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= 0095.0004.p (207 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herba... 350 5e-98 gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 109 2e-25 gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel A... 104 5e-24 gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 77 8e-16 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 62 4e-11 >gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 356 Score = 350 bits (898), Expect = 5e-98, Method: Compositional matrix adjust. Identities = 172/194 (88%), Positives = 184/194 (94%) Query: 14 LVLVGYSIPGFVLGVFLLVVFGGGSFVQWFPLRGLTSDDWATLSLLGKVKDYLWHITLPV 73 LVLVGYSIPGFVLGVFLLV+F GGSFVQWFPLRGLTSD+W +LSL+GK+ DYLWHITLPV Sbjct: 163 LVLVGYSIPGFVLGVFLLVLFAGGSFVQWFPLRGLTSDNWESLSLMGKITDYLWHITLPV 222 Query: 74 IASVAGSFAVMTMLTKNTFLEEIRKQYVLTARAKGLSENTVLYKHVFRNALIPLVTGFPA 133 ASV GSFAV+TMLT+NTFLEEIRKQYVLTARAKGLSE VLYKHVFRNALIPLVTGFP+ Sbjct: 223 TASVIGSFAVITMLTRNTFLEEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPS 282 Query: 134 AFIGAFFTGSLLIETLFSLDGLGLLSYESVIRRDYPVVMGTLYLFTLIGLVVKLLGDLCY 193 AFI +FF GSLLIETLFSLDG+GLL+YES IRRDYPVVMGTLYLFTLIGLVVKL+GDLCY Sbjct: 283 AFIASFFAGSLLIETLFSLDGMGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCY 342 Query: 194 VWADPRVQFESLAK 207 VWADPRVQFESLAK Sbjct: 343 VWADPRVQFESLAK 356 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 109 bits (272), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 70/190 (36%), Positives = 103/190 (54%), Gaps = 18/190 (9%) Query: 14 LVLVGYSIPGFVLGVFLLVVFGGGSFVQWFPLRGLTSDDWATLSLLGKVKDYLWHITLPV 73 L + G S P F LG+ L+ VF + W P G D W H LP Sbjct: 135 LAVSGISFPAFSLGILLVQVFSVK--LGWLPTVG--DDTWL-------------HYILPS 177 Query: 74 IASVAGSFAVMTMLTKNTFLEEIRKQYVLTARAKGLSENTVLYKHVFRNALIPLVTGFPA 133 I A AVM T+++F+E +++ +V TARAKGL+E V+ KH RNALIP+VT Sbjct: 178 ITLGAAVAAVMARFTRSSFIEILQEDFVRTARAKGLTETVVVIKHCLRNALIPVVTMMGL 237 Query: 134 AFIGAFFTGSLLIETLFSLDGLGLLSYESVIRRDYPVVMGTLYLFTLIGLVVKLLGDLCY 193 F G GS+L+E +F+ G+G L ++V RDYPV+ + LF+L + + L+ D+ Y Sbjct: 238 QF-GFLLGGSILVEVVFNWPGMGRLLVDAVEMRDYPVIQAEILLFSLEFIFINLVVDVLY 296 Query: 194 VWADPRVQFE 203 +P ++F+ Sbjct: 297 AVINPSIRFK 306 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 104 bits (260), Expect = 5e-24, Method: Compositional matrix adjust. Identities = 60/188 (31%), Positives = 104/188 (55%), Gaps = 18/188 (9%) Query: 14 LVLVGYSIPGFVLGVFLLVVFGGGSFVQWFPLRGLTSDDWATLSLLGKVKDYLWHITLPV 73 + +VG ++P F G+ L+++F + W P+ G ++ W H LP Sbjct: 134 IAVVGQAMPSFWFGLTLILIFA--VTLHWLPVAG--NESWQ-------------HFILPA 176 Query: 74 IASVAGSFAVMTMLTKNTFLEEIRKQYVLTARAKGLSENTVLYKHVFRNALIPLVTGFPA 133 +A + M LT++ LE + Y+ TARAKGLS++ V++KH RNA+IP+V A Sbjct: 177 VALGYYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVIPVV-ALAA 235 Query: 134 AFIGAFFTGSLLIETLFSLDGLGLLSYESVIRRDYPVVMGTLYLFTLIGLVVKLLGDLCY 193 +G GS++IE+++S+ GLG L+++++ R DYPVV + + + + + L D+ Sbjct: 236 VELGFMLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVIN 295 Query: 194 VWADPRVQ 201 DPR++ Sbjct: 296 ALLDPRIR 303 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 77.4 bits (189), Expect = 8e-16, Method: Compositional matrix adjust. Identities = 60/193 (31%), Positives = 99/193 (51%), Gaps = 14/193 (7%) Query: 18 GYSIPGFVLGVFLLVVFGGGSFVQWFPL--RGLTSD----DWATLSLLGKVKDYLWHITL 71 G+S+P F +G+ L++ F + W P RG T++ W+ L+ D H+ L Sbjct: 138 GFSLPTFWIGLMLIMAFS--VTLGWLPSGGRGQTAELFGVQWSWLT-----ADGWRHMIL 190 Query: 72 PVIASVAGSFAVMTMLTKNTFLEEIRKQYVLTARAKGLSENTVLYKHVFRNALIPLVTGF 131 P I +++ LT+ E + +V ARAKGLS V+ +V RN LIPLVT Sbjct: 191 PAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLRNTLIPLVTVV 250 Query: 132 PAAFIGAFFTGSLLIETLFSLDGLGLLSYESVIRRDYPVVMGTLYLFTLIGLVVKLLGDL 191 F G+ +++ E++F+ G G L +S+ D PV++ L + + + + L+ D+ Sbjct: 251 GLEF-GSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDV 309 Query: 192 CYVWADPRVQFES 204 Y DPRV+ E+ Sbjct: 310 LYKLLDPRVRVEA 322 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 61.6 bits (148), Expect = 4e-11, Method: Compositional matrix adjust. Identities = 45/183 (24%), Positives = 90/183 (49%), Gaps = 12/183 (6%) Query: 20 SIPGFVLGVFLLVVFGGGSFVQWFPLRGLT-SDDWATLSLLGKVKDYLWHITLPVIASVA 78 S+P F++ +++F ++W L L+ + D ATL +K Y +PV+ Sbjct: 145 SVPEFLVATVAVMIFAVK--LRW--LSALSHAGDAATLGAF--IKAY----AMPVLTLCC 194 Query: 79 GSFAVMTMLTKNTFLEEIRKQYVLTARAKGLSENTVLYKHVFRNALIPLVTGFPAAFIGA 138 A MT +T+ ++++R Y A KG+ ++ +H NA+ P+ A + Sbjct: 195 VIVAQMTRMTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPNAIGPIANAV-ALSLSY 253 Query: 139 FFTGSLLIETLFSLDGLGLLSYESVIRRDYPVVMGTLYLFTLIGLVVKLLGDLCYVWADP 198 G +++E++F+ G+ L ++V RD P+V +F L++ L D+ + ++P Sbjct: 254 LLGGVIIVESIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYLLLVLTADVLAIVSNP 313 Query: 199 RVQ 201 R++ Sbjct: 314 RLK 316 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 0.145 0.448 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: 579,289 Number of extensions: 21150 Number of successful extensions: 91 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 86 Number of HSP's successfully gapped: 6 Length of query: 207 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 126 Effective length of database: 1,236,335 Effective search space: 155778210 Effective search space used: 155778210 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: 128 (53.9 bits)