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= 0001.0012.p (334 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310351|ref|YP_003774443.1| sugar ABC transporter periplasm... 667 0.0 gi|300313729|ref|YP_003777821.1| sugar ABC transporter periplasm... 114 1e-26 gi|300310384|ref|YP_003774476.1| sugar ABC transporter periplasm... 68 1e-12 gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasm... 56 4e-09 >gi|300310351|ref|YP_003774443.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 335 Score = 667 bits (1722), Expect = 0.0, Method: Compositional matrix adjust. Identities = 328/334 (98%), Positives = 332/334 (99%) Query: 1 MNKKSACVLGSALAAIGFASALQAQNKPIDIVTVVKITGISWFNRMEVGVKEFAAANPGV 60 MNKKSACVL SALAA+GFASALQAQNKPIDIVTVVKITGISWFNRMEVGVKEFAAANPGV Sbjct: 2 MNKKSACVLVSALAAVGFASALQAQNKPIDIVTVVKITGISWFNRMEVGVKEFAAANPGV 61 Query: 61 TTRQIGPAQSDAAQQQRLVEDLVAKKVDAIAVVSMDPPTLEPVLKRALDRGIKVVTHEAD 120 TTRQIGPAQSDAAQQQRLVEDLVAKKVDAIAVVSMDPPTLEPVLKRALDRGIKVVTHEAD Sbjct: 62 TTRQIGPAQSDAAQQQRLVEDLVAKKVDAIAVVSMDPPTLEPVLKRALDRGIKVVTHEAD 121 Query: 121 NQKNTLVDIEAFDNTAYGARLNDRLAACMGETGKWSSLVGSLGSQSQVQWADGGASNAAK 180 NQKNTLVDIEAFDNTAYGARLNDRLAACMG+ GKWSSLVGSLGSQSQVQWADGGA+NAAK Sbjct: 122 NQKNTLVDIEAFDNTAYGARLNDRLAACMGQAGKWSSLVGSLGSQSQVQWADGGAANAAK 181 Query: 181 KYPKMTLVDAKNESANDAEKAYAKAKEILRKHPDIKGFQGSSSLDVLGIGRAVEEAGLQG 240 KYPKMTLVDAKNESANDAEKAYAKAKEILRKHPDIKGFQGSSSLDVLGIGRAVEEAGLQG Sbjct: 182 KYPKMTLVDAKNESANDAEKAYAKAKEILRKHPDIKGFQGSSSLDVLGIGRAVEEAGLQG 241 Query: 241 KVCVYGTGLPSEAAKFLESGAVGGIAFWDPKDAGLAMNKAAMMLVQGKKITDGMDLGIPG 300 KVCVYGTGLPSEAAKFLESGAVGGIAFWDPKDAGLAMNKAAMMLVQGKKITDGMDLGIPG Sbjct: 242 KVCVYGTGLPSEAAKFLESGAVGGIAFWDPKDAGLAMNKAAMMLVQGKKITDGMDLGIPG 301 Query: 301 YNKVSVKKGPGVGVIVTGQAWVEVDKKNYKQYAF 334 YNKV+VKKGPGVGVIVTGQAWVEVDKKNYKQYAF Sbjct: 302 YNKVTVKKGPGVGVIVTGQAWVEVDKKNYKQYAF 335 >gi|300313729|ref|YP_003777821.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 114 bits (285), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 84/262 (32%), Positives = 131/262 (50%), Gaps = 3/262 (1%) Query: 29 IDIVTVVKITGISWFNRMEVGVKEFAAANPGVTTRQIGPAQSDAAQQQRLVEDLVAKKVD 88 + I VVK G +F+ G KE A V GP A Q +V L+++KVD Sbjct: 39 VRIAMVVKSLGNGFFDAAHEGAKEAARELGDVEVIYTGPTTPTAEGQIEIVNSLISQKVD 98 Query: 89 AIAVVSMDPPTLEPVLKRALDRGIKVVTHEADNQKN-TLVDIEAFDNTAYGARLNDRLAA 147 AI + + D L P+ KRA+ RG+KV++ ++ K L+ + + G + A Sbjct: 99 AIVISANDANALVPITKRAMQRGVKVLSFDSGIAKGGRLMQLNPSNAELIGLKQIQMAAE 158 Query: 148 CMGETGKWSSLVGSLGSQSQVQW-ADGGASNAAKKYPKMTLVDAKNESANDAEKAYAKAK 206 +G G + L + + +Q W + + A ++ +M LV A + ++K+Y +A Sbjct: 159 AIGGAGDVAILSATAQATNQNIWIGEMKKALARPEFSRMKLV-ATVYGDDQSDKSYREAI 217 Query: 207 EILRKHPDIKGFQGSSSLDVLGIGRAVEEAGLQGKVCVYGTGLPSEAAKFLESGAVGGIA 266 +LR HP +K +++ + G+AV + L GKV V G GLPSE A ++SGAV A Sbjct: 218 GLLRSHPGLKAIIAPTTVGINAAGKAVVDEKLVGKVYVTGLGLPSEMAGHVKSGAVKSFA 277 Query: 267 FWDPKDAGLAMNKAAMMLVQGK 288 W+P D G A AA V+GK Sbjct: 278 IWNPIDLGYAATYAAYQFVKGK 299 >gi|300310384|ref|YP_003774476.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 312 Score = 68.2 bits (165), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 59/233 (25%), Positives = 108/233 (46%), Gaps = 3/233 (1%) Query: 74 QQQRLVEDLVAKKVDAIAVVSMDPPTLEPVLKRALDRGIKVVTHEADNQKNTLVDIEAFD 133 +Q ++ +AKK AI ++D P+LK+A I VV ++ + V D Sbjct: 72 KQIDMLSAALAKKPQAIGFAALDSKAAIPLLKKAQAAKIPVVAFDSGVDSDIPVTTATTD 131 Query: 134 NTAYGARLNDRLAACMGETGKWSSLVGSLGSQSQVQWADGGASNAAKKYPKMTLVDAKNE 193 N A A D++A +G+ G+ + + S++ V DG YPK+ +V + Sbjct: 132 NRAAAALAADKMAELVGKEGEVAVVAHDQTSRTGVDRRDGFLERIKSAYPKIKVVSVQY- 190 Query: 194 SANDAEKAYAKAKEILRKHPDIKGFQGSSSLDVLGIGRAVEEAGLQGKVCVYGTGLPSEA 253 A D K+ K IL+ +P IKG G++ +G+ V+E ++ K+ + G + Sbjct: 191 GAGDQLKSTEVTKSILQAYPKIKGIFGTNEGSAIGVVNGVKE--MKRKIIIIGYDSGKQQ 248 Query: 254 AKFLESGAVGGIAFWDPKDAGLAMNKAAMMLVQGKKITDGMDLGIPGYNKVSV 306 + G + G +P G +AA+ ++G+K+ +D G Y+K ++ Sbjct: 249 KDAIREGIMAGAITQNPVGIGYKTVEAAVKAIKGEKLPKVIDTGFYWYDKSNI 301 >gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 56.2 bits (134), Expect = 4e-09, Method: Compositional matrix adjust. Identities = 76/274 (27%), Positives = 113/274 (41%), Gaps = 49/274 (17%) Query: 1 MNK---KSACVLGSALAAIGFASALQAQNKPIDIVTVVKITGISWFNRMEVGVKEFAAAN 57 MNK + + A A + A+ Q KP + V+K +F ME G +E+ AN Sbjct: 1 MNKFTRRHFAIAALACAVLPGAAMAQTPAKP-KVALVMKSLANEFFLNMENGAREYQKAN 59 Query: 58 P--------GVTTRQIGPAQSDAAQQQRLVEDLVAKKVDAIAVVSMDPPTLEPVLKRALD 109 G+ Q D A Q ++VE ++ KV+A+ + D L PV+K+A+D Sbjct: 60 ASKFDLIANGIKDEQ------DTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAID 113 Query: 110 RGIKVVTHE------ADNQKNTLVDIEAFDNTAYGARL-----------NDRLAACMGET 152 GI VV + A +K V DN GA+L D++A G + Sbjct: 114 AGIIVVNIDNKLDDAALKEKGITVPFVGPDNR-KGAKLAGDYLGKQLQKGDKVAIIEGVS 172 Query: 153 GKWSSLVGSLGSQSQVQWADGGASNAAKKYPKMTLVDAKNESANDAEKAYAKAKEILRKH 212 +++ +LG Q ++ D GA N +D N+ A IL H Sbjct: 173 TTFNAQQRTLGFQDAMK--DVGA-NVVTVQSGQWEIDQGNKV----------AASILNAH 219 Query: 213 PDIKGFQGSSSLDVLGIGRAVEEAGLQGKVCVYG 246 PDIK + LG A+ AG GKV + G Sbjct: 220 PDIKAILAGNDNMALGAVAAIRAAGKTGKVQLVG 253 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 0.314 0.130 0.373 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: 956,856 Number of extensions: 37885 Number of successful extensions: 129 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 128 Number of HSP's successfully gapped: 4 Length of query: 334 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 248 Effective length of database: 1,212,660 Effective search space: 300739680 Effective search space used: 300739680 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 (22.0 bits) S2: 131 (55.1 bits)