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= 0001.3140.p (305 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... 597 e-172 gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 236 2e-63 gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 196 2e-51 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 167 8e-43 gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herba... 149 3e-37 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 597 bits (1538), Expect = e-172, Method: Compositional matrix adjust. Identities = 297/305 (97%), Positives = 302/305 (99%) Query: 1 MLIYILRRLAIALCVALTVSIVSFTLLHMSGDLAVSIAGPEATAAQVESVRTQFGLDRPM 60 MLIYILRRLAIALCVA+TVS+VSFTLLHMSGDLAVSIAGPEATAAQVESVRTQFGLDRPM Sbjct: 1 MLIYILRRLAIALCVAVTVSVVSFTLLHMSGDLAVSIAGPEATAAQVESVRTQFGLDRPM 60 Query: 61 ATQYMDWLGRAVRLDFGNSFYFQGPVMEMITERLPITFKLGGSALLLAILTAIPLGVLAA 120 ATQY+DWLGRAV+LDFG SFYFQGPVMEMI ERLPITFKLGGSALLLA+LTAIPLGVLAA Sbjct: 61 ATQYLDWLGRAVQLDFGKSFYFQGPVMEMIAERLPITFKLGGSALLLAVLTAIPLGVLAA 120 Query: 121 IYRDTWLDRIALLIAVVGQAMPSFWFGLTLILIFAVTLHWLPVAGNESWQHFILPAVALG 180 IYRDTWLDR ALLIAVVGQAMPSFWFGLTLILIFAVTLHWLPVAGNESWQHFILPAVALG Sbjct: 121 IYRDTWLDRAALLIAVVGQAMPSFWFGLTLILIFAVTLHWLPVAGNESWQHFILPAVALG 180 Query: 181 YYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVIPVVALAAVELGF 240 YYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVIPVVALAAVELGF Sbjct: 181 YYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVIPVVALAAVELGF 240 Query: 241 MLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVINALLDP 300 MLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVINALLDP Sbjct: 241 MLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVINALLDP 300 Query: 301 RIRTR 305 RIRTR Sbjct: 301 RIRTR 305 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 236 bits (602), Expect = 2e-63, Method: Compositional matrix adjust. Identities = 121/306 (39%), Positives = 198/306 (64%), Gaps = 1/306 (0%) Query: 1 MLIYILRRLAIALCVALTVSIVSFTLLHM-SGDLAVSIAGPEATAAQVESVRTQFGLDRP 59 M ++++RL + L V+++ F +H+ GD A AGPEA V VR GLD+P Sbjct: 1 MFSFVIKRLLGLIPTLLLVAVLVFLFVHLLPGDPARLAAGPEADDKTVALVRADLGLDKP 60 Query: 60 MATQYMDWLGRAVRLDFGNSFYFQGPVMEMITERLPITFKLGGSALLLAILTAIPLGVLA 119 + Q++++ A R DFG+S + PV E I+ R T L A++ A+L + +G+ + Sbjct: 61 LPEQFVNFFLNAARGDFGHSIRTKRPVSEEISARFWPTLWLTVVAMVWAVLFGLIIGISS 120 Query: 120 AIYRDTWLDRIALLIAVVGQAMPSFWFGLTLILIFAVTLHWLPVAGNESWQHFILPAVAL 179 A++R+ W DR+ + +AV G + P+F G+ L+ +F+V L WLP G+++W H+ILP++ L Sbjct: 121 AVWRNQWPDRLGMTLAVSGISFPAFSLGILLVQVFSVKLGWLPTVGDDTWLHYILPSITL 180 Query: 180 GYYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVIPVVALAAVELG 239 G M R TRS +E+L D++RTARAKGL+++ VV KH LRNA+IPVV + ++ G Sbjct: 181 GAAVAAVMARFTRSSFIEILQEDFVRTARAKGLTETVVVIKHCLRNALIPVVTMMGLQFG 240 Query: 240 FMLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVINALLD 299 F+LGGS+++E V++ G+G+L DA+ DYPV+QA +L+ ++ +I + + DV+ A+++ Sbjct: 241 FLLGGSILVEVVFNWPGMGRLLVDAVEMRDYPVIQAEILLFSLEFIFINLVVDVLYAVIN 300 Query: 300 PRIRTR 305 P IR + Sbjct: 301 PSIRFK 306 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 196 bits (497), Expect = 2e-51, Method: Compositional matrix adjust. Identities = 113/317 (35%), Positives = 185/317 (58%), Gaps = 16/317 (5%) Query: 5 ILRRLAIALCVALTVSIVSFTLLHMSGDLAVSIAGPEATAAQVESVRTQFGLDRPMATQY 64 I R + AL V L ++++ F LHM G+ + G + + + GLD+P+ QY Sbjct: 5 IARSVVQALMVVLLMTVIVFFGLHMIGNPVDILIGQDVDQVDRLRIIQELGLDQPVWRQY 64 Query: 65 MDWLGRAVRLDFGNSFYFQGPVMEMITERLPITFKLGGSALLLAILTAIPLGVLAAIYRD 124 + +L A+ + GNSF + P + +I +RLP T +L +ALLLA++ +PLG+ A + D Sbjct: 65 LAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVPLGLFAGMKPD 124 Query: 125 TWLDRIALLIAVVGQAMPSFWFGLTLILIFAVTLHWLPVAGN----------------ES 168 R+ + ++ G ++P+FW GL LI+ F+VTL WLP G + Sbjct: 125 HPFSRLVMTTSIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWLTADG 184 Query: 169 WQHFILPAVALGYYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVI 228 W+H ILPA+ L + + ++RLTR+ + EVL D+++ ARAKGLS +RVV + LRN +I Sbjct: 185 WRHMILPAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLRNTLI 244 Query: 229 PVVALAAVELGFMLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLT 288 P+V + +E G + +VV ES+++ G G+L D+I+ D PV+ A +++I ++ + Sbjct: 245 PLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMFVTIN 304 Query: 289 FLADVINALLDPRIRTR 305 + DV+ LLDPR+R Sbjct: 305 LVVDVLYKLLDPRVRVE 321 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 167 bits (424), Expect = 8e-43, Method: Compositional matrix adjust. Identities = 95/285 (33%), Positives = 158/285 (55%), Gaps = 8/285 (2%) Query: 29 MSGDLAVSIAGPEATAAQVESVRTQFGLDRPMATQYMDWLGRAVRLDFGNSFYFQGPVME 88 + GD A + G AT V ++R Q+GLD P +Y WLG + + G S PV + Sbjct: 34 LPGDAAQTALGQAATPETVAALRLQYGLDLPAPLRYAHWLGNLLSGNPGMSLVNNVPVAQ 93 Query: 89 MITERLPITFKLGGSALLLAILTAIPLGVLAAIYRDTWLDRIALLIAVVGQAMPSFWFGL 148 MI RLP + L L+++ A+ LG+ +A+YR ++ DR + AV ++P F Sbjct: 94 MIGGRLPASLMLAAVTALVSVPLALFLGIFSAMYRGSFFDRAVNVSAVSMVSVPEFLVAT 153 Query: 149 TLILIFAVTLHWLPV---AGNESW-----QHFILPAVALGYYAMPAMMRLTRSGMLEVLG 200 ++IFAV L WL AG+ + + + +P + L + M R+TR+ +++ L Sbjct: 154 VAVMIFAVKLRWLSALSHAGDAATLGAFIKAYAMPVLTLCCVIVAQMTRMTRAAVIDQLR 213 Query: 201 SDYIRTARAKGLSKSRVVFKHALRNAVIPVVALAAVELGFMLGGSVVIESVYSMQGLGQL 260 S Y A KG+ ++R+V +HAL NA+ P+ A+ L ++LGG +++ES+++ G+ L Sbjct: 214 SSYAEMALLKGVKRTRIVLRHALPNAIGPIANAVALSLSYLLGGVIIVESIFNYPGIATL 273 Query: 261 AWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVINALLDPRIRTR 305 DA++ D P+VQA +I Y+ L ADV+ + +PR++TR Sbjct: 274 MIDAVTTRDMPLVQACSMIFCAGYLLLVLTADVLAIVSNPRLKTR 318 >gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 356 Score = 149 bits (375), Expect = 3e-37, Method: Compositional matrix adjust. Identities = 85/278 (30%), Positives = 151/278 (54%), Gaps = 22/278 (7%) Query: 46 QVESVRTQFGLDRPMATQYMDWLGRAVRLDFGNSFYFQGPVMEMITERLPITFKLGGSAL 105 ++ ++ +G D+P ++ L + D G SFY G V ++ +LP++ +G Sbjct: 75 RIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVKSKLPVSISIGLWTF 134 Query: 106 LLAILTAIPLGVLAAIYRDTWLDRIALLIAVVGQAMPSFWFGLTLILIFA--VTLHWLPV 163 LL+ L ++PLG+ A+ T D + +VG ++P F G+ L+++FA + W P+ Sbjct: 135 LLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLLVLFAGGSFVQWFPL 194 Query: 164 AG--NESWQ-------------HFILPAVA--LGYYAMPAMMRLTRSGMLEVLGSDYIRT 206 G +++W+ H LP A +G +A+ M LTR+ LE + Y+ T Sbjct: 195 RGLTSDNWESLSLMGKITDYLWHITLPVTASVIGSFAVITM--LTRNTFLEEIRKQYVLT 252 Query: 207 ARAKGLSKSRVVFKHALRNAVIPVV-ALAAVELGFMLGGSVVIESVYSMQGLGQLAWDAI 265 ARAKGLS+ RV++KH RNA+IP+V + + GS++IE+++S+ G+G LA+++ Sbjct: 253 ARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFSLDGMGLLAYESA 312 Query: 266 SRNDYPVVQAVVLIIAMFYIGLTFLADVINALLDPRIR 303 R DYPVV + + + + + + D+ DPR++ Sbjct: 313 IRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQ 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 0.141 0.421 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: 836,940 Number of extensions: 32275 Number of successful extensions: 181 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 177 Number of HSP's successfully gapped: 6 Length of query: 305 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 220 Effective length of database: 1,217,395 Effective search space: 267826900 Effective search space used: 267826900 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)