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= 0006.0008.p (360 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... 711 0.0 gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel A... 152 3e-38 gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 119 4e-28 gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 110 2e-25 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 93 3e-20 >gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 356 Score = 711 bits (1835), Expect = 0.0, Method: Compositional matrix adjust. Identities = 356/356 (100%), Positives = 356/356 (100%) Query: 5 MNIWSYIVKRVLLMIPTLFGVVAITFAVIQFVPGGPVEQAMLEMKGRGGGGEASGGGAAS 64 MNIWSYIVKRVLLMIPTLFGVVAITFAVIQFVPGGPVEQAMLEMKGRGGGGEASGGGAAS Sbjct: 1 MNIWSYIVKRVLLMIPTLFGVVAITFAVIQFVPGGPVEQAMLEMKGRGGGGEASGGGAAS 60 Query: 65 GASAYRGRQGIDEQRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVK 124 GASAYRGRQGIDEQRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVK Sbjct: 61 GASAYRGRQGIDEQRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVK 120 Query: 125 SKLPVSISIGLWTFLLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLL 184 SKLPVSISIGLWTFLLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLL Sbjct: 121 SKLPVSISIGLWTFLLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLL 180 Query: 185 VLFAGGSFVQWFPLRGLTSDNWESLSLMGKITDYLWHITLPVTASVIGSFAVITMLTRNT 244 VLFAGGSFVQWFPLRGLTSDNWESLSLMGKITDYLWHITLPVTASVIGSFAVITMLTRNT Sbjct: 181 VLFAGGSFVQWFPLRGLTSDNWESLSLMGKITDYLWHITLPVTASVIGSFAVITMLTRNT 240 Query: 245 FLEEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFS 304 FLEEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFS Sbjct: 241 FLEEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFS 300 Query: 305 LDGMGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQFESLAK 360 LDGMGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQFESLAK Sbjct: 301 LDGMGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQFESLAK 356 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 152 bits (385), Expect = 3e-38, Method: Compositional matrix adjust. Identities = 87/278 (31%), Positives = 153/278 (55%), Gaps = 22/278 (7%) Query: 79 RIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVKSKLPVSISIGLWTF 138 ++ ++ +G D+P ++ L + D GKSFY G V ++ +LP++ +G Sbjct: 46 QVESVRTQFGLDRPMATQYLDWLGRAVQLDFGKSFYFQGPVMEMIAERLPITFKLGGSAL 105 Query: 139 LLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLLVLFAGGSFVQWFPL 198 LL+ L ++PLG+ A+ T D A + +VG ++P F G+ L+++FA + W P+ Sbjct: 106 LLAVLTAIPLGVLAAIYRDTWLDRAALLIAVVGQAMPSFWFGLTLILIFA--VTLHWLPV 163 Query: 199 RGLTSDNWESLSLMGKITDYLWHITLPVTASVIGSFAVITM--LTRNTFLEEIRKQYVLT 256 G +++W+ H LP A +G +A+ M LTR+ LE + Y+ T Sbjct: 164 AG--NESWQ-------------HFILPAVA--LGYYAMPAMMRLTRSGMLEVLGSDYIRT 206 Query: 257 ARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFSLDGMGLLAYESA 316 ARAKGLS+ RV++KH RNA+IP+V + + GS++IE+++S+ G+G LA+++ Sbjct: 207 ARAKGLSKSRVVFKHALRNAVIPVV-ALAAVELGFMLGGSVVIESVYSMQGLGQLAWDAI 265 Query: 317 IRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQ 354 R DYPVV + + + + + + D+ DPR++ Sbjct: 266 SRNDYPVVQAVVLIIAMFYIGLTFLADVINALLDPRIR 303 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 119 bits (298), Expect = 4e-28, Method: Compositional matrix adjust. Identities = 91/291 (31%), Positives = 138/291 (47%), Gaps = 38/291 (13%) Query: 76 DEQRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVKSKLPVSISIG- 134 D++ +A ++ G DKP E+F D G S +++K PVS I Sbjct: 44 DDKTVALVRADLGLDKPLPEQFVNFFLNAARGDFGHS----------IRTKRPVSEEISA 93 Query: 135 -----LW----TFLLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLLV 185 LW + + L + +GI+ AV D L + G S P F LG+ L+ Sbjct: 94 RFWPTLWLTVVAMVWAVLFGLIIGISSAVWRNQWPDRLGMTLAVSGISFPAFSLGILLVQ 153 Query: 186 LFAGGSFVQWFPLRGLTSDNWESLSLMGKITDYLWHITLPVTASVIGSFAVITMLTRNTF 245 +F+ + W P G D W H LP AV+ TR++F Sbjct: 154 VFSVK--LGWLPTVG--DDTW-------------LHYILPSITLGAAVAAVMARFTRSSF 196 Query: 246 LEEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFSL 305 +E +++ +V TARAKGL+E V+ KH RNALIP+VT F GS+L+E +F+ Sbjct: 197 IEILQEDFVRTARAKGLTETVVVIKHCLRNALIPVVTMMGLQF-GFLLGGSILVEVVFNW 255 Query: 306 DGMGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQFE 356 GMG L ++ RDYPV+ + LF+L + + LV D+ Y +P ++F+ Sbjct: 256 PGMGRLLVDAVEMRDYPVIQAEILLFSLEFIFINLVVDVLYAVINPSIRFK 306 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 110 bits (275), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 87/291 (29%), Positives = 143/291 (49%), Gaps = 14/291 (4%) Query: 73 QGIDEQRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVKSKLPVSIS 132 Q +D+ I Q G D+P ++ L G L +LG SF ++ L+ +LP ++ Sbjct: 40 QDVDQVDRLRIIQELGLDQPVWRQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLE 99 Query: 133 IGLWTFLLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLLVLFAGGSF 192 + LL+ ++ VPLG+ ++ F + G+S+P F +G+ L++ F+ Sbjct: 100 LACAALLLALVVGVPLGLFAGMKPDHPFSRLVMTTSIFGFSLPTFWIGLMLIMAFS--VT 157 Query: 193 VQWFPL--RGLTSD----NWESLSLMGKITDYLWHITLPVTASVIGSFAVITMLTRNTFL 246 + W P RG T++ W L+ D H+ LP + +++ LTR Sbjct: 158 LGWLPSGGRGQTAELFGVQWSWLT-----ADGWRHMILPAINLSLFKISLVIRLTRANVR 212 Query: 247 EEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFSLD 306 E + +V ARAKGLS RV+ +V RN LIPLVT F S A +++ E++F+ Sbjct: 213 EVLPMDFVKFARAKGLSPARVVLMYVLRNTLIPLVTVVGLEF-GSTIAFAVVTESIFAWP 271 Query: 307 GMGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQFES 357 G G L +S D PV++ L + + + + LV D+ Y DPRV+ E+ Sbjct: 272 GAGKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDVLYKLLDPRVRVEA 322 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 93.2 bits (230), Expect = 3e-20, Method: Compositional matrix adjust. Identities = 67/282 (23%), Positives = 134/282 (47%), Gaps = 10/282 (3%) Query: 73 QGIDEQRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVKSKLPVSIS 132 Q + +A ++ YG D P R+ L L+ + G S ++ V ++ +LP S+ Sbjct: 45 QAATPETVAALRLQYGLDLPAPLRYAHWLGNLLSGNPGMSLVNNVPVAQMIGGRLPASLM 104 Query: 133 IGLWTFLLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLLVLFAGGSF 192 + T L+S +++ LGI A+ G+ FD A + S+P F++ +++FA Sbjct: 105 LAAVTALVSVPLALFLGIFSAMYRGSFFDRAVNVSAVSMVSVPEFLVATVAVMIFAVK-- 162 Query: 193 VQWFPLRGLTSDNWESLSLMGKITDYLWHITLPVTASVIGSFAVITMLTRNTFLEEIRKQ 252 ++W S ++ +L I Y +PV A +T +TR ++++R Sbjct: 163 LRWL---SALSHAGDAATLGAFIKAY----AMPVLTLCCVIVAQMTRMTRAAVIDQLRSS 215 Query: 253 YVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFSLDGMGLLA 312 Y A KG+ R++ +H NA+ P+ + ++ G +++E++F+ G+ L Sbjct: 216 YAEMALLKGVKRTRIVLRHALPNAIGPIANAV-ALSLSYLLGGVIIVESIFNYPGIATLM 274 Query: 313 YESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQ 354 ++ RD P+V +F L++ L D+ + ++PR++ Sbjct: 275 IDAVTTRDMPLVQACSMIFCAGYLLLVLTADVLAIVSNPRLK 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 0.326 0.143 0.436 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: 977,631 Number of extensions: 35973 Number of successful extensions: 177 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 167 Number of HSP's successfully gapped: 6 Length of query: 360 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 274 Effective length of database: 1,212,660 Effective search space: 332268840 Effective search space used: 332268840 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 (21.6 bits) S2: 131 (55.1 bits)