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= 0038.0008.p (303 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313777|ref|YP_003777869.1| D-xylose ABC transporter ATPase... 556 e-160 gi|300310371|ref|YP_003774463.1| sugar ABC transporter ATPase [H... 261 4e-71 gi|300310382|ref|YP_003774474.1| sugar ABC transporter ATPase [H... 236 1e-63 gi|300310396|ref|YP_003774488.1| sugar ABC transporter ATPase [H... 223 1e-59 gi|300310063|ref|YP_003774155.1| sugar ABC transporter ATPase [H... 206 1e-54 >gi|300313777|ref|YP_003777869.1| D-xylose ABC transporter ATPase [Herbaspirillum seropedicae SmR1] Length = 518 Score = 556 bits (1432), Expect = e-160, Method: Compositional matrix adjust. Identities = 264/294 (89%), Positives = 282/294 (95%) Query: 1 MKGIVKQFDGVRALDGIDLKIKAGECVGLCGENGAGKSTLMKILSGVYPHGTWDGDILWD 60 MKGIVK F GVRAL+GID+KI+ GECVGLCGENGAGKSTLMKILSGVYPHGTW+G+ILWD Sbjct: 8 MKGIVKSFGGVRALNGIDIKIRPGECVGLCGENGAGKSTLMKILSGVYPHGTWEGEILWD 67 Query: 61 GKPLVAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHELTLPGGRMNYPAMYRRAEE 120 GKPL AHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHE+TLPGGRMNYPAMYRRAEE Sbjct: 68 GKPLQAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHEITLPGGRMNYPAMYRRAEE 127 Query: 121 LMRELNMPDINVALPVMQYGGGHQQLVEIAKALNKKARLLILDEPSSSLTASEIAVLLKI 180 LMRELNMPDINVALPV QYGGGHQQLVEIAKALNK ARLLILDEPSSSLTASEI VLLKI Sbjct: 128 LMRELNMPDINVALPVSQYGGGHQQLVEIAKALNKDARLLILDEPSSSLTASEIGVLLKI 187 Query: 181 IKDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTPMEELDVDRIITQMVGREIT 240 IKDLKA+GVACVYISHKLDEVA VCDTISVIRDGKHIATTPM+E+DVD+IITQMVGREIT Sbjct: 188 IKDLKARGVACVYISHKLDEVAEVCDTISVIRDGKHIATTPMQEMDVDKIITQMVGREIT 247 Query: 241 AMYPSRDHEVGEIVFEAHHMTCFDVDNPKRKRVDDVSFSVRRGEILGIAGLVGA 294 AMYP R+H +GE+V EA ++TC+D+DNP+RKRVDDVSFSVRRGEILGIAGLVGA Sbjct: 248 AMYPERNHAIGEVVLEARNITCYDIDNPRRKRVDDVSFSVRRGEILGIAGLVGA 301 Score = 89.4 bits (220), Expect = 4e-19, Method: Compositional matrix adjust. Identities = 57/208 (27%), Positives = 109/208 (52%), Gaps = 5/208 (2%) Query: 12 RALDGIDLKIKAGECVGLCGENGAGKSTLMKILSGVYPHGTWDGDILWDGKPLVAHSVRD 71 + +D + ++ GE +G+ G GAG++ L+ + G Y G ++G +L +GKP S Sbjct: 278 KRVDDVSFSVRRGEILGIAGLVGAGRTELVSAIFGAY-RGRYEGQVLLEGKPADTSSPLK 336 Query: 72 TEAAGIVIIHQELM---LVPELSVAENIFMGHELTLP-GGRMNYPAMYRRAEELMRELNM 127 + G+ ++ ++ +VP+L V +NI + G R++ A + ++ + + + Sbjct: 337 SIRRGLCMVPEDRKHHGIVPDLDVGQNITLTVLNRFSRGSRIDGSAELKTIQDEIGRMRV 396 Query: 128 PDINVALPVMQYGGGHQQLVEIAKALNKKARLLILDEPSSSLTASEIAVLLKIIKDLKAK 187 LP+ GG+QQ +AK L + ++LILDEP+ + A + ++I +L Sbjct: 397 KTATPFLPITSLSGGNQQKAVLAKMLLAQPKVLILDEPTRGVDVGAKAEIYRLISELAKA 456 Query: 188 GVACVYISHKLDEVAAVCDTISVIRDGK 215 G+A + +S +L EV V D + VI +G+ Sbjct: 457 GLAIIMVSSELAEVLGVSDRVLVIGEGR 484 >gi|300310371|ref|YP_003774463.1| sugar ABC transporter ATPase [Herbaspirillum seropedicae SmR1] Length = 518 Score = 261 bits (667), Expect = 4e-71, Method: Compositional matrix adjust. Identities = 143/299 (47%), Positives = 205/299 (68%), Gaps = 10/299 (3%) Query: 1 MKGIVKQFDGVRALDGIDLKIKAGECVGLCGENGAGKSTLMKILSGVYPHGTWDGDILWD 60 M+GI K F GV+AL+ ++L ++ GE + GENGAGKSTLMK+LSGVYPHG++ GDI++ Sbjct: 7 MRGIEKSFPGVKALNNVNLAVREGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGDIVYK 66 Query: 61 GKPLVAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHELTLPGGRMNYPAMYRRAEE 120 G+ +RD+E GI+IIHQEL LVP LSV EN+F+G+E GG +++ Y RA+E Sbjct: 67 GEVRAFKDIRDSEHLGIIIIHQELALVPLLSVMENLFLGNE-QARGGVIDWEQSYVRAKE 125 Query: 121 LMRELNMPDINVALPVMQYGG---GHQQLVEIAKALNKKARLLILDEPSSSLTASEIAVL 177 L+ ++ + + P+ Q G G QQL+EIAKAL+K+ +LLILDEP++SL S+ L Sbjct: 126 LLAKVGLKE----SPLTQVGDLGVGKQQLIEIAKALSKEVKLLILDEPTASLNESDSDAL 181 Query: 178 LKIIKDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIAT--TPMEELDVDRIITQMV 235 L+++ +LK +G+A + ISHKL+E++ V D+I+V+RDG + T E + DRII MV Sbjct: 182 LELLLELKRQGIASILISHKLNEISKVADSITVLRDGTTVDTFDCRAEPISEDRIIQHMV 241 Query: 236 GREITAMYPSRDHEVGEIVFEAHHMTCFDVDNPKRKRVDDVSFSVRRGEILGIAGLVGA 294 GRE+ YP RD ++GE++FE + R + DV+ SVR GEI+GIAGL+GA Sbjct: 242 GREMADRYPQRDPQIGEVIFEVRDWRVHHPLHTDRLAIKDVNMSVRAGEIVGIAGLMGA 300 Score = 77.4 bits (189), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 59/227 (25%), Positives = 110/227 (48%), Gaps = 12/227 (5%) Query: 13 ALDGIDLKIKAGECVGLCGENGAGKSTLMKILSGVYPHGTWDGDILWDGKPLVAHSVRDT 72 A+ +++ ++AGE VG+ G GAG++ L K + G G GK + ++ Sbjct: 278 AIKDVNMSVRAGEIVGIAGLMGAGRTELAKSIFGRAYGKKITGQAFLHGKEVDLSTIEKA 337 Query: 73 EAAGIVIIHQELM---LVPELSVAENIFMGH-----ELTLPGGRMNYPAMYRRAEELMRE 124 A GI + ++ LV E + +NI + + E T+ ++ Y+ A + ++ Sbjct: 338 IAKGIAYVTEDRKGDGLVLEEDIKKNISLANLGGVSERTV----IDEAREYKIAADFKQQ 393 Query: 125 LNMPDINVALPVMQYGGGHQQLVEIAKALNKKARLLILDEPSSSLTASEIAVLLKIIKDL 184 + + +V V+ GG+QQ V ++K L + +LILDEP+ + + II L Sbjct: 394 MRIRCSSVLQKVVNLSGGNQQKVVLSKWLFSQPEVLILDEPTRGIDVGAKFEIYNIISKL 453 Query: 185 KAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTPMEELDVDRII 231 A+G + IS ++ E+ +CD I V+ +G+ + P E + I+ Sbjct: 454 AAEGKCIIMISSEMPELLGMCDRIYVMNEGQFVGHLPKAEATQENIM 500 >gi|300310382|ref|YP_003774474.1| sugar ABC transporter ATPase [Herbaspirillum seropedicae SmR1] Length = 520 Score = 236 bits (603), Expect = 1e-63, Method: Compositional matrix adjust. Identities = 135/296 (45%), Positives = 191/296 (64%), Gaps = 12/296 (4%) Query: 1 MKGIVKQFDGVRALDGIDLKIKAGECVGLCGENGAGKSTLMKILSGVYPHGTWDGDILWD 60 ++ + K+F GV ALD ++ AGE L GENGAGKSTLMKILSGVY + GDIL D Sbjct: 25 LRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS--GDILLD 82 Query: 61 GKPLVAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHELTLPGG-RMNYPAMYRRAE 119 GKP+ R +A GI IIHQEL L+ LS A+NIF+G E G ++ + R+A Sbjct: 83 GKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAA 142 Query: 120 ELMRELNMPDINVALPVMQYGGGHQQLVEIAKALNKKARLLILDEPSSSLTASEIAVLLK 179 + + + D++ + PV + QQ+VEIAKAL+ +R+LI+DEP+++L +EIA L + Sbjct: 143 AIFARMRL-DMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201 Query: 180 IIKDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTPMEELDVDRIITQMVGREI 239 II+DL+A+GV VYISHK+DE+ + D +SV+RDGK+IAT PM+E +D II+ MVGR + Sbjct: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261 Query: 240 TA-MYPSRDHEVGEIVFEAHHMTCFDVDNPKRKRVDDVSFSVRRGEILGIAGLVGA 294 D ++V E + + + + DVSF++R+GEILG AGL+GA Sbjct: 262 DGEQRIPPDTSRNDVVLEVRGLN-------RGRAIRDVSFTLRKGEILGFAGLMGA 310 Score = 62.8 bits (151), Expect = 4e-11, Method: Compositional matrix adjust. Identities = 58/217 (26%), Positives = 101/217 (46%), Gaps = 10/217 (4%) Query: 5 VKQFDGVRALDGIDLKIKAGECVGLCGENGAGKSTLMKILSGVYPHGTWDGDILWDGKPL 64 V+ + RA+ + ++ GE +G G GAG++ + + + G P G+I+ G Sbjct: 280 VRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADP--LEAGEIIIHGGKA 337 Query: 65 VAHSVRDTEAAGIVIIHQE---LMLVPELSVAENIF---MGHELTLPGGRMNYPAMYRRA 118 V S D A GI + ++ L + V NI MG + G M+ A+ A Sbjct: 338 VIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRV--GFMDQRAIREAA 395 Query: 119 EELMRELNMPDINVALPVMQYGGGHQQLVEIAKALNKKARLLILDEPSSSLTASEIAVLL 178 + +R+L + +V GG+QQ + IAK L + +L DEP+ + + + Sbjct: 396 QMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIY 455 Query: 179 KIIKDLKAKGVACVYISHKLDEVAAVCDTISVIRDGK 215 K++ L +G A V IS +L EV + + V+ +G+ Sbjct: 456 KLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGR 492 >gi|300310396|ref|YP_003774488.1| sugar ABC transporter ATPase [Herbaspirillum seropedicae SmR1] Length = 506 Score = 223 bits (569), Expect = 1e-59, Method: Compositional matrix adjust. Identities = 126/299 (42%), Positives = 182/299 (60%), Gaps = 16/299 (5%) Query: 1 MKGIVKQFDGVRALDGIDLKIKAGECVGLCGENGAGKSTLMKILSG-VYPHGTWDGDILW 59 + GI K F V L G+DL+++AGE L GENGAGKSTLMKIL G V P G+I Sbjct: 8 LTGIKKNFGPVTVLRGVDLEVRAGEVHALLGENGAGKSTLMKILCGIVRPDA---GEIRI 64 Query: 60 DGKPLVAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHELTLPGGRMNYPAMYRRAE 119 DG+P S R A G+ ++ QE L+P L +N+F+ EL G + AM RRA+ Sbjct: 65 DGQPCRFDSYRAAIAGGVGVVFQEFSLIPYLDAVDNMFLARELRSRWGWLQRAAMRRRAQ 124 Query: 120 ELMRELNMPDINVALPVMQYGGGHQQLVEIAKALNKKARLLILDEPSSSLTASEIAVLLK 179 E++ +L + I + +PV + QQ VEIAKAL AR+L+LDEP+++LT +E+ L Sbjct: 125 EIIGQLGVA-IPLDVPVCKLSVAQQQFVEIAKALALDARILVLDEPTATLTPAEVEHLFA 183 Query: 180 IIKDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTPMEELDVDRIITQMVGREI 239 +++ L+A+GVA ++ISH L+E+ +CD I+V+RDG ++AT E+D R++ MVGR I Sbjct: 184 VMRSLRAQGVAIIFISHHLEEIFEICDRITVLRDGAYVATCATAEVDQARLVEMMVGRRI 243 Query: 240 TAMYPSRDHE----VGEIVFEAHHMTCFDVDNPKRKRVDDVSFSVRRGEILGIAGLVGA 294 +P + + GE+V E H + R++ F +RRGEILG AGLVG+ Sbjct: 244 ENCFPPKPAKGGEGEGEVVLEVHALQL-------RRQAPVSQFQLRRGEILGFAGLVGS 295 Score = 74.7 bits (182), Expect = 9e-15, Method: Compositional matrix adjust. Identities = 56/225 (24%), Positives = 105/225 (46%), Gaps = 17/225 (7%) Query: 18 DLKIKAGECVGLCGENGAGKSTLMKILSGVYPHGTWDGDILWDGKPLVAHSVRDTEAAGI 77 +++ GE +G G G+G++ +L+ + H + G PL AGI Sbjct: 278 QFQLRRGEILGFAGLVGSGRTE--TVLAMLGAHAALSCKLSMHGVPLRFADPAQALQAGI 335 Query: 78 VII---HQELMLVPELSVAENIFMGHELTLPGGRMNYPAMY--RRAEELMRELNMPDINV 132 ++ +E L+ S+ N+ + + G+ ++ RR E+ E M + V Sbjct: 336 GLLPESRKEQGLITSFSILHNVSLNNY-----GKYRLGGLFLDRRREQQATEAAMQRVRV 390 Query: 133 ALPVMQ-----YGGGHQQLVEIAKALNKKARLLILDEPSSSLTASEIAVLLKIIKDLKAK 187 P Q GG+QQ V IA+ +N ++LI DEP+ + + + +++++ A+ Sbjct: 391 KAPGAQVRVDTLSGGNQQKVVIARWINHAMKVLIFDEPTRGIDVGAKSEIYQLMREFTAQ 450 Query: 188 GVACVYISHKLDEVAAVCDTISVIRDGKHIATTPMEELDVDRIIT 232 G + + IS +L EV + D + V R G +AT E ++ + I+T Sbjct: 451 GYSILMISSELPEVVGMADRVCVFRGGGIVATLEGEAVNAEEIMT 495 >gi|300310063|ref|YP_003774155.1| sugar ABC transporter ATPase [Herbaspirillum seropedicae SmR1] Length = 521 Score = 206 bits (525), Expect = 1e-54, Method: Compositional matrix adjust. Identities = 119/298 (39%), Positives = 176/298 (59%), Gaps = 14/298 (4%) Query: 1 MKGIVKQFDGVRALDGIDLKIKAGECVGLCGENGAGKSTLMKILSGVYPHGTWDGDILWD 60 M+GI K F AL + L I+ GE L GENGAGKSTLMK+LSGV H G+IL D Sbjct: 9 MRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGV--HAPDQGEILLD 66 Query: 61 GKPLVAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHELTLPGGRMNYPAMYRRAEE 120 G+P+ + AAGI +I+QEL + P +SVA N+FMG EL G +++ AM R + Sbjct: 67 GRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDA 126 Query: 121 LMRELNM----PDINVALPVMQYGGGHQQLVEIAKALNKKARLLILDEPSSSLTASEIAV 176 ++R+L D+ L + + QQ VEIA+AL ++R++I+DEP+++L+ E Sbjct: 127 VLRQLGAGFGASDLAGRLSIAE-----QQQVEIARALVHRSRIVIMDEPTAALSERETEQ 181 Query: 177 LLKIIKDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTPMEELDVDRIITQMVG 236 L +++ L+ +G+A +YISH++ EV A+ D ++V+RDG + +E+D +RI+ MVG Sbjct: 182 LFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 241 Query: 237 REITAMYPSRDHEVGEIVFEAHHMTCFDVDNPKRKRVDDVSFSVRRGEILGIAGLVGA 294 R ++ Y H+ A T V ++ SF VR GE+LG AGLVGA Sbjct: 242 RSLSEFY---QHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGA 296 Score = 88.6 bits (218), Expect = 5e-19, Method: Compositional matrix adjust. Identities = 67/221 (30%), Positives = 109/221 (49%), Gaps = 27/221 (12%) Query: 11 VRALDGIDLK-----IKAGECVGLCGENGAGKSTLMKILSGVYPHGTWDGDILWDGKPLV 65 VRAL G ++ ++AGE +G G GAG++ L ++L G P GDIL +G+P+ Sbjct: 267 VRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRS--GGDILLEGRPVH 324 Query: 66 AHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHELTLPGGRMNYPAMYRR-------- 117 R AGI VPE + +F+ + MN + + R Sbjct: 325 IDQPRAAMRAGIA-------YVPEDRKGQGLFLQMAVA-ANATMNVASRHTRLGLVRSRS 376 Query: 118 ----AEELMRELNMPDINVALPVMQYGGGHQQLVEIAKALNKKARLLILDEPSSSLTASE 173 A ++ LN+ + PV + GG+QQ V +A+ L ++LILDEP+ + Sbjct: 377 LGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYA 436 Query: 174 IAVLLKIIKDLKAKGVACVYISHKLDEVAAVCDTISVIRDG 214 + + +++ L ++GVA V IS +L EV +CD + V+R+G Sbjct: 437 KSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREG 477 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 0.320 0.138 0.401 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: 952,121 Number of extensions: 40894 Number of successful extensions: 540 Number of sequences better than 1.0e-08: 117 Number of HSP's gapped: 355 Number of HSP's successfully gapped: 132 Length of query: 303 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 218 Effective length of database: 1,217,395 Effective search space: 265392110 Effective search space used: 265392110 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 130 (54.7 bits)