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= 0002.0212.p (313 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310384|ref|YP_003774476.1| sugar ABC transporter periplasm... 545 e-156 gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasm... 85 9e-18 gi|300313729|ref|YP_003777821.1| sugar ABC transporter periplasm... 75 6e-15 gi|300310351|ref|YP_003774443.1| sugar ABC transporter periplasm... 65 8e-12 gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasm... 59 4e-10 >gi|300310384|ref|YP_003774476.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 312 Score = 545 bits (1404), Expect = e-156, Method: Compositional matrix adjust. Identities = 273/313 (87%), Positives = 296/313 (94%), Gaps = 1/313 (0%) Query: 1 MIKRRALNIALGLSFAFGASGIAQAQEIYIPLVSKGFQHQFWQAVKAGANQAATDYKVKV 60 M K + L ALGL+FA GAS AQAQE YIPL+SKGFQHQFWQAVKAGA+QA DYKVKV Sbjct: 1 MFKNKLLGAALGLAFAMGASA-AQAQEAYIPLISKGFQHQFWQAVKAGADQAGKDYKVKV 59 Query: 61 TFEGPETEAMVDKQIDMLSAALAKKPQAIGFAALDSKAALPLLKKAQAAKIPVIAFDSGV 120 TFEGPETEAMVDKQIDMLSAALAKKPQAIGFAALDSKAA+PLLKKAQAAKIPV+AFDSGV Sbjct: 60 TFEGPETEAMVDKQIDMLSAALAKKPQAIGFAALDSKAAIPLLKKAQAAKIPVVAFDSGV 119 Query: 121 DSDIPVTTTTTDNKAAAALAADKMAELIGKEGEVAVVAHDQTSRTGIDRRDGFVDRMKSA 180 DSDIPVTT TTDN+AAAALAADKMAEL+GKEGEVAVVAHDQTSRTG+DRRDGF++R+KSA Sbjct: 120 DSDIPVTTATTDNRAAAALAADKMAELVGKEGEVAVVAHDQTSRTGVDRRDGFLERIKSA 179 Query: 181 YPKIKIVSIQYGAGDQLKSTEVTKSILQAYPKLKGAFGTNEGSAIGVLNGAREMKRKVVI 240 YPKIK+VS+QYGAGDQLKSTEVTKSILQAYPK+KG FGTNEGSAIGV+NG +EMKRK++I Sbjct: 180 YPKIKVVSVQYGAGDQLKSTEVTKSILQAYPKIKGIFGTNEGSAIGVVNGVKEMKRKIII 239 Query: 241 IGFDSGKQQKDAIRDGQMAGAITQNPVGIGYKTVEAAVKALKGEKLPKIIDTGFYWYDKS 300 IG+DSGKQQKDAIR+G MAGAITQNPVGIGYKTVEAAVKA+KGEKLPK+IDTGFYWYDKS Sbjct: 240 IGYDSGKQQKDAIREGIMAGAITQNPVGIGYKTVEAAVKAIKGEKLPKVIDTGFYWYDKS 299 Query: 301 NIADPKIAAVLYD 313 NI D KIAAVLYD Sbjct: 300 NIDDAKIAAVLYD 312 >gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 84.7 bits (208), Expect = 9e-18, Method: Compositional matrix adjust. Identities = 84/296 (28%), Positives = 137/296 (46%), Gaps = 14/296 (4%) Query: 4 RRALNIA-LGLSFAFGASGIAQAQEIYIPLVSKGFQHQFWQAVKAGAN--QAATDYKVKV 60 RR IA L + GA+ + + LV K ++F+ ++ GA Q A K + Sbjct: 6 RRHFAIAALACAVLPGAAMAQTPAKPKVALVMKSLANEFFLNMENGAREYQKANASKFDL 65 Query: 61 TFEGPETEAMVDKQIDMLSAALAKKPQAIGFAALDSKAALPLLKKAQAAKIPVIAFDSGV 120 G + E QI ++ + K A+ A DSKA +P++KKA A I V+ D+ + Sbjct: 66 IANGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVNIDNKL 125 Query: 121 DS------DIPVTTTTTDNKAAAALAADKMAELIGKEGEVAVVAHDQTSRTGIDRRDGFV 174 D I V DN+ A LA D + + + K +VA++ T+ R GF Sbjct: 126 DDAALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQRTLGFQ 185 Query: 175 DRMKSAYPKIKIVSIQYGAGDQLKSTEVTKSILQAYPKLKGAFGTNEGSAIGVLNGAREM 234 D MK + V++Q G + + +V SIL A+P +K N+ A+G + R Sbjct: 186 DAMKDVGANV--VTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAAIRAA 243 Query: 235 KR--KVVIIGFDSGKQQKDAIRDGQMAGAITQNPVGIGYKTVEAAVKALKGEKLPK 288 + KV ++G+D+ K ++DG++ + Q +E A+KAL EK P+ Sbjct: 244 GKTGKVQLVGYDNINAIKPMLKDGRVLATVDQFAQQQAVFGIETALKAL-SEKKPQ 298 >gi|300313729|ref|YP_003777821.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 75.5 bits (184), Expect = 6e-15, Method: Compositional matrix adjust. Identities = 71/273 (26%), Positives = 131/273 (47%), Gaps = 24/273 (8%) Query: 26 QEIYIPLVSKGFQHQFWQAVKAGANQAATDY-KVKVTFEGPETEAMVDKQIDMLSAALAK 84 +++ I +V K + F+ A GA +AA + V+V + GP T + QI+++++ +++ Sbjct: 37 EKVRIAMVVKSLGNGFFDAAHEGAKEAARELGDVEVIYTGPTTPT-AEGQIEIVNSLISQ 95 Query: 85 KPQAIGFAALDSKAALPLLKKAQAAKIPVIAFDSGVDSDIPVTTTTTDNKAAAALAADKM 144 K AI +A D+ A +P+ K+A + V++FDSG+ + N L +M Sbjct: 96 KVDAIVISANDANALVPITKRAMQRGVKVLSFDSGIAKGGRLMQLNPSNAELIGLKQIQM 155 Query: 145 -AELIGKEGEVAVV-AHDQTSRTGIDRRDGFVDRMKSA-----YPKIKIVSIQYGAGDQL 197 AE IG G+VA++ A Q + I ++ MK A + ++K+V+ YG Sbjct: 156 AAEAIGGAGDVAILSATAQATNQNI-----WIGEMKKALARPEFSRMKLVATVYGDDQSD 210 Query: 198 KSTEVTKSILQAYPKLKGAFGTNEGSAIGVLNGA------REMKRKVVIIGFDSGKQQKD 251 KS +L+++P LK + +G+ N A ++ KV + G + Sbjct: 211 KSYREAIGLLRSHPGLKAIIAP---TTVGI-NAAGKAVVDEKLVGKVYVTGLGLPSEMAG 266 Query: 252 AIRDGQMAGAITQNPVGIGYKTVEAAVKALKGE 284 ++ G + NP+ +GY AA + +KG+ Sbjct: 267 HVKSGAVKSFAIWNPIDLGYAATYAAYQFVKGK 299 >gi|300310351|ref|YP_003774443.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 335 Score = 64.7 bits (156), Expect = 8e-12, Method: Compositional matrix adjust. Identities = 56/233 (24%), Positives = 105/233 (45%), Gaps = 3/233 (1%) Query: 73 KQIDMLSAALAKKPQAIGFAALDSKAALPLLKKAQAAKIPVIAFDSGVDSDIPVTTTTTD 132 +Q ++ +AKK AI ++D P+LK+A I V+ ++ + V D Sbjct: 75 QQQRLVEDLVAKKVDAIAVVSMDPPTLEPVLKRALDRGIKVVTHEADNQKNTLVDIEAFD 134 Query: 133 NKAAAALAADKMAELIGKEGEVAVVAHDQTSRTGIDRRDGFVDRMKSAYPKIKIVSIQY- 191 N A A D++A +G+ G+ + + S++ + DG YPK+ +V + Sbjct: 135 NTAYGARLNDRLAACMGQAGKWSSLVGSLGSQSQVQWADGGAANAAKKYPKMTLVDAKNE 194 Query: 192 GAGDQLKSTEVTKSILQAYPKLKGAFGTNEGSAIGVLNGARE--MKRKVVIIGFDSGKQQ 249 A D K+ K IL+ +P +KG G++ +G+ E ++ KV + G + Sbjct: 195 SANDAEKAYAKAKEILRKHPDIKGFQGSSSLDVLGIGRAVEEAGLQGKVCVYGTGLPSEA 254 Query: 250 KDAIRDGQMAGAITQNPVGIGYKTVEAAVKALKGEKLPKIIDTGFYWYDKSNI 302 + G + G +P G +AA+ ++G+K+ +D G Y+K + Sbjct: 255 AKFLESGAVGGIAFWDPKDAGLAMNKAAMMLVQGKKITDGMDLGIPGYNKVTV 307 >gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 59.3 bits (142), Expect = 4e-10, Method: Compositional matrix adjust. Identities = 79/313 (25%), Positives = 144/313 (46%), Gaps = 34/313 (10%) Query: 3 KRRALNIALGLSFAFGASGIAQAQEIYIPLVSKGFQH----QFWQ-----AVKAGANQAA 53 KRRAL + + + G+S ++ ++ GF W+ ++K A QA Sbjct: 4 KRRAL-LGAAICLSLGSSAMSLPAFAADKPLTMGFSQVGAESEWRTANTVSIKDAAKQAG 62 Query: 54 TDYKVKVTFEGPETEAMVDKQIDMLSAALAKKPQAIGFAALDSKAALPLLKKAQAAKIPV 113 + K + + + Q+ + + +A+K I F+ + +L++A+AAKIPV Sbjct: 63 VNLKF------ADAQQKQENQVKAIRSFIAQKVDVIAFSPVVESGWETVLREAKAAKIPV 116 Query: 114 IAFDSGV---DSDIPVTTTTTD----NKAAAALAADKMAELIGKEGEVAVVAHDQT--SR 164 I D V D + VT +D + A +K + G++ +V T S Sbjct: 117 ILTDRAVNVSDKSLYVTFIGSDFVEEGRRAGRWLLEKAKSM--PAGDINIVELQGTVGSA 174 Query: 165 TGIDRRDGFVDRMKSAYPKIKIVSIQYGAGDQLKSTEVTKSILQAY-PKLKGAFGTNEGS 223 IDR+ GF + +K P++KI+ Q G + K EV ++ L+A K+ + N+ Sbjct: 175 PAIDRKAGFEEVIK-GEPRLKIIRSQTGDFTRAKGKEVMEAFLKAEGKKINVLYAHNDDM 233 Query: 224 AIGVLNGARE--MK--RKVVIIGFDSGKQQKDAIRDGQMAGAITQNPVGIGYKTVEAAVK 279 AIG + E MK + ++II D K +A+ G++ + +P+ +G + ++ A Sbjct: 234 AIGAIQAIEEAGMKPGKDIIIISIDGVKGAFEAMMAGKLNVTVECSPL-LGPQLMQIAKD 292 Query: 280 ALKGEKLPKIIDT 292 G+++PK I T Sbjct: 293 IKAGKEVPKRITT 305 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 0.316 0.132 0.364 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: 824,800 Number of extensions: 30433 Number of successful extensions: 126 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 120 Number of HSP's successfully gapped: 8 Length of query: 313 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 228 Effective length of database: 1,217,395 Effective search space: 277566060 Effective search space used: 277566060 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 130 (54.7 bits)