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= 0020.0029.p (306 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... 486 e-138 gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel A... 240 1e-64 gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 193 2e-50 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 189 2e-49 gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herba... 142 3e-35 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 486 bits (1251), Expect = e-138, Method: Compositional matrix adjust. Identities = 250/306 (81%), Positives = 287/306 (93%) Query: 1 MFSYVLKRLLGLIPTLLLVAVMVFLFVHLLPGDPARLAAGPEADEQTVALIRADLGLDQP 60 MFS+V+KRLLGLIPTLLLVAV+VFLFVHLLPGDPARLAAGPEAD++TVAL+RADLGLD+P Sbjct: 1 MFSFVIKRLLGLIPTLLLVAVLVFLFVHLLPGDPARLAAGPEADDKTVALVRADLGLDKP 60 Query: 61 IHKQFVRFFVNAAHGDFGTSLRSKLPVSQEIMERFWPTLWLTVTSMIWAVIFGLFIGVFS 120 + +QFV FF+NAA GDFG S+R+K PVS+EI RFWPTLWLTV +M+WAV+FGL IG+ S Sbjct: 61 LPEQFVNFFLNAARGDFGHSIRTKRPVSEEISARFWPTLWLTVVAMVWAVLFGLIIGISS 120 Query: 121 AVWRNEWPDRAGMTLAVSGISFPPFALGMVLMEVFSVQLGWLPTVGADSWRHYVLPSLTL 180 AVWRN+WPDR GMTLAVSGISFP F+LG++L++VFSV+LGWLPTVG D+W HY+LPS+TL Sbjct: 121 AVWRNQWPDRLGMTLAVSGISFPAFSLGILLVQVFSVKLGWLPTVGDDTWLHYILPSITL 180 Query: 181 GAGVAAIMARFTRSSFIEIMKEDFVRTARAKGLNERIVIAKHCLRNALIPVVTMMGLQFG 240 GA VAA+MARFTRSSFIEI++EDFVRTARAKGL E +V+ KHCLRNALIPVVTMMGLQFG Sbjct: 181 GAAVAAVMARFTRSSFIEILQEDFVRTARAKGLTETVVVIKHCLRNALIPVVTMMGLQFG 240 Query: 241 FLLGGSIVVEKVFNWPGMGRLLIDAVEMRDYPIIQAEILLFSLEFIFINLIVDVLYAVIN 300 FLLGGSI+VE VFNWPGMGRLL+DAVEMRDYP+IQAEILLFSLEFIFINL+VDVLYAVIN Sbjct: 241 FLLGGSILVEVVFNWPGMGRLLVDAVEMRDYPVIQAEILLFSLEFIFINLVVDVLYAVIN 300 Query: 301 PSIRYK 306 PSIR+K Sbjct: 301 PSIRFK 306 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 240 bits (612), Expect = 1e-64, Method: Compositional matrix adjust. Identities = 120/306 (39%), Positives = 194/306 (63%), Gaps = 1/306 (0%) Query: 1 MFSYVLKRLLGLIPTLLLVAVMVFLFVHLLPGDPARLAAGPEADEQTVALIRADLGLDQP 60 M Y+L+RL + + V+V+ F +H+ GD A AGPEA V +R GLD+P Sbjct: 1 MLIYILRRLAIALCVAVTVSVVSFTLLHM-SGDLAVSIAGPEATAAQVESVRTQFGLDRP 59 Query: 61 IHKQFVRFFVNAAHGDFGTSLRSKLPVSQEIMERFWPTLWLTVTSMIWAVIFGLFIGVFS 120 + Q++ + A DFG S + PV + I ER T L ++++ AV+ + +GV + Sbjct: 60 MATQYLDWLGRAVQLDFGKSFYFQGPVMEMIAERLPITFKLGGSALLLAVLTAIPLGVLA 119 Query: 121 AVWRNEWPDRAGMTLAVSGISFPPFALGMVLMEVFSVQLGWLPTVGADSWRHYVLPSLTL 180 A++R+ W DRA + +AV G + P F G+ L+ +F+V L WLP G +SW+H++LP++ L Sbjct: 120 AIYRDTWLDRAALLIAVVGQAMPSFWFGLTLILIFAVTLHWLPVAGNESWQHFILPAVAL 179 Query: 181 GAGVAAIMARFTRSSFIEIMKEDFVRTARAKGLNERIVIAKHCLRNALIPVVTMMGLQFG 240 G M R TRS +E++ D++RTARAKGL++ V+ KH LRNA+IPVV + ++ G Sbjct: 180 GYYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVIPVVALAAVELG 239 Query: 241 FLLGGSIVVEKVFNWPGMGRLLIDAVEMRDYPIIQAEILLFSLEFIFINLIVDVLYAVIN 300 F+LGGS+V+E V++ G+G+L DA+ DYP++QA +L+ ++ +I + + DV+ A+++ Sbjct: 240 FMLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVINALLD 299 Query: 301 PSIRYK 306 P IR + Sbjct: 300 PRIRTR 305 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 193 bits (490), Expect = 2e-50, Method: Compositional matrix adjust. Identities = 110/307 (35%), Positives = 183/307 (59%), Gaps = 17/307 (5%) Query: 16 LLLVAVMVFLFVHLLPGDPARLAAGPEADEQTVALIRADLGLDQPIHKQFVRFFVNAAHG 75 +LL+ V+VF +H++ G+P + G + D+ I +LGLDQP+ +Q++ F A HG Sbjct: 16 VLLMTVIVFFGLHMI-GNPVDILIGQDVDQVDRLRIIQELGLDQPVWRQYLAFLNGALHG 74 Query: 76 DFGTSLRSKLPVSQEIMERFWPTLWLTVTSMIWAVIFGLFIGVFSAVWRNEWPDRAGMTL 135 + G S P I +R TL L +++ A++ G+ +G+F+ + + R MT Sbjct: 75 NLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVPLGLFAGMKPDHPFSRLVMTT 134 Query: 136 AVSGISFPPFALGMVLMEVFSVQLGWLPTVG----------------ADSWRHYVLPSLT 179 ++ G S P F +G++L+ FSV LGWLP+ G AD WRH +LP++ Sbjct: 135 SIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWLTADGWRHMILPAIN 194 Query: 180 LGAGVAAIMARFTRSSFIEIMKEDFVRTARAKGLNERIVIAKHCLRNALIPVVTMMGLQF 239 L +++ R TR++ E++ DFV+ ARAKGL+ V+ + LRN LIP+VT++GL+F Sbjct: 195 LSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLRNTLIPLVTVVGLEF 254 Query: 240 GFLLGGSIVVEKVFNWPGMGRLLIDAVEMRDYPIIQAEILLFSLEFIFINLIVDVLYAVI 299 G + ++V E +F WPG G+L++D++ D P+I A +++ F+ INL+VDVLY ++ Sbjct: 255 GSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDVLYKLL 314 Query: 300 NPSIRYK 306 +P +R + Sbjct: 315 DPRVRVE 321 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 189 bits (481), Expect = 2e-49, Method: Compositional matrix adjust. Identities = 107/297 (36%), Positives = 167/297 (56%), Gaps = 10/297 (3%) Query: 19 VAVMVFLFVHLLPGDPARLAAGPEADEQTVALIRADLGLDQPIHKQFVRFFVNAAHGDFG 78 V+ VF +LLPGD A+ A G A +TVA +R GLD P ++ + N G+ G Sbjct: 23 VSAGVFFITNLLPGDAAQTALGQAATPETVAALRLQYGLDLPAPLRYAHWLGNLLSGNPG 82 Query: 79 TSLRSKLPVSQEIMERFWPTLWLTVTSMIWAVIFGLFIGVFSAVWRNEWPDRAGMTLAVS 138 SL + +PV+Q I R +L L + + +V LF+G+FSA++R + DRA AVS Sbjct: 83 MSLVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALFLGIFSAMYRGSFFDRAVNVSAVS 142 Query: 139 GISFPPFALGMVLMEVFSVQLGWLP---------TVGADSWRHYVLPSLTLGAGVAAIMA 189 +S P F + V + +F+V+L WL T+GA + Y +P LTL + A M Sbjct: 143 MVSVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLGA-FIKAYAMPVLTLCCVIVAQMT 201 Query: 190 RFTRSSFIEIMKEDFVRTARAKGLNERIVIAKHCLRNALIPVVTMMGLQFGFLLGGSIVV 249 R TR++ I+ ++ + A KG+ ++ +H L NA+ P+ + L +LLGG I+V Sbjct: 202 RMTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPNAIGPIANAVALSLSYLLGGVIIV 261 Query: 250 EKVFNWPGMGRLLIDAVEMRDYPIIQAEILLFSLEFIFINLIVDVLYAVINPSIRYK 306 E +FN+PG+ L+IDAV RD P++QA ++F ++ + L DVL V NP ++ + Sbjct: 262 ESIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYLLLVLTADVLAIVSNPRLKTR 318 >gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 356 Score = 142 bits (359), Expect = 3e-35, Method: Compositional matrix adjust. Identities = 113/362 (31%), Positives = 176/362 (48%), Gaps = 68/362 (18%) Query: 1 MFSYVLKRLLGLIPTLLLVAVMVFLFVHLLPGDPARLAA--------------------- 39 ++SY++KR+L +IPTL V + F + +PG P A Sbjct: 3 IWSYIVKRVLLMIPTLFGVVAITFAVIQFVPGGPVEQAMLEMKGRGGGGEASGGGAASGA 62 Query: 40 ----GPEA-DEQTVALIRADLGLDQP-------IHKQFVRFFVNAA---HGDFGTSLRSK 84 G + DEQ +A I+ G D+P + K F+ F + + HGD T ++SK Sbjct: 63 SAYRGRQGIDEQRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVKSK 122 Query: 85 LPVSQEIMERFWPTLWLTVTSMIWAVIFGLFIGVFSAVWRNEWPDRAGMTLAVSGISFPP 144 LPVS I LW + S + +V +G+ AV D A L + G S P Sbjct: 123 LPVSISI------GLWTFLLSYLISVP----LGIAKAVREGTRFDTATTGLVLVGYSIPG 172 Query: 145 FALGMVLMEVFS----VQLGWLPTVG--ADSWR-------------HYVLPSLTLGAGVA 185 F LG+ L+ +F+ VQ W P G +D+W H LP G Sbjct: 173 FVLGVFLLVLFAGGSFVQ--WFPLRGLTSDNWESLSLMGKITDYLWHITLPVTASVIGSF 230 Query: 186 AIMARFTRSSFIEIMKEDFVRTARAKGLNERIVIAKHCLRNALIPVVTMMGLQF-GFLLG 244 A++ TR++F+E +++ +V TARAKGL+ER V+ KH RNALIP+VT F Sbjct: 231 AVITMLTRNTFLEEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFA 290 Query: 245 GSIVVEKVFNWPGMGRLLIDAVEMRDYPIIQAEILLFSLEFIFINLIVDVLYAVINPSIR 304 GS+++E +F+ GMG L ++ RDYP++ + LF+L + + L+ D+ Y +P ++ Sbjct: 291 GSLLIETLFSLDGMGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQ 350 Query: 305 YK 306 ++ Sbjct: 351 FE 352 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 0.330 0.144 0.446 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: 889,607 Number of extensions: 35369 Number of successful extensions: 167 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 158 Number of HSP's successfully gapped: 6 Length of query: 306 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 221 Effective length of database: 1,217,395 Effective search space: 269044295 Effective search space used: 269044295 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)