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= 0001.1458.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... 595 e-171 gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel A... 208 6e-55 gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 186 3e-48 gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herba... 122 5e-29 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 120 1e-28 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 595 bits (1535), Expect = e-171, Method: Compositional matrix adjust. Identities = 312/323 (96%), Positives = 318/323 (98%) Query: 1 MSAAIAKSVLQALMVVLLMTVIVFFGLHMIGNPVDILIGQDVDQVDRLRIIQELGLDQPV 60 MS AIA+SV+QALMVVLLMTVIVFFGLHMIGNPVDILIGQDVDQVDRLRIIQELGLDQPV Sbjct: 1 MSGAIARSVVQALMVVLLMTVIVFFGLHMIGNPVDILIGQDVDQVDRLRIIQELGLDQPV 60 Query: 61 WRQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLELAFAALLLALLVGVPLGLLAG 120 WRQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLELA AALLLAL+VGVPLGL AG Sbjct: 61 WRQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVPLGLFAG 120 Query: 121 MKPDHPFSRLVMTTSILGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWL 180 MKPDHPFSRLVMTTSI GFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWL Sbjct: 121 MKPDHPFSRLVMTTSIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWL 180 Query: 181 TVDGWRHMILPALNLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLR 240 T DGWRHMILPA+NLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLR Sbjct: 181 TADGWRHMILPAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLR 240 Query: 241 NTLIPLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMF 300 NTLIPLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMF Sbjct: 241 NTLIPLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMF 300 Query: 301 VTINLVVDVLYKILDPRVRVEAR 323 VTINLVVDVLYK+LDPRVRVEA+ Sbjct: 301 VTINLVVDVLYKLLDPRVRVEAK 323 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 208 bits (529), Expect = 6e-55, Method: Compositional matrix adjust. Identities = 112/310 (36%), Positives = 182/310 (58%), Gaps = 16/310 (5%) Query: 12 ALMVVLLMTVIVFFGLHMIGNPVDILIGQDVDQVDRLRIIQELGLDQPVWRQYLAFLNGA 71 AL V + ++V+ F LHM G+ + G + + + GLD+P+ QYL +L A Sbjct: 12 ALCVAVTVSVVSFTLLHMSGDLAVSIAGPEATAAQVESVRTQFGLDRPMATQYLDWLGRA 71 Query: 72 LHGNLGNSFVYNTPAILLIFQRLPATLELAFAALLLALLVGVPLGLLAGMKPDHPFSRLV 131 + + G SF + P + +I +RLP T +L +ALLLA+L +PLG+LA + D R Sbjct: 72 VQLDFGKSFYFQGPVMEMIAERLPITFKLGGSALLLAVLTAIPLGVLAAIYRDTWLDRAA 131 Query: 132 MTTSILGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWLTVDGWRHMILP 191 + +++G ++P+FW GL LI+ F+VTL WLP G + W+H ILP Sbjct: 132 LLIAVVGQAMPSFWFGLTLILIFAVTLHWLPVAGN----------------ESWQHFILP 175 Query: 192 ALNLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLRNTLIPLVTVVG 251 A+ L + + ++RLTR+ + EVL D+++ ARAKGLS +RVV + LRN +IP+V + Sbjct: 176 AVALGYYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVIPVVALAA 235 Query: 252 LEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDVLY 311 +E G + +VV ES+++ G G+L D+I+ D PV+ A +++I ++ + + DV+ Sbjct: 236 VELGFMLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVIN 295 Query: 312 KILDPRVRVE 321 +LDPR+R Sbjct: 296 ALLDPRIRTR 305 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 186 bits (471), Expect = 3e-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 FQRLPATLELAFAALLLALLVGVPLGLLAGMKPDHPFSRLVMTTSILGFSLPTFWIGLML 150 R TL L A++ A+L G+ +G+ + + + RL MT ++ G S P F +G++L Sbjct: 92 SARFWPTLWLTVVAMVWAVLFGLIIGISSAVWRNQWPDRLGMTLAVSGISFPAFSLGILL 151 Query: 151 IMAFSVTLGWLPSGGRGQTAELFGVQWSWLTVDGWRHMILPALNLSLFKISLVIRLTRAN 210 + FSV LGWLP+ G D W H ILP++ 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 PGAGKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDVLYKILDPRVRVE 321 PG G+L++D++ D PVI A +++ F+ INLVVDVLY +++P +R + Sbjct: 256 PGMGRLLVDAVEMRDYPVIQAEILLFSLEFIFINLVVDVLYAVINPSIRFK 306 >gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 356 Score = 122 bits (305), Expect = 5e-29, Method: Compositional matrix adjust. Identities = 90/294 (30%), Positives = 147/294 (50%), Gaps = 16/294 (5%) Query: 40 QDVDQVDRLRIIQELGLDQPVWRQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLE 99 Q +D+ I Q G D+P ++ L G L +LG SF ++ L+ +LP ++ Sbjct: 69 QGIDEQRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVKSKLPVSIS 128 Query: 100 LAFAALLLALLVGVPLGLLAGMKPDHPFSRLVMTTSILGFSLPTFWIGLMLIMAFS--VT 157 + LL+ L+ VPLG+ ++ F ++G+S+P F +G+ L++ F+ Sbjct: 129 IGLWTFLLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLLVLFAGGSF 188 Query: 158 LGWLPSGGRGQTAELFGVQWSWLTVDG------WRHMILPALNLSLFKISLVIRLTRANV 211 + W P RG T++ W L++ G W H+ LP + +++ LTR Sbjct: 189 VQWFPL--RGLTSD----NWESLSLMGKITDYLW-HITLPVTASVIGSFAVITMLTRNTF 241 Query: 212 REVLPMDFVKFARAKGLSPARVVLMYVLRNTLIPLVTVVGLEF-GSTIAFAVVTESIFAW 270 E + +V ARAKGLS RV+ +V RN LIPLVT F S A +++ E++F+ Sbjct: 242 LEEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFSL 301 Query: 271 PGAGKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDVLYKILDPRVRVEARA 324 G G L +S D PV++ L + + + + LV D+ Y DPRV+ E+ A Sbjct: 302 DGMGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQFESLA 355 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 120 bits (302), Expect = 1e-28, Method: Compositional matrix adjust. Identities = 87/302 (28%), Positives = 147/302 (48%), Gaps = 13/302 (4%) Query: 23 VFFGLHMI-GNPVDILIGQDV--DQVDRLRIIQELGLDQPVWRQYLAFLNGALHGNLGNS 79 VFF +++ G+ +GQ + V LR+ + GLD P +Y +L L GN G S Sbjct: 27 VFFITNLLPGDAAQTALGQAATPETVAALRL--QYGLDLPAPLRYAHWLGNLLSGNPGMS 84 Query: 80 FVYNTPAILLIFQRLPATLELAFAALLLALLVGVPLGLLAGMKPDHPFSRLVMTTSILGF 139 V N P +I RLPA+L LA L+++ + + LG+ + M F R V +++ Sbjct: 85 LVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALFLGIFSAMYRGSFFDRAVNVSAVSMV 144 Query: 140 SLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWLTVDGWRHMILPALNLSLFK 199 S+P F + + +M F+V L WL + A G + +P L L Sbjct: 145 SVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLGAFI--------KAYAMPVLTLCCVI 196 Query: 200 ISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLRNTLIPLVTVVGLEFGSTIA 259 ++ + R+TRA V + L + + A KG+ R+VL + L N + P+ V L + Sbjct: 197 VAQMTRMTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPNAIGPIANAVALSLSYLLG 256 Query: 260 FAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDVLYKILDPRVR 319 ++ ESIF +PG L++D++ D P++ A M+ ++ + L DVL + +PR++ Sbjct: 257 GVIIVESIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYLLLVLTADVLAIVSNPRLK 316 Query: 320 VE 321 Sbjct: 317 TR 318 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 0.435 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: 915,939 Number of extensions: 35904 Number of successful extensions: 169 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 159 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)