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= 0029.0106.p (324 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 643 0.0 gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel A... 208 4e-55 gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 185 4e-48 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 124 1e-29 gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herba... 119 5e-28 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 643 bits (1658), Expect = 0.0, Method: Compositional matrix adjust. Identities = 324/324 (100%), Positives = 324/324 (100%) Query: 1 MSGAIARSVVQALMVVLLMTVIVFFGLHMIGNPVDILIGQDVDQVDRLRIIQELGLDQPV 60 MSGAIARSVVQALMVVLLMTVIVFFGLHMIGNPVDILIGQDVDQVDRLRIIQELGLDQPV Sbjct: 1 MSGAIARSVVQALMVVLLMTVIVFFGLHMIGNPVDILIGQDVDQVDRLRIIQELGLDQPV 60 Query: 61 WRQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVPLGLFAG 120 WRQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVPLGLFAG Sbjct: 61 WRQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVPLGLFAG 120 Query: 121 MKPDHPFSRLVMTTSIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWL 180 MKPDHPFSRLVMTTSIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWL Sbjct: 121 MKPDHPFSRLVMTTSIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWL 180 Query: 181 TADGWRHMILPAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLR 240 TADGWRHMILPAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLR Sbjct: 181 TADGWRHMILPAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLR 240 Query: 241 NTLIPLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMF 300 NTLIPLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMF Sbjct: 241 NTLIPLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMF 300 Query: 301 VTINLVVDVLYKLLDPRVRVEAKP 324 VTINLVVDVLYKLLDPRVRVEAKP Sbjct: 301 VTINLVVDVLYKLLDPRVRVEAKP 324 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 208 bits (530), Expect = 4e-55, Method: Compositional matrix adjust. Identities = 113/317 (35%), Positives = 183/317 (57%), Gaps = 16/317 (5%) Query: 5 IARSVVQALMVVLLMTVIVFFGLHMIGNPVDILIGQDVDQVDRLRIIQELGLDQPVWRQY 64 I R + AL V + ++V+ F LHM G+ + G + + + GLD+P+ QY Sbjct: 5 ILRRLAIALCVAVTVSVVSFTLLHMSGDLAVSIAGPEATAAQVESVRTQFGLDRPMATQY 64 Query: 65 LAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVPLGLFAGMKPD 124 L +L A+ + G SF + P + +I +RLP T +L +ALLLA++ +PLG+ A + D Sbjct: 65 LDWLGRAVQLDFGKSFYFQGPVMEMIAERLPITFKLGGSALLLAVLTAIPLGVLAAIYRD 124 Query: 125 HPFSRLVMTTSIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWLTADG 184 R + ++ G ++P+FW GL LI+ F+VTL WLP G + Sbjct: 125 TWLDRAALLIAVVGQAMPSFWFGLTLILIFAVTLHWLPVAGN----------------ES 168 Query: 185 WRHMILPAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLRNTLI 244 W+H ILPA+ L + + ++RLTR+ + EVL D+++ ARAKGLS +RVV + LRN +I Sbjct: 169 WQHFILPAVALGYYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVI 228 Query: 245 PLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMFVTIN 304 P+V + +E G + +VV ES+++ G G+L D+I+ D PV+ A +++I ++ + Sbjct: 229 PVVALAAVELGFMLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLT 288 Query: 305 LVVDVLYKLLDPRVRVE 321 + DV+ LLDPR+R Sbjct: 289 FLADVINALLDPRIRTR 305 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 185 bits (470), Expect = 4e-48, Method: Compositional matrix adjust. Identities = 105/291 (36%), Positives = 167/291 (57%), Gaps = 16/291 (5%) Query: 31 GNPVDILIGQDVDQVDRLRIIQELGLDQPVWRQYLAFLNGALHGNLGNSFVYNTPAILLI 90 G+P + G + D + +LGLD+P+ Q++ F A G+ G+S P I Sbjct: 32 GDPARLAAGPEADDKTVALVRADLGLDKPLPEQFVNFFLNAARGDFGHSIRTKRPVSEEI 91 Query: 91 FQRLPATLELACAALLLALVVGVPLGLFAGMKPDHPFSRLVMTTSIFGFSLPTFWIGLML 150 R TL L A++ A++ G+ +G+ + + + RL MT ++ G S P F +G++L Sbjct: 92 SARFWPTLWLTVVAMVWAVLFGLIIGISSAVWRNQWPDRLGMTLAVSGISFPAFSLGILL 151 Query: 151 IMAFSVTLGWLPSGGRGQTAELFGVQWSWLTADGWRHMILPAINLSLFKISLVIRLTRAN 210 + FSV LGWLP+ G D W H ILP+I L +++ R TR++ Sbjct: 152 VQVFSVKLGWLPTVGD----------------DTWLHYILPSITLGAAVAAVMARFTRSS 195 Query: 211 VREVLPMDFVKFARAKGLSPARVVLMYVLRNTLIPLVTVVGLEFGSTIAFAVVTESIFAW 270 E+L DFV+ ARAKGL+ VV+ + LRN LIP+VT++GL+FG + +++ E +F W Sbjct: 196 FIEILQEDFVRTARAKGLTETVVVIKHCLRNALIPVVTMMGLQFGFLLGGSILVEVVFNW 255 Query: 271 PGAGKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDVLYKLLDPRVRVE 321 PG G+L++D++ D PVI A +++ F+ INLVVDVLY +++P +R + Sbjct: 256 PGMGRLLVDAVEMRDYPVIQAEILLFSLEFIFINLVVDVLYAVINPSIRFK 306 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 124 bits (311), Expect = 1e-29, Method: Compositional matrix adjust. Identities = 95/320 (29%), Positives = 165/320 (51%), Gaps = 13/320 (4%) Query: 5 IARSVVQALMVVLLMTVIVFFGLHMI-GNPVDILIGQDV--DQVDRLRIIQELGLDQPVW 61 IAR ++QA++ +LL++ VFF +++ G+ +GQ + V LR+ + GLD P Sbjct: 9 IARRLLQAVLTLLLVSAGVFFITNLLPGDAAQTALGQAATPETVAALRL--QYGLDLPAP 66 Query: 62 RQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVPLGLFAGM 121 +Y +L L GN G S V N P +I RLPA+L LA L+++ + + LG+F+ M Sbjct: 67 LRYAHWLGNLLSGNPGMSLVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALFLGIFSAM 126 Query: 122 KPDHPFSRLVMTTSIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWLT 181 F R V +++ S+P F + + +M F+V L WL + A G +++ Sbjct: 127 YRGSFFDRAVNVSAVSMVSVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLG---AFIK 183 Query: 182 ADGWRHMILPAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLRN 241 A +P + L ++ + R+TRA V + L + + A KG+ R+VL + L N Sbjct: 184 AYA-----MPVLTLCCVIVAQMTRMTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPN 238 Query: 242 TLIPLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMFV 301 + P+ V L + ++ ESIF +PG L++D++ D P++ A M+ ++ Sbjct: 239 AIGPIANAVALSLSYLLGGVIIVESIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYL 298 Query: 302 TINLVVDVLYKLLDPRVRVE 321 + L DVL + +PR++ Sbjct: 299 LLVLTADVLAIVSNPRLKTR 318 >gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 356 Score = 119 bits (297), Expect = 5e-28, Method: Compositional matrix adjust. Identities = 87/291 (29%), Positives = 143/291 (49%), Gaps = 14/291 (4%) Query: 40 QDVDQVDRLRIIQELGLDQPVWRQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLE 99 Q +D+ I Q G D+P ++ L G L +LG SF ++ L+ +LP ++ Sbjct: 69 QGIDEQRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVKSKLPVSIS 128 Query: 100 LACAALLLALVVGVPLGLFAGMKPDHPFSRLVMTTSIFGFSLPTFWIGLMLIMAFS--VT 157 + LL+ ++ VPLG+ ++ F + G+S+P F +G+ L++ F+ Sbjct: 129 IGLWTFLLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLLVLFAGGSF 188 Query: 158 LGWLPSGGRGQTAELFGVQWSWLT-----ADGWRHMILPAINLSLFKISLVIRLTRANVR 212 + W P RG T++ W L+ D H+ LP + +++ LTR Sbjct: 189 VQWFPL--RGLTSD----NWESLSLMGKITDYLWHITLPVTASVIGSFAVITMLTRNTFL 242 Query: 213 EVLPMDFVKFARAKGLSPARVVLMYVLRNTLIPLVTVVGLEF-GSTIAFAVVTESIFAWP 271 E + +V ARAKGLS RV+ +V RN LIPLVT F S A +++ E++F+ Sbjct: 243 EEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFSLD 302 Query: 272 GAGKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDVLYKLLDPRVRVEA 322 G G L +S D PV++ L + + + + LV D+ Y DPRV+ E+ Sbjct: 303 GMGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQFES 353 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 0.440 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: 925,598 Number of extensions: 36418 Number of successful extensions: 171 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 163 Number of HSP's successfully gapped: 6 Length of query: 324 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 239 Effective length of database: 1,217,395 Effective search space: 290957405 Effective search space used: 290957405 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: 131 (55.1 bits)