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= 0006.0002.p (154 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... 295 1e-81 gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 152 2e-38 gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 120 4e-29 gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herba... 99 2e-22 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 98 3e-22 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 295 bits (754), Expect = 1e-81, Method: Compositional matrix adjust. Identities = 140/154 (90%), Positives = 151/154 (98%) Query: 1 MVLSVTLHWFPVSGNENWEHFVLPAIALGYYAMPAMMRLTRAGMLEVLGSDYIRTARAKG 60 ++ +VTLHW PV+GNE+W+HF+LPA+ALGYYAMPAMMRLTR+GMLEVLGSDYIRTARAKG Sbjct: 152 LIFAVTLHWLPVAGNESWQHFILPAVALGYYAMPAMMRLTRSGMLEVLGSDYIRTARAKG 211 Query: 61 LSKGKVIFKHALRNAVIPVVALAAVELGFMLGGSVVIESVYSMQGLGQLAWDAISRNDYP 120 LSK +V+FKHALRNAVIPVVALAAVELGFMLGGSVVIESVYSMQGLGQLAWDAISRNDYP Sbjct: 212 LSKSRVVFKHALRNAVIPVVALAAVELGFMLGGSVVIESVYSMQGLGQLAWDAISRNDYP 271 Query: 121 VVQAVVLIIAMFYIGLTFLADVINALLDPRIRTR 154 VVQAVVLIIAMFYIGLTFLADVINALLDPRIRTR Sbjct: 272 VVQAVVLIIAMFYIGLTFLADVINALLDPRIRTR 305 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 152 bits (383), Expect = 2e-38, Method: Compositional matrix adjust. Identities = 67/153 (43%), Positives = 106/153 (69%) Query: 2 VLSVTLHWFPVSGNENWEHFVLPAIALGYYAMPAMMRLTRAGMLEVLGSDYIRTARAKGL 61 V SV L W P G++ W H++LP+I LG M R TR+ +E+L D++RTARAKGL Sbjct: 154 VFSVKLGWLPTVGDDTWLHYILPSITLGAAVAAVMARFTRSSFIEILQEDFVRTARAKGL 213 Query: 62 SKGKVIFKHALRNAVIPVVALAAVELGFMLGGSVVIESVYSMQGLGQLAWDAISRNDYPV 121 ++ V+ KH LRNA+IPVV + ++ GF+LGGS+++E V++ G+G+L DA+ DYPV Sbjct: 214 TETVVVIKHCLRNALIPVVTMMGLQFGFLLGGSILVEVVFNWPGMGRLLVDAVEMRDYPV 273 Query: 122 VQAVVLIIAMFYIGLTFLADVINALLDPRIRTR 154 +QA +L+ ++ +I + + DV+ A+++P IR + Sbjct: 274 IQAEILLFSLEFIFINLVVDVLYAVINPSIRFK 306 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 120 bits (302), Expect = 4e-29, Method: Compositional matrix adjust. Identities = 62/170 (36%), Positives = 97/170 (57%), Gaps = 16/170 (9%) Query: 1 MVLSVTLHWFPVSGN----------------ENWEHFVLPAIALGYYAMPAMMRLTRAGM 44 M SVTL W P G + W H +LPAI L + + ++RLTRA + Sbjct: 152 MAFSVTLGWLPSGGRGQTAELFGVQWSWLTADGWRHMILPAINLSLFKISLVIRLTRANV 211 Query: 45 LEVLGSDYIRTARAKGLSKGKVIFKHALRNAVIPVVALAAVELGFMLGGSVVIESVYSMQ 104 EVL D+++ ARAKGLS +V+ + LRN +IP+V + +E G + +VV ES+++ Sbjct: 212 REVLPMDFVKFARAKGLSPARVVLMYVLRNTLIPLVTVVGLEFGSTIAFAVVTESIFAWP 271 Query: 105 GLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVINALLDPRIRTR 154 G G+L D+I+ D PV+ A +++I ++ + + DV+ LLDPR+R Sbjct: 272 GAGKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDVLYKLLDPRVRVE 321 >gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 356 Score = 98.6 bits (244), Expect = 2e-22, Method: Compositional matrix adjust. Identities = 56/164 (34%), Positives = 92/164 (56%), Gaps = 20/164 (12%) Query: 7 LHWFPVSG--NENWE-------------HFVLPAIA--LGYYAMPAMMRLTRAGMLEVLG 49 + WFP+ G ++NWE H LP A +G +A+ M LTR LE + Sbjct: 189 VQWFPLRGLTSDNWESLSLMGKITDYLWHITLPVTASVIGSFAVITM--LTRNTFLEEIR 246 Query: 50 SDYIRTARAKGLSKGKVIFKHALRNAVIPVV-ALAAVELGFMLGGSVVIESVYSMQGLGQ 108 Y+ TARAKGLS+ +V++KH RNA+IP+V + + GS++IE+++S+ G+G Sbjct: 247 KQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFSLDGMGL 306 Query: 109 LAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVINALLDPRIR 152 LA+++ R DYPVV + + + + + + D+ DPR++ Sbjct: 307 LAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQ 350 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 98.2 bits (243), Expect = 3e-22, Method: Compositional matrix adjust. Identities = 49/162 (30%), Positives = 89/162 (54%), Gaps = 8/162 (4%) Query: 1 MVLSVTLHWFPVSGNEN--------WEHFVLPAIALGYYAMPAMMRLTRAGMLEVLGSDY 52 M+ +V L W + + + +P + L + M R+TRA +++ L S Y Sbjct: 157 MIFAVKLRWLSALSHAGDAATLGAFIKAYAMPVLTLCCVIVAQMTRMTRAAVIDQLRSSY 216 Query: 53 IRTARAKGLSKGKVIFKHALRNAVIPVVALAAVELGFMLGGSVVIESVYSMQGLGQLAWD 112 A KG+ + +++ +HAL NA+ P+ A+ L ++LGG +++ES+++ G+ L D Sbjct: 217 AEMALLKGVKRTRIVLRHALPNAIGPIANAVALSLSYLLGGVIIVESIFNYPGIATLMID 276 Query: 113 AISRNDYPVVQAVVLIIAMFYIGLTFLADVINALLDPRIRTR 154 A++ D P+VQA +I Y+ L ADV+ + +PR++TR Sbjct: 277 AVTTRDMPLVQACSMIFCAGYLLLVLTADVLAIVSNPRLKTR 318 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 0.327 0.140 0.418 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: 476,664 Number of extensions: 18444 Number of successful extensions: 106 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 105 Number of HSP's successfully gapped: 6 Length of query: 154 Length of database: 1,619,870 Length adjustment: 77 Effective length of query: 77 Effective length of database: 1,255,275 Effective search space: 96656175 Effective search space used: 96656175 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: 126 (53.1 bits)