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= 0001.1710.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... 210 1e-55 gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 198 4e-52 gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 174 9e-45 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 169 3e-43 gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herba... 137 1e-33 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 210 bits (535), Expect = 1e-55, Method: Compositional matrix adjust. Identities = 120/307 (39%), Positives = 182/307 (59%), Gaps = 9/307 (2%) Query: 4 LVKRLLLSLPTLLLVSMVVFSLLAVLPGDPVAAILGMEATPEAAAALRLKLGLDDPLLVQ 63 +++RL ++L + VS+V F+LL + GD +I G EAT ++R + GLD P+ Q Sbjct: 5 ILRRLAIALCVAVTVSVVSFTLLH-MSGDLAVSIAGPEATAAQVESVRTQFGLDRPMATQ 63 Query: 64 YGRWLWAVLHGDLGRSFIDNTPVAEALWQRLPVTIELAIGSFLVAVIIAVPAGILSAARP 123 Y WL + D G+SF PV E + +RLP+T +L + L+AV+ A+P G+L+A Sbjct: 64 YLDWLGRAVQLDFGKSFYFQGPVMEMIAERLPITFKLGGSALLLAVLTAIPLGVLAAIYR 123 Query: 124 RGWANAIGTLIALFGMSVPHFWLGMLFIILFAVKLGWLPASGFVPLSVDWHANLIAMVMP 183 W + LIA+ G ++P FW G+ I++FAV L WLP +G + W ++P Sbjct: 124 DTWLDRAALLIAVVGQAMPSFWFGLTLILIFAVTLHWLPVAG----NESWQ----HFILP 175 Query: 184 MVVTGLRESAILMRMVRSSLLEVLNEDYIRTAFSKGLRDWQVVLGHALRNAMIPVVTASG 243 V G +MR+ RS +LEVL DYIRTA +KGL +VV HALRNA+IPVV + Sbjct: 176 AVALGYYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVIPVVALAA 235 Query: 244 LMVSGMLGGLVITESIFGIPGMGKMIVDAIFQRDYVTVQAGVLAATVMVVIVNLCVDLLY 303 + + MLGG V+ ES++ + G+G++ DAI + DY VQA VL + + + D++ Sbjct: 236 VELGFMLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVIN 295 Query: 304 SVIDPRI 310 +++DPRI Sbjct: 296 ALLDPRI 302 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 198 bits (504), Expect = 4e-52, Method: Compositional matrix adjust. Identities = 111/283 (39%), Positives = 165/283 (58%), Gaps = 8/283 (2%) Query: 28 VLPGDPVAAILGMEATPEAAAALRLKLGLDDPLLVQYGRWLWAVLHGDLGRSFIDNTPVA 87 +LPGDP G EA + A +R LGLD PL Q+ + GD G S PV+ Sbjct: 29 LLPGDPARLAAGPEADDKTVALVRADLGLDKPLPEQFVNFFLNAARGDFGHSIRTKRPVS 88 Query: 88 EALWQRLPVTIELAIGSFLVAVIIAVPAGILSAARPRGWANAIGTLIALFGMSVPHFWLG 147 E + R T+ L + + + AV+ + GI SA W + +G +A+ G+S P F LG Sbjct: 89 EEISARFWPTLWLTVVAMVWAVLFGLIIGISSAVWRNQWPDRLGMTLAVSGISFPAFSLG 148 Query: 148 MLFIILFAVKLGWLPASGFVPLSVDWHANLIAMVMPMVVTGLRESAILMRMVRSSLLEVL 207 +L + +F+VKLGWLP G + ++P + G +A++ R RSS +E+L Sbjct: 149 ILLVQVFSVKLGWLPTVG--------DDTWLHYILPSITLGAAVAAVMARFTRSSFIEIL 200 Query: 208 NEDYIRTAFSKGLRDWQVVLGHALRNAMIPVVTASGLMVSGMLGGLVITESIFGIPGMGK 267 ED++RTA +KGL + VV+ H LRNA+IPVVT GL +LGG ++ E +F PGMG+ Sbjct: 201 QEDFVRTARAKGLTETVVVIKHCLRNALIPVVTMMGLQFGFLLGGSILVEVVFNWPGMGR 260 Query: 268 MIVDAIFQRDYVTVQAGVLAATVMVVIVNLCVDLLYSVIDPRI 310 ++VDA+ RDY +QA +L ++ + +NL VD+LY+VI+P I Sbjct: 261 LLVDAVEMRDYPVIQAEILLFSLEFIFINLVVDVLYAVINPSI 303 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 174 bits (441), Expect = 9e-45, Method: Compositional matrix adjust. Identities = 111/315 (35%), Positives = 188/315 (59%), Gaps = 9/315 (2%) Query: 4 LVKRLLLSLPTLLLVSMVVFSLLAVLPGDPVAAILGMEATPEAAAALRLKLGLDDPLLVQ 63 + + ++ +L +LL++++VF L ++ G+PV ++G + + +LGLD P+ Q Sbjct: 5 IARSVVQALMVVLLMTVIVFFGLHMI-GNPVDILIGQDVDQVDRLRIIQELGLDQPVWRQ 63 Query: 64 YGRWLWAVLHGDLGRSFIDNTPVAEALWQRLPVTIELAIGSFLVAVIIAVPAGILSAARP 123 Y +L LHG+LG SF+ NTP ++QRLP T+ELA + L+A+++ VP G+ + +P Sbjct: 64 YLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVPLGLFAGMKP 123 Query: 124 RGWANAIGTLIALFGMSVPHFWLGMLFIILFAVKLGWLPASGFVP----LSVDWH----A 175 + + ++FG S+P FW+G++ I+ F+V LGWLP+ G V W Sbjct: 124 DHPFSRLVMTTSIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWLTAD 183 Query: 176 NLIAMVMPMVVTGLRESAILMRMVRSSLLEVLNEDYIRTAFSKGLRDWQVVLGHALRNAM 235 M++P + L + ++++R+ R+++ EVL D+++ A +KGL +VVL + LRN + Sbjct: 184 GWRHMILPAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLRNTL 243 Query: 236 IPVVTASGLMVSGMLGGLVITESIFGIPGMGKMIVDAIFQRDYVTVQAGVLAATVMVVIV 295 IP+VT GL + V+TESIF PG GK+I+D+I D + A ++ M V + Sbjct: 244 IPLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMFVTI 303 Query: 296 NLCVDLLYSVIDPRI 310 NL VD+LY ++DPR+ Sbjct: 304 NLVVDVLYKLLDPRV 318 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 169 bits (428), Expect = 3e-43, Method: Compositional matrix adjust. Identities = 107/293 (36%), Positives = 166/293 (56%) Query: 18 VSMVVFSLLAVLPGDPVAAILGMEATPEAAAALRLKLGLDDPLLVQYGRWLWAVLHGDLG 77 VS VF + +LPGD LG ATPE AALRL+ GLD P ++Y WL +L G+ G Sbjct: 23 VSAGVFFITNLLPGDAAQTALGQAATPETVAALRLQYGLDLPAPLRYAHWLGNLLSGNPG 82 Query: 78 RSFIDNTPVAEALWQRLPVTIELAIGSFLVAVIIAVPAGILSAARPRGWANAIGTLIALF 137 S ++N PVA+ + RLP ++ LA + LV+V +A+ GI SA + + + A+ Sbjct: 83 MSLVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALFLGIFSAMYRGSFFDRAVNVSAVS 142 Query: 138 GMSVPHFWLGMLFIILFAVKLGWLPASGFVPLSVDWHANLIAMVMPMVVTGLRESAILMR 197 +SVP F + + +++FAVKL WL A + A + A MP++ A + R Sbjct: 143 MVSVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLGAFIKAYAMPVLTLCCVIVAQMTR 202 Query: 198 MVRSSLLEVLNEDYIRTAFSKGLRDWQVVLGHALRNAMIPVVTASGLMVSGMLGGLVITE 257 M R+++++ L Y A KG++ ++VL HAL NA+ P+ A L +S +LGG++I E Sbjct: 203 MTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPNAIGPIANAVALSLSYLLGGVIIVE 262 Query: 258 SIFGIPGMGKMIVDAIFQRDYVTVQAGVLAATVMVVIVNLCVDLLYSVIDPRI 310 SIF PG+ +++DA+ RD VQA + +++ L D+L V +PR+ Sbjct: 263 SIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYLLLVLTADVLAIVSNPRL 315 >gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 356 Score = 137 bits (345), Expect = 1e-33, Method: Compositional matrix adjust. Identities = 102/346 (29%), Positives = 173/346 (50%), Gaps = 42/346 (12%) Query: 4 LVKRLLLSLPTLLLVSMVVFSLLAVLPGDPVA-AILGMEAT------------------- 43 +VKR+LL +PTL V + F+++ +PG PV A+L M+ Sbjct: 7 IVKRVLLMIPTLFGVVAITFAVIQFVPGGPVEQAMLEMKGRGGGGEASGGGAASGASAYR 66 Query: 44 ------PEAAAALRLKLGLDDPLLVQYGRWLWAVLHGDLGRSFIDNTPVAEALWQRLPVT 97 + A ++ G D P + ++ L L DLG+SF + V + +LPV+ Sbjct: 67 GRQGIDEQRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVKSKLPVS 126 Query: 98 IELAIGSFLVAVIIAVPAGILSAARPRGWANAIGTLIALFGMSVPHFWLGMLFIILFA-- 155 I + + +FL++ +I+VP GI A R + T + L G S+P F LG+ ++LFA Sbjct: 127 ISIGLWTFLLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLLVLFAGG 186 Query: 156 VKLGWLPASGFVPLSVDWHA---------NLIAMVMPMVVTGLRESAILMRMVRSSLLEV 206 + W P G S +W + L + +P+ + + A++ + R++ LE Sbjct: 187 SFVQWFPLRGLT--SDNWESLSLMGKITDYLWHITLPVTASVIGSFAVITMLTRNTFLEE 244 Query: 207 LNEDYIRTAFSKGLRDWQVVLGHALRNAMIPVVTA--SGLMVSGMLGGLVITESIFGIPG 264 + + Y+ TA +KGL + +V+ H RNA+IP+VT S + S G L+I E++F + G Sbjct: 245 IRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLI-ETLFSLDG 303 Query: 265 MGKMIVDAIFQRDYVTVQAGVLAATVMVVIVNLCVDLLYSVIDPRI 310 MG + ++ +RDY V + T++ ++V L DL Y DPR+ Sbjct: 304 MGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRV 349 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 0.142 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: 839,087 Number of extensions: 32378 Number of successful extensions: 209 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 203 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)