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= 0001.2487.p (314 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasm... 617 e-178 gi|300310384|ref|YP_003774476.1| sugar ABC transporter periplasm... 84 2e-17 gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasm... 68 8e-13 gi|300313729|ref|YP_003777821.1| sugar ABC transporter periplasm... 62 5e-11 gi|300310351|ref|YP_003774443.1| sugar ABC transporter periplasm... 59 6e-10 >gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 617 bits (1592), Expect = e-178, Method: Compositional matrix adjust. Identities = 311/314 (99%), Positives = 312/314 (99%) Query: 1 MNKFTRRHFAIAALACAVLPGAAMAQTPAKPKVALVMKSLANEFFLNMENGARDYQKANA 60 MNKFTRRHFAIAALACAVLPGAAMAQTPAKPKVALVMKSLANEFFLNMENGAR+YQKANA Sbjct: 1 MNKFTRRHFAIAALACAVLPGAAMAQTPAKPKVALVMKSLANEFFLNMENGAREYQKANA 60 Query: 61 GKFDLIANGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVN 120 KFDLIANGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVN Sbjct: 61 SKFDLIANGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVN 120 Query: 121 IDNKLDDAALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQR 180 IDNKLDDAALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQR Sbjct: 121 IDNKLDDAALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQR 180 Query: 181 TLGFQDAMKDVGANVVTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAAI 240 TLGFQDAMKDVGANVVTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAAI Sbjct: 181 TLGFQDAMKDVGANVVTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAAI 240 Query: 241 RAAGKTGKVLLVGYDNINAIKPMLKDGRVLATVDQFAQQQAVFGIETALKALSEKKPQSA 300 RAAGKTGKV LVGYDNINAIKPMLKDGRVLATVDQFAQQQAVFGIETALKALSEKKPQSA Sbjct: 241 RAAGKTGKVQLVGYDNINAIKPMLKDGRVLATVDQFAQQQAVFGIETALKALSEKKPQSA 300 Query: 301 LGGVVETKVSLVTK 314 LGGVVETKVSLVTK Sbjct: 301 LGGVVETKVSLVTK 314 >gi|300310384|ref|YP_003774476.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 312 Score = 83.6 bits (205), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 86/294 (29%), Positives = 140/294 (47%), Gaps = 22/294 (7%) Query: 12 AALACAVLPGAAMAQTPAKPKVALVMKSLANEFFLNMENGA----RDYQKANAGKFDLIA 67 AAL A GA+ AQ + + L+ K ++F+ ++ GA +DY K + Sbjct: 9 AALGLAFAMGASAAQA-QEAYIPLISKGFQHQFWQAVKAGADQAGKDY------KVKVTF 61 Query: 68 NGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVNIDNKLDD 127 G + E QI ++ + K A+ A DSKA +P++KKA A I VV D+ +D Sbjct: 62 EGPETEAMVDKQIDMLSAALAKKPQAIGFAALDSKAAIPLLKKAQAAKIPVVAFDSGVDS 121 Query: 128 AALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQRTLGFQDA 187 I V DNR A LA D + + + K +VA++ T+ R GF + Sbjct: 122 ------DIPVTTATTDNRAAAALAADKMAELVGKEGEVAVVAHDQTSRTGVDRRDGFLER 175 Query: 188 MKDVGA--NVVTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAAIRAAGK 245 +K VV+VQ G + + +V SIL A+P IK I N+ A+G V ++ + Sbjct: 176 IKSAYPKIKVVSVQYGAGDQLKSTEVTKSILQAYPKIKGIFGTNEGSAIGVVNGVKEMKR 235 Query: 246 TGKVLLVGYDNINAIKPMLKDGRVLATVDQFAQQQAVFGIETALKAL-SEKKPQ 298 K++++GYD+ K +++G + + Q +E A+KA+ EK P+ Sbjct: 236 --KIIIIGYDSGKQQKDAIREGIMAGAITQNPVGIGYKTVEAAVKAIKGEKLPK 287 >gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 302 Score = 68.2 bits (165), Expect = 8e-13, Method: Compositional matrix adjust. Identities = 74/270 (27%), Positives = 126/270 (46%), Gaps = 20/270 (7%) Query: 24 MAQTPAKPKVALVMKSLANEFFLNMENGARDYQKANAGKFDLIANGIKDEQDTANQIKIV 83 MAQ +K K+ + + + N +F++M+ + K+ K +IA + A QI + Sbjct: 19 MAQEVSKLKIGMSFQEMNNPYFVSMKKALDEAAKSLGAK--VIAT--DAAHNVAKQIADI 74 Query: 84 EQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVNIDNKLDDAALKEKGITVPFVGPD 143 E M+ ++ L+I P DS + VK A +IVV +D G FVG Sbjct: 75 EDMLQQNIDILLINPTDSAGVEAAVKAAKARNVIVVAVD-------ANASGPVDMFVGSK 127 Query: 144 NRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQRTLGFQDAM---KDVGANVVTVQS 200 N+ + L + +VAI++G+ QR G + A+ KD+ +V Q+ Sbjct: 128 NKDAGYQSCRALADAIGGKGEVAILDGIPVV-PILQRVEGCKQALAEYKDI--KLVATQN 184 Query: 201 GQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAAIRAAGKTGKVLLVGYDNI-NA 259 G+ + V +++ + P++K I + ND A+GA+AAI+ +GK + L D A Sbjct: 185 GRQDRSVALGVVENMIQSRPNLKGIFSVNDGGAMGALAAIQGSGKD--IKLTSVDGAPEA 242 Query: 260 IKPMLKDGRVLATVDQFAQQQAVFGIETAL 289 +K + G + T QF + Q G+ AL Sbjct: 243 VKAIADGGPFVETTAQFPRDQVRVGLAMAL 272 >gi|300313729|ref|YP_003777821.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 62.4 bits (150), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 76/261 (29%), Positives = 120/261 (45%), Gaps = 46/261 (17%) Query: 30 KPKVALVMKSLANEFFLNMENGARDYQKANAGKFDLIANGIKDEQDTANQIKIVEQMIVS 89 K ++A+V+KSL N FF GA++ + G ++I G QI+IV +I Sbjct: 38 KVRIAMVVKSLGNGFFDAAHEGAKEAAR-ELGDVEVIYTG-PTTPTAEGQIEIVNSLISQ 95 Query: 90 KVNALVIAPADSKALVPVVKKAIDAGIIVVNIDNKLDDAALKEKGITVPFVGPDNRKGAK 149 KV+A+VI+ D+ ALVP+ K+A+ G+ V++ D+ + KG + + P N A+ Sbjct: 96 KVDAIVISANDANALVPITKRAMQRGVKVLSFDSGI------AKGGRLMQLNPSN---AE 146 Query: 150 LAGDYLGKQLQ--------KGDKVAIIEGVSTTFNAQQRTLGFQDAMKDVG------ANV 195 L G KQ+Q GD VAI+ S T A + + + K + + Sbjct: 147 LIGL---KQIQMAAEAIGGAGD-VAIL---SATAQATNQNIWIGEMKKALARPEFSRMKL 199 Query: 196 VTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAAIRAAGK-------TGK 248 V G + D+ + A +L +HP +KAI+A I AAGK GK Sbjct: 200 VATVYGDDQSDKSYREAIGLLRSHPGLKAIIAPT-------TVGINAAGKAVVDEKLVGK 252 Query: 249 VLLVGYDNINAIKPMLKDGRV 269 V + G + + +K G V Sbjct: 253 VYVTGLGLPSEMAGHVKSGAV 273 >gi|300310351|ref|YP_003774443.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 335 Score = 58.5 bits (140), Expect = 6e-10, Method: Compositional matrix adjust. Identities = 71/249 (28%), Positives = 105/249 (42%), Gaps = 18/249 (7%) Query: 11 IAALACAVLPGAAMAQTPAKP-KVALVMKSLANEFFLNMENGARDYQKANAGKFDLIANG 69 ++ALA A AQ KP + V+K +F ME G +++ AN G + Sbjct: 11 VSALAAVGFASALQAQN--KPIDIVTVVKITGISWFNRMEVGVKEFAAANPG---VTTRQ 65 Query: 70 IKDEQ-DTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVNIDNKLDDA 128 I Q D A Q ++VE ++ KV+A+ + D L PV+K+A+D GI VV + Sbjct: 66 IGPAQSDAAQQQRLVEDLVAKKVDAIAVVSMDPPTLEPVLKRALDRGIKVVTHE------ 119 Query: 129 ALKEKGITVPFVGPDNR-KGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQRTLGFQDA 187 A +K V DN GA+L Q G +++ + + Q G +A Sbjct: 120 ADNQKNTLVDIEAFDNTAYGARLNDRLAACMGQAGKWSSLVGSLGSQSQVQWADGGAANA 179 Query: 188 MKDVGANVVTVQSGQWEIDQGNKVAA---SILNAHPDIKAILAGNDNMALGAVAAIRAAG 244 K + V + + K A IL HPDIK + LG A+ AG Sbjct: 180 AKKY-PKMTLVDAKNESANDAEKAYAKAKEILRKHPDIKGFQGSSSLDVLGIGRAVEEAG 238 Query: 245 KTGKVLLVG 253 GKV + G Sbjct: 239 LQGKVCVYG 247 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 0.359 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: 802,939 Number of extensions: 30289 Number of successful extensions: 167 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 158 Number of HSP's successfully gapped: 8 Length of query: 314 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 229 Effective length of database: 1,217,395 Effective search space: 278783455 Effective search space used: 278783455 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)