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= 0001.0690.p (316 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasm... 524 e-150 gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasm... 132 5e-32 gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasm... 75 7e-15 gi|300310384|ref|YP_003774476.1| sugar ABC transporter periplasm... 73 3e-14 gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter peripl... 70 3e-13 >gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 316 Score = 524 bits (1349), Expect = e-150, Method: Compositional matrix adjust. Identities = 284/315 (90%), Positives = 299/315 (94%) Query: 1 MIKNTLAIACATLSLAAIASSSQAADKPLKSVGVTLGDLANPFFVAIAKGAESGAHKINP 60 MIKNT+AIAC+TL LAA A + AADKPLKSVGVT+GDLANPFFVAIAKGAESGAHKINP Sbjct: 1 MIKNTIAIACSTLLLAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINP 60 Query: 61 EAKVTVVSSKYDLNTQVGQIENFIANKVDMIVLNAADSKGVGPAVKKARKAGIVVVAVDV 120 +AKVTVVSSKYDLNTQVGQIENFIANKVD+IVLNAADSKGVGPAVKKA+KAGIVVVAVDV Sbjct: 61 DAKVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDV 120 Query: 121 AAEGADVTVMSDNTMAGAQSCKFIADKLQGKGNVVIVNGPPVSAVMDRVTGCKSEFKKSP 180 AA GADVTVMSDNTMAGA+SCKF+A+KLQGKGNVVIVNGPPVSAVMDRVTGCK+EFKKSP Sbjct: 121 AAAGADVTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKSP 180 Query: 181 GIKILSDNQNAGGSRDGGMTTMSNLLAAHAKIDGVFAINDPTAIGAELAIRQAKRSDIKV 240 GIKILSDNQNAGGSRDGGMTTMSNLLAA KID VFAINDPTAIGAELAIRQAKRSDIK Sbjct: 181 GIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIKW 240 Query: 241 ITGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYQVMNGHPPANSIKLLPVKL 300 I+GVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGY VMNG P +KLLPVKL Sbjct: 241 ISGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLPVKL 300 Query: 301 ITRENVADYKGWVPA 315 ITR+NVADY+GWVPA Sbjct: 301 ITRDNVADYQGWVPA 315 >gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 302 Score = 132 bits (331), Expect = 5e-32, Method: Compositional matrix adjust. Identities = 96/285 (33%), Positives = 155/285 (54%), Gaps = 14/285 (4%) Query: 32 VGVTLGDLANPFFVAIAKGAESGAHKINPEAKVTVVSSKYDLNTQVGQIENFIANKVDMI 91 +G++ ++ NP+FV++ K + A + AKV + +++ Q+ IE+ + +D++ Sbjct: 28 IGMSFQEMNNPYFVSMKKALDEAAKSLG--AKVIATDAAHNVAKQIADIEDMLQQNIDIL 85 Query: 92 VLNAADSKGVGPAVKKARKAGIVVVAVDVAAEG-ADVTVMSDNTMAGAQSCKFIADKLQG 150 ++N DS GV AVK A+ ++VVAVD A G D+ V S N AG QSC+ +AD + G Sbjct: 86 LINPTDSAGVEAAVKAAKARNVIVVAVDANASGPVDMFVGSKNKDAGYQSCRALADAIGG 145 Query: 151 KGNVVIVNGPPVSAVMDRVTGCKSEFKKSPGIKILSDNQNAGGSRDGGMTTMSNLLAAHA 210 KG V I++G PV ++ RV GCK + IK+++ QN R + + N++ + Sbjct: 146 KGEVAILDGIPVVPILQRVEGCKQALAEYKDIKLVA-TQNGRQDRSVALGVVENMIQSRP 204 Query: 211 KIDGVFAINDPTAIGAELAIRQAKRSDIKVITGVDGAPDAERALKDSKSLFAASPAQDPY 270 + G+F++ND A+GA AI Q DIK +T VDGAP+A +A+ D F + AQ P Sbjct: 205 NLKGIFSVNDGGAMGALAAI-QGSGKDIK-LTSVDGAPEAVKAIADGGP-FVETTAQFPR 261 Query: 271 GMAAESVAIGYQVMNGH---PPANSIKLLPVKLITRENVADYKGW 312 +A+ G P I ++PV T++N A + W Sbjct: 262 DQVRVGLAMALAKKWGARVVPKEVPIDVMPV---TKKNAAGFS-W 302 >gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 75.1 bits (183), Expect = 7e-15, Method: Compositional matrix adjust. Identities = 79/266 (29%), Positives = 127/266 (47%), Gaps = 20/266 (7%) Query: 7 AIACATLSLAAIASSSQAADKPLKSVGVTLGDLANPFFVAIAKGAESGAHKINPEAKVTV 66 A+ACA L AA+A Q KP V + + LAN FF+ + GA K N +K + Sbjct: 13 ALACAVLPGAAMA---QTPAKP--KVALVMKSLANEFFLNMENGARE-YQKANA-SKFDL 65 Query: 67 VSS----KYDLNTQVGQIENFIANKVDMIVLNAADSKGVGPAVKKARKAGIVVVAVD--- 119 +++ + D Q+ +E I +KV+ +V+ ADSK + P VKKA AGI+VV +D Sbjct: 66 IANGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVNIDNKL 125 Query: 120 ----VAAEGADVTVMSDNTMAGAQ-SCKFIADKLQGKGNVVIVNGPPVSAVMDRVTGCKS 174 + +G V + + GA+ + ++ +LQ V I+ G + + T Sbjct: 126 DDAALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQRTLGFQ 185 Query: 175 EFKKSPGIKILSDNQNAGGSRDGGMTTMSNLLAAHAKIDGVFAINDPTAIGAELAIRQAK 234 + K G +++ Q+ D G +++L AH I + A ND A+GA AIR A Sbjct: 186 DAMKDVGANVVT-VQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAAIRAAG 244 Query: 235 RSDIKVITGVDGAPDAERALKDSKSL 260 ++ + G D + LKD + L Sbjct: 245 KTGKVQLVGYDNINAIKPMLKDGRVL 270 >gi|300310384|ref|YP_003774476.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 312 Score = 72.8 bits (177), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 86/296 (29%), Positives = 139/296 (46%), Gaps = 22/296 (7%) Query: 1 MIKNTLAIACATLSLAAIASSSQAADK--PLKSVGVTLGDLANPFFVAIAKGAESGAHKI 58 M KN L A L+ A AS++QA + PL S G + F+ A+ GA+ Sbjct: 1 MFKNKLLGAALGLAFAMGASAAQAQEAYIPLISKG-----FQHQFWQAVKAGADQAGK-- 53 Query: 59 NPEAKVTVVSSKYD--LNTQVGQIENFIANKVDMIVLNAADSKGVGPAVKKARKAGIVVV 116 + + KVT + + ++ Q+ + +A K I A DSK P +KKA+ A I VV Sbjct: 54 DYKVKVTFEGPETEAMVDKQIDMLSAALAKKPQAIGFAALDSKAAIPLLKKAQAAKIPVV 113 Query: 117 AVDVAAEGADV---TVMSDNTMAGAQSCKFIADKLQGKGNVVIVNGPPVSAV-MDRVTGC 172 A D + +D+ T +DN A A + +A+ + +G V +V S +DR G Sbjct: 114 AFDSGVD-SDIPVTTATTDNRAAAALAADKMAELVGKEGEVAVVAHDQTSRTGVDRRDGF 172 Query: 173 KSEFKKS-PGIKILSDNQNAGGSRDGGMTTMSNLLAAHAKIDGVFAINDPTAIGAELAIR 231 K + P IK++S AG T S +L A+ KI G+F N+ +AIG ++ Sbjct: 173 LERIKSAYPKIKVVSVQYGAGDQLKSTEVTKS-ILQAYPKIKGIFGTNEGSAIGVVNGVK 231 Query: 232 QAKRSDIKVITGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYQVMNGH 287 + KR I I G D + A+++ + A + Q+P G+ ++V + + G Sbjct: 232 EMKRKII--IIGYDSGKQQKDAIRE--GIMAGAITQNPVGIGYKTVEAAVKAIKGE 283 >gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 69.7 bits (169), Expect = 3e-13, Method: Compositional matrix adjust. Identities = 90/323 (27%), Positives = 149/323 (46%), Gaps = 22/323 (6%) Query: 1 MIKNTLAIACATLSLAAIASSSQAADKPLKSVGVTLGDLANPFFVAIAKGAESGAHKINP 60 M+K T+ +A T++ ++ + S AD +G ++ DL + + A K+ Sbjct: 4 MLKKTV-LALMTVTTLSMVAGSAMADAKNPKIGFSIDDLRVERWARDRDFFTAAAEKLG- 61 Query: 61 EAKVTVVSSKYDLNTQVGQIENFIANKVDMIVLNAADSKGVGPAVKKARKAGIVVVAVDV 120 AKV V S+ Q+ QIEN I+ VD+IV+ ++ + +K+A+KAGI V++ D Sbjct: 62 -AKVYVQSADASEQRQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDR 120 Query: 121 AAEGADV--TVMSDNTMAGAQSCKFIADKLQGKGNVVIVNGPPV--SAVMDRVTGCKS-- 174 ADV + DN G + I K++ KGN ++ G P +A M R K+ Sbjct: 121 LILNADVDAYISFDNEKVGEMQAEGIL-KVKNKGNFFLLGGSPTDNNAKMFREGQMKALK 179 Query: 175 EFKKSPGIKILSDNQNAGGSRDGGMTTMSNLLAA-HAKIDGVFAINDPTAIGAELAIRQA 233 + IKI+ + ++ + N L A + KID + A ND TA GA A+ Sbjct: 180 PYIDKGDIKIVGQQWVKEWNPTEALSIVENALTANNNKIDAIVASNDGTAGGAIQALAAQ 239 Query: 234 KRSDIKVITGVDGAPDA-ERALKDSKSLFAASPAQDPYGMAA---------ESVAIGYQV 283 K + ++G D A +R + ++++ P + AA E Q Sbjct: 240 KLAGKVPVSGQDADLAAVKRVVAGTQTMTVYKPLKQIATEAAKLSVELARNEKPTYNAQY 299 Query: 284 MNGHPPANSIKLLPVKLITRENV 306 NG +S+ L P+ L+T+ENV Sbjct: 300 DNGFKKVDSLLLKPI-LLTKENV 321 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 0.313 0.129 0.357 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: 844,376 Number of extensions: 31188 Number of successful extensions: 114 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 109 Number of HSP's successfully gapped: 8 Length of query: 316 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 231 Effective length of database: 1,217,395 Effective search space: 281218245 Effective search space used: 281218245 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 130 (54.7 bits)