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= 0001.3374.p (351 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... 578 e-166 gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel A... 148 6e-37 gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 129 4e-31 gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 110 1e-25 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 95 8e-21 >gi|300312718|ref|YP_003776810.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 356 Score = 578 bits (1491), Expect = e-166, Method: Compositional matrix adjust. Identities = 289/356 (81%), Positives = 323/356 (90%), Gaps = 5/356 (1%) Query: 1 MNIWAYILKRILLMIPTLLGVIAITFAVIQFVPGGPVEQMVQELRGRSGVHESAGGGGA- 59 MNIW+YI+KR+LLMIPTL GV+AITFAVIQFVPGGPVEQ + E++GR G E++GGG A Sbjct: 1 MNIWSYIVKRVLLMIPTLFGVVAITFAVIQFVPGGPVEQAMLEMKGRGGGGEASGGGAAS 60 Query: 60 ----YRGRQGVDPERVKEIKALYGFDKPPLERFWLMLKGFATFDLGRSFYHHADVWALVK 115 YRGRQG+D +R+ EIK LYGFDKPP+ERFW MLKGF TFDLG+SFYHH DVW LVK Sbjct: 61 GASAYRGRQGIDEQRIAEIKQLYGFDKPPVERFWTMLKGFLTFDLGKSFYHHGDVWTLVK 120 Query: 116 SKMPVSISIGLWTFFITYLISVPLGIAKAVRAGSRFDSITSAVVLVGYSIPGFVLGVFLL 175 SK+PVSISIGLWTF ++YLISVPLGIAKAVR G+RFD+ T+ +VLVGYSIPGFVLGVFLL Sbjct: 121 SKLPVSISIGLWTFLLSYLISVPLGIAKAVREGTRFDTATTGLVLVGYSIPGFVLGVFLL 180 Query: 176 VVFGGGSFLQWFPLRGLTSDNWEQLSWFGKISDYLWHITLPIIASVAGAFATMTMLTKNT 235 V+F GGSF+QWFPLRGLTSDNWE LS GKI+DYLWHITLP+ ASV G+FA +TMLT+NT Sbjct: 181 VLFAGGSFVQWFPLRGLTSDNWESLSLMGKITDYLWHITLPVTASVIGSFAVITMLTRNT 240 Query: 236 FLEEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPAAFIGAFFAGSLLIETLFS 295 FLEEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFP+AFI +FFAGSLLIETLFS Sbjct: 241 FLEEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPSAFIASFFAGSLLIETLFS 300 Query: 296 LDGLGLLSYESVLRRDYPVVMGTLYLFTLIGLVVKLIGDLCYVWVDPRVQFESLAK 351 LDG+GLL+YES +RRDYPVVMGTLYLFTLIGLVVKL+GDLCYVW DPRVQFESLAK Sbjct: 301 LDGMGLLAYESAIRRDYPVVMGTLYLFTLIGLVVKLVGDLCYVWADPRVQFESLAK 356 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 148 bits (374), Expect = 6e-37, Method: Compositional matrix adjust. Identities = 92/340 (27%), Positives = 171/340 (50%), Gaps = 40/340 (11%) Query: 6 YILKRILLMIPTLLGVIAITFAVIQFVPGGPVEQMVQELRGRSGVHESAGGGGAYRGRQG 65 YIL+R+ + + +A+T +V+ F + +H S + G + Sbjct: 4 YILRRLAIAL-----CVAVTVSVVSF----------------TLLHMSGDLAVSIAGPEA 42 Query: 66 VDPERVKEIKALYGFDKPPLERFWLMLKGFATFDLGRSFYHHADVWALVKSKMPVSISIG 125 + V+ ++ +G D+P ++ L D G+SFY V ++ ++P++ +G Sbjct: 43 TAAQ-VESVRTQFGLDRPMATQYLDWLGRAVQLDFGKSFYFQGPVMEMIAERLPITFKLG 101 Query: 126 LWTFFITYLISVPLGIAKAVRAGSRFDSITSAVVLVGYSIPGFVLGVFLLVVFGGGSFLQ 185 + L ++PLG+ A+ + D + +VG ++P F G+ L+++F L Sbjct: 102 GSALLLAVLTAIPLGVLAAIYRDTWLDRAALLIAVVGQAMPSFWFGLTLILIF--AVTLH 159 Query: 186 WFPLRGLTSDNWEQLSWFGKISDYLWHITLPIIASVAGAFATMTMLTKNTFLEEIRKQYV 245 W P+ G +++W+ H LP +A A M LT++ LE + Y+ Sbjct: 160 WLPVAG--NESWQ-------------HFILPAVALGYYAMPAMMRLTRSGMLEVLGSDYI 204 Query: 246 LTARAKGLSERRVLYKHVFRNALIPLVTGFPAAFIGAFFAGSLLIETLFSLDGLGLLSYE 305 TARAKGLS+ RV++KH RNA+IP+V A +G GS++IE+++S+ GLG L+++ Sbjct: 205 RTARAKGLSKSRVVFKHALRNAVIPVV-ALAAVELGFMLGGSVVIESVYSMQGLGQLAWD 263 Query: 306 SVLRRDYPVVMGTLYLFTLIGLVVKLIGDLCYVWVDPRVQ 345 ++ R DYPVV + + + + + + D+ +DPR++ Sbjct: 264 AISRNDYPVVQAVVLIIAMFYIGLTFLADVINALLDPRIR 303 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 129 bits (323), Expect = 4e-31, Method: Compositional matrix adjust. Identities = 95/292 (32%), Positives = 144/292 (49%), Gaps = 40/292 (13%) Query: 67 DPERVKEIKALYGFDKPPLERFWLMLKGFATFDLGRSFYHHADVWALVKSKMPVS--ISI 124 D + V ++A G DKP E+F A D G S +++K PVS IS Sbjct: 44 DDKTVALVRADLGLDKPLPEQFVNFFLNAARGDFGHS----------IRTKRPVSEEISA 93 Query: 125 GLW-TFFITY-------LISVPLGIAKAVRAGSRFDSITSAVVLVGYSIPGFVLGVFLLV 176 W T ++T L + +GI+ AV D + + + G S P F LG+ L+ Sbjct: 94 RFWPTLWLTVVAMVWAVLFGLIIGISSAVWRNQWPDRLGMTLAVSGISFPAFSLGILLVQ 153 Query: 177 VFGGGSFLQWFPLRGLTSDNWEQLSWFGKISDYLW-HITLPIIASVAGAFATMTMLTKNT 235 VF +L W + D W H LP I A A M T+++ Sbjct: 154 VFS------------------VKLGWLPTVGDDTWLHYILPSITLGAAVAAVMARFTRSS 195 Query: 236 FLEEIRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPAAFIGAFFAGSLLIETLFS 295 F+E +++ +V TARAKGL+E V+ KH RNALIP+VT F G GS+L+E +F+ Sbjct: 196 FIEILQEDFVRTARAKGLTETVVVIKHCLRNALIPVVTMMGLQF-GFLLGGSILVEVVFN 254 Query: 296 LDGLGLLSYESVLRRDYPVVMGTLYLFTLIGLVVKLIGDLCYVWVDPRVQFE 347 G+G L ++V RDYPV+ + LF+L + + L+ D+ Y ++P ++F+ Sbjct: 255 WPGMGRLLVDAVEMRDYPVIQAEILLFSLEFIFINLVVDVLYAVINPSIRFK 306 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 110 bits (276), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 86/289 (29%), Positives = 148/289 (51%), Gaps = 10/289 (3%) Query: 64 QGVDP-ERVKEIKALYGFDKPPLERFWLMLKGFATFDLGRSFYHHADVWALVKSKMPVSI 122 Q VD +R++ I+ L G D+P ++ L G +LG SF ++ L+ ++P ++ Sbjct: 40 QDVDQVDRLRIIQEL-GLDQPVWRQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATL 98 Query: 123 SIGLWTFFITYLISVPLGIAKAVRAGSRFDSITSAVVLVGYSIPGFVLGVFLLVVFGGGS 182 + + ++ VPLG+ ++ F + + G+S+P F +G+ L++ F Sbjct: 99 ELACAALLLALVVGVPLGLFAGMKPDHPFSRLVMTTSIFGFSLPTFWIGLMLIMAF--SV 156 Query: 183 FLQWFPL--RGLTSDNW-EQLSWFGKISDYLWHITLPIIASVAGAFATMTMLTKNTFLEE 239 L W P RG T++ + Q SW +D H+ LP I + + LT+ E Sbjct: 157 TLGWLPSGGRGQTAELFGVQWSWL--TADGWRHMILPAINLSLFKISLVIRLTRANVREV 214 Query: 240 IRKQYVLTARAKGLSERRVLYKHVFRNALIPLVTGFPAAFIGAFFAGSLLIETLFSLDGL 299 + +V ARAKGLS RV+ +V RN LIPLVT F G+ A +++ E++F+ G Sbjct: 215 LPMDFVKFARAKGLSPARVVLMYVLRNTLIPLVTVVGLEF-GSTIAFAVVTESIFAWPGA 273 Query: 300 GLLSYESVLRRDYPVVMGTLYLFTLIGLVVKLIGDLCYVWVDPRVQFES 348 G L +S+ D PV++ L + + + + L+ D+ Y +DPRV+ E+ Sbjct: 274 GKLILDSINALDRPVIVAYLMVIVCMFVTINLVVDVLYKLLDPRVRVEA 322 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 95.1 bits (235), Expect = 8e-21, Method: Compositional matrix adjust. Identities = 63/282 (22%), Positives = 128/282 (45%), Gaps = 10/282 (3%) Query: 64 QGVDPERVKEIKALYGFDKPPLERFWLMLKGFATFDLGRSFYHHADVWALVKSKMPVSIS 123 Q PE V ++ YG D P R+ L + + G S ++ V ++ ++P S+ Sbjct: 45 QAATPETVAALRLQYGLDLPAPLRYAHWLGNLLSGNPGMSLVNNVPVAQMIGGRLPASLM 104 Query: 124 IGLWTFFITYLISVPLGIAKAVRAGSRFDSITSAVVLVGYSIPGFVLGVFLLVVFGGGSF 183 + T ++ +++ LGI A+ GS FD + + S+P F++ +++F Sbjct: 105 LAAVTALVSVPLALFLGIFSAMYRGSFFDRAVNVSAVSMVSVPEFLVATVAVMIFAVK-- 162 Query: 184 LQWFPLRGLTSDNWEQLSWFGKISDYLWHITLPIIASVAGAFATMTMLTKNTFLEEIRKQ 243 L+W D + ++ +P++ A MT +T+ ++++R Sbjct: 163 LRWLSALSHAGDA-------ATLGAFIKAYAMPVLTLCCVIVAQMTRMTRAAVIDQLRSS 215 Query: 244 YVLTARAKGLSERRVLYKHVFRNALIPLVTGFPAAFIGAFFAGSLLIETLFSLDGLGLLS 303 Y A KG+ R++ +H NA+ P+ A + G +++E++F+ G+ L Sbjct: 216 YAEMALLKGVKRTRIVLRHALPNAIGPIANAV-ALSLSYLLGGVIIVESIFNYPGIATLM 274 Query: 304 YESVLRRDYPVVMGTLYLFTLIGLVVKLIGDLCYVWVDPRVQ 345 ++V 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 0.328 0.144 0.449 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: 949,163 Number of extensions: 33622 Number of successful extensions: 175 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 162 Number of HSP's successfully gapped: 6 Length of query: 351 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 265 Effective length of database: 1,212,660 Effective search space: 321354900 Effective search space used: 321354900 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 (21.7 bits) S2: 131 (55.1 bits)