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= 0057.0013.p (174 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 146 9e-37 gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel A... 134 5e-33 gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 121 3e-29 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 103 5e-24 gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herba... 94 9e-21 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 146 bits (369), Expect = 9e-37, Method: Compositional matrix adjust. Identities = 78/173 (45%), Positives = 110/173 (63%), Gaps = 8/173 (4%) Query: 1 MSVPHFWLGMMFIILFAVKLGWLPASGYVPFTEDWRGNLAAMCMPVLATGLRESAILMRM 60 +S P F LG++ + +F+VKLGWLP G + W +P + G +A++ R Sbjct: 140 ISFPAFSLGILLVQVFSVKLGWLPTVG----DDTW----LHYILPSITLGAAVAAVMARF 191 Query: 61 VRSSLLEVLNEDYIRTAFSKGLRDWQVVIGHALRNALIPVVTASGLMVSVLLGGLVITES 120 RSS +E+L ED++RTA +KGL + VVI H LRNALIPVVT GL LLGG ++ E Sbjct: 192 TRSSFIEILQEDFVRTARAKGLTETVVVIKHCLRNALIPVVTMMGLQFGFLLGGSILVEV 251 Query: 121 IFAIPGMGKMIVDAIFQRDYVMVQGGVLAAALMVVIVNLAVDVLYTVIDPRIE 173 +F PGMG+++VDA+ RDY ++Q +L +L + +NL VDVLY VI+P I Sbjct: 252 VFNWPGMGRLLVDAVEMRDYPVIQAEILLFSLEFIFINLVVDVLYAVINPSIR 304 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 134 bits (336), Expect = 5e-33, Method: Compositional matrix adjust. Identities = 71/172 (41%), Positives = 106/172 (61%), Gaps = 8/172 (4%) Query: 2 SVPHFWLGMMFIILFAVKLGWLPASGYVPFTEDWRGNLAAMCMPVLATGLRESAILMRMV 61 ++P FW G+ I++FAV L WLP +G E W+ +P +A G +MR+ Sbjct: 140 AMPSFWFGLTLILIFAVTLHWLPVAG----NESWQH----FILPAVALGYYAMPAMMRLT 191 Query: 62 RSSLLEVLNEDYIRTAFSKGLRDWQVVIGHALRNALIPVVTASGLMVSVLLGGLVITESI 121 RS +LEVL DYIRTA +KGL +VV HALRNA+IPVV + + + +LGG V+ ES+ Sbjct: 192 RSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVIPVVALAAVELGFMLGGSVVIESV 251 Query: 122 FAIPGMGKMIVDAIFQRDYVMVQGGVLAAALMVVIVNLAVDVLYTVIDPRIE 173 +++ G+G++ DAI + DY +VQ VL A+ + + DV+ ++DPRI Sbjct: 252 YSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVINALLDPRIR 303 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 121 bits (304), Expect = 3e-29, Method: Compositional matrix adjust. Identities = 70/184 (38%), Positives = 108/184 (58%), Gaps = 16/184 (8%) Query: 2 SVPHFWLGMMFIILFAVKLGWLPASGYVPFTE------------DWRGNLAAMCMPVLAT 49 S+P FW+G+M I+ F+V LGWLP+ G E WR M +P + Sbjct: 140 SLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWLTADGWR----HMILPAINL 195 Query: 50 GLRESAILMRMVRSSLLEVLNEDYIRTAFSKGLRDWQVVIGHALRNALIPVVTASGLMVS 109 L + ++++R+ R+++ EVL D+++ A +KGL +VV+ + LRN LIP+VT GL Sbjct: 196 SLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLRNTLIPLVTVVGLEFG 255 Query: 110 VLLGGLVITESIFAIPGMGKMIVDAIFQRDYVMVQGGVLAAALMVVIVNLAVDVLYTVID 169 + V+TESIFA PG GK+I+D+I D ++ ++ M V +NL VDVLY ++D Sbjct: 256 STIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDVLYKLLD 315 Query: 170 PRIE 173 PR+ Sbjct: 316 PRVR 319 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 103 bits (258), Expect = 5e-24, Method: Compositional matrix adjust. Identities = 60/173 (34%), Positives = 96/173 (55%) Query: 2 SVPHFWLGMMFIILFAVKLGWLPASGYVPFTEDWRGNLAAMCMPVLATGLRESAILMRMV 61 SVP F + + +++FAVKL WL A + + A MPVL A + RM Sbjct: 145 SVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLGAFIKAYAMPVLTLCCVIVAQMTRMT 204 Query: 62 RSSLLEVLNEDYIRTAFSKGLRDWQVVIGHALRNALIPVVTASGLMVSVLLGGLVITESI 121 R+++++ L Y A KG++ ++V+ HAL NA+ P+ A L +S LLGG++I ESI Sbjct: 205 RAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPNAIGPIANAVALSLSYLLGGVIIVESI 264 Query: 122 FAIPGMGKMIVDAIFQRDYVMVQGGVLAAALMVVIVNLAVDVLYTVIDPRIEK 174 F PG+ +++DA+ RD +VQ + +++ L DVL V +PR++ Sbjct: 265 FNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYLLLVLTADVLAIVSNPRLKT 317 >gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 356 Score = 93.6 bits (231), Expect = 9e-21, Method: Compositional matrix adjust. Identities = 59/185 (31%), Positives = 102/185 (55%), Gaps = 16/185 (8%) Query: 2 SVPHFWLGMMFIILFA--VKLGWLPASGYVPFTEDWRG---------NLAAMCMPVLATG 50 S+P F LG+ ++LFA + W P G +++W L + +PV A+ Sbjct: 169 SIPGFVLGVFLLVLFAGGSFVQWFPLRGLT--SDNWESLSLMGKITDYLWHITLPVTASV 226 Query: 51 LRESAILMRMVRSSLLEVLNEDYIRTAFSKGLRDWQVVIGHALRNALIPVVTA--SGLMV 108 + A++ + R++ LE + + Y+ TA +KGL + +V+ H RNALIP+VT S + Sbjct: 227 IGSFAVITMLTRNTFLEEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIA 286 Query: 109 SVLLGGLVITESIFAIPGMGKMIVDAIFQRDYVMVQGGVLAAALMVVIVNLAVDVLYTVI 168 S G L+I E++F++ GMG + ++ +RDY +V G + L+ ++V L D+ Y Sbjct: 287 SFFAGSLLI-ETLFSLDGMGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWA 345 Query: 169 DPRIE 173 DPR++ Sbjct: 346 DPRVQ 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 0.142 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: 472,628 Number of extensions: 15557 Number of successful extensions: 101 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 95 Number of HSP's successfully gapped: 6 Length of query: 174 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 95 Effective length of database: 1,245,805 Effective search space: 118351475 Effective search space used: 118351475 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: 127 (53.5 bits)