAAVAAVMARFTRSSFIEIL 200 Query: 208 NEDYIRTAFSKGLRDWQVVIGHALRNALIPVVTASGLMVSVLLGGLVITESIFAIPGMGK 267 ED++RTA +KGL + VVI H LRNALIPVVT GL LLGG ++ E +F PGMG+ Sbjct: 201 QEDFVRTARAKGLTETVVVIKHCLRNALIPVVTMMGLQFGFLLGGSILVEVVFNWPGMGR 260 Query: 268 MIVDAIFQRDYVMVQGGVLAAALMVVIVNLAVDVLYTVIDPRIE 311 ++VDA+ RDY ++Q +L +L + +NL VDVLY VI+P I Sbjct: 261 LLVDAVEMRDYPVIQAEILLFSLEFIFINLVVDVLYAVINPSIR 304 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 179 bits (454), Expect = 2e-46, Method: Compositional matrix adjust. Identities = 112/309 (36%), Positives = 178/309 (57%), Gaps = 18/309 (5%) Query: 15 LLLVSMVIFSLLAILPGDPVTAILGLEATPEAAAALRLQLGLDDPLYVQYARWLWNVLHG 74 LL+ +V F L I G+PV ++G + + +LGLD P++ QY +L LHG Sbjct: 17 LLMTVIVFFGLHMI--GNPVDILIGQDVDQVDRLRIIQELGLDQPVWRQYLAFLNGALHG 74 Query: 75 DLGRSFIDRTPVIDVLMQRLPVTIELAVGSFAVGILIAVPAGILSAVRPRGIANYFTTLV 134 +LG SF+ TP I ++ QRLP T+ELA + + +++ VP G+ + ++P + Sbjct: 75 NLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVPLGLFAGMKPDHPFSRLVMTT 134 Query: 135 ALFGMSVPHFWLGMMFIILFAVKLGWLPASGYVPFTE------------DWRGNLAAMCM 182 ++FG S+P FW+G+M I+ F+V LGWLP+ G E WR M + Sbjct: 135 SIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWLTADGWR----HMIL 190 Query: 183 PVLATGLRESAILMRMVRSSLLEVLNEDYIRTAFSKGLRDWQVVIGHALRNALIPVVTAS 242 P + L + ++++R+ R+++ EVL D+++ A +KGL +VV+ + LRN LIP+VT Sbjct: 191 PAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLRNTLIPLVTVV 250 Query: 243 GLMVSVLLGGLVITESIFAIPGMGKMIVDAIFQRDYVMVQGGVLAAALMVVIVNLAVDVL 302 GL + V+TESIFA PG GK+I+D+I D ++ ++ M V +NL VDVL Sbjct: 251 GLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDVL 310 Query: 303 YTVIDPRIE 311 Y ++DPR+ Sbjct: 311 YKLLDPRVR 319 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 173 bits (438), Expect = 2e-44, Method: Compositional matrix adjust. Identities = 106/294 (36%), Positives = 164/294 (55%) Query: 18 VSMVIFSLLAILPGDPVTAILGLEATPEAAAALRLQLGLDDPLYVQYARWLWNVLHGDLG 77 VS +F + +LPGD LG ATPE AALRLQ GLD P ++YA WL N+L G+ G Sbjct: 23 VSAGVFFITNLLPGDAAQTALGQAATPETVAALRLQYGLDLPAPLRYAHWLGNLLSGNPG 82 Query: 78 RSFIDRTPVIDVLMQRLPVTIELAVGSFAVGILIAVPAGILSAVRPRGIANYFTTLVALF 137 S ++ PV ++ RLP ++ LA + V + +A+ GI SA+ + + A+ Sbjct: 83 MSLVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALFLGIFSAMYRGSFFDRAVNVSAVS 142 Query: 138 GMSVPHFWLGMMFIILFAVKLGWLPASGYVPFTEDWRGNLAAMCMPVLATGLRESAILMR 197 +SVP F + + +++FAVKL WL A + + A MPVL A + R Sbjct: 143 MVSVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLGAFIKAYAMPVLTLCCVIVAQMTR 202 Query: 198 MVRSSLLEVLNEDYIRTAFSKGLRDWQVVIGHALRNALIPVVTASGLMVSVLLGGLVITE 257 M R+++++ L Y A KG++ ++V+ HAL NA+ P+ A L +S LLGG++I E Sbjct: 203 MTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPNAIGPIANAVALSLSYLLGGVIIVE 262 Query: 258 SIFAIPGMGKMIVDAIFQRDYVMVQGGVLAAALMVVIVNLAVDVLYTVIDPRIE 311 SIF PG+ +++DA+ RD +VQ + +++ L DVL V +PR++ Sbjct: 263 SIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYLLLVLTADVLAIVSNPRLK 316 >gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 356 Score = 147 bits (370), Expect = 1e-36, Method: Compositional matrix adjust. Identities = 108/349 (30%), Positives = 176/349 (50%), Gaps = 42/349 (12%) Query: 2 SPLIKRILLVIPTLLLVSMVIFSLLAILPGDPVTAIL----------------------- 38 S ++KR+LL+IPTL V + F+++ +PG PV + Sbjct: 5 SYIVKRVLLMIPTLFGVVAITFAVIQFVPGGPVEQAMLEMKGRGGGGEASGGGAASGASA 64 Query: 39 --GLEATPEAAAALRLQL-GLDDPLYVQYARWLWNVLHGDLGRSFIDRTPVIDVLMQRLP 95 G + E A QL G D P ++ L L DLG+SF V ++ +LP Sbjct: 65 YRGRQGIDEQRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVKSKLP 124 Query: 96 VTIELAVGSFAVGILIAVPAGILSAVRPRGIANYFTTLVALFGMSVPHFWLGMMFIILFA 155 V+I + + +F + LI+VP GI AVR + TT + L G S+P F LG+ ++LFA Sbjct: 125 VSISIGLWTFLLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLLVLFA 184 Query: 156 --VKLGWLPASGYVPFTEDWRG---------NLAAMCMPVLATGLRESAILMRMVRSSLL 204 + W P G +++W L + +PV A+ + A++ + R++ L Sbjct: 185 GGSFVQWFPLRGLT--SDNWESLSLMGKITDYLWHITLPVTASVIGSFAVITMLTRNTFL 242 Query: 205 EVLNEDYIRTAFSKGLRDWQVVIGHALRNALIPVVTA--SGLMVSVLLGGLVITESIFAI 262 E + + Y+ TA +KGL + +V+ H RNALIP+VT S + S G L+I E++F++ Sbjct: 243 EEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLI-ETLFSL 301 Query: 263 PGMGKMIVDAIFQRDYVMVQGGVLAAALMVVIVNLAVDVLYTVIDPRIE 311 GMG + ++ +RDY +V G + L+ ++V L D+ Y DPR++ Sbjct: 302 DGMGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQ 350 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: 955,378 Number of extensions: 40502 Number of successful extensions: 234 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 224 Number of HSP's successfully gapped: 6 Length of query: 312 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 227 Effective length of database: 1,217,395 Effective search space: 276348665 Effective search space used: 276348665 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)