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= 0001.0257.p (412 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309614|ref|YP_003773706.1| sugar ABC transporter periplasm... 777 0.0 gi|300313831|ref|YP_003777923.1| sugar ABC transporter periplasm... 65 1e-11 gi|300313992|ref|YP_003778084.1| extracellular solute-binding, f... 64 3e-11 >gi|300309614|ref|YP_003773706.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 415 Score = 777 bits (2006), Expect = 0.0, Method: Compositional matrix adjust. Identities = 383/412 (92%), Positives = 399/412 (96%) Query: 1 MIRMTVIAGCLAASAAWSAAAMAGTLAVNIAYKGAVQRNVWQSTVDEFKKANPDVDVKVS 60 MIRM VIAGCLAA+AAW+ AA AGTLA+NIAYKGAVQR VWQST+DEFKKANPDVD+K S Sbjct: 4 MIRMGVIAGCLAATAAWNTAATAGTLAINIAYKGAVQRAVWQSTMDEFKKANPDVDIKPS 63 Query: 61 FMEEEAYKVQLPGWLSTQAPDIINWHNGERMAFYASRGLLEDLSEDWKKNGWDSTYASTK 120 F+EEEAYKVQLPGWLSTQAPDIINWHNGERMAFYASRGLLED+SEDWKKNGWD+TYASTK Sbjct: 64 FIEEEAYKVQLPGWLSTQAPDIINWHNGERMAFYASRGLLEDVSEDWKKNGWDATYASTK 123 Query: 121 EASSWQGKQYSAPTVYYSWGMFYRKDLFKKVGIASEPKTWDEFLEACKKLKAAGIAPVAV 180 EASSW GKQYS PTVYYSWGMFYRKDLFKKVGIA EPKTWDEFL+ACKKLKAAGIAP+AV Sbjct: 124 EASSWHGKQYSVPTVYYSWGMFYRKDLFKKVGIAGEPKTWDEFLDACKKLKAAGIAPIAV 183 Query: 181 GGRDAWTLAGWFDYLDLRINGNAFHQQLMAGDIAYTDPRVKKVYTTWKSLIDNKIFIDNA 240 GGRDAWTLAGWFDYLDLRINGNAFHQQLMAGDIAYTD RVKKV+T WKSLIDNK FIDNA Sbjct: 184 GGRDAWTLAGWFDYLDLRINGNAFHQQLMAGDIAYTDARVKKVHTAWKSLIDNKYFIDNA 243 Query: 241 LSYDLDGAQPFLFQGKAAMMLMGTFIAKGFPAKLAPEMGYFQFPIIDANVPTAEEGPTES 300 LSYDLDGAQPFLFQGKAAMMLMGTFIAKGFPAKLAPEMGYFQFPIIDANVPTAEEGPTES Sbjct: 244 LSYDLDGAQPFLFQGKAAMMLMGTFIAKGFPAKLAPEMGYFQFPIIDANVPTAEEGPTES 303 Query: 301 IHIPAKARNKADAHRFIAFVGTPAISAKLAEGLGSLPANSKSPAPADPISRIGFDILSNA 360 IHIPAKARNKADA RFIAFVGTPAISAKLAEGLGSLPANSKSPAP +PISRIGF+ILSNA Sbjct: 304 IHIPAKARNKADARRFIAFVGTPAISAKLAEGLGSLPANSKSPAPTEPISRIGFEILSNA 363 Query: 361 KGGISQFYDRDMTKEMADEGMKGMQKFVSDPSKLDDVLNELEQSRKRIYKKS 412 KGGISQFYDRDMTKEMADEGMKGMQKFVSDP+++DDVLNELEQSRKRIYKKS Sbjct: 364 KGGISQFYDRDMTKEMADEGMKGMQKFVSDPTRIDDVLNELEQSRKRIYKKS 415 >gi|300313831|ref|YP_003777923.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 446 Score = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 58/210 (27%), Positives = 103/210 (49%), Gaps = 32/210 (15%) Query: 75 LSTQAPDIINWHNGERMAFYASRGLLEDLSE-----DWKKNGWDSTYASTKEASSWQGKQ 129 L+ +AP++ NG +A GLL +L +W+K + + ++ G Sbjct: 105 LANRAPEVTQL-NGVVFGEWADLGLLLELDNVAVQGNWEKQMFPTVWSLLNN----HGHV 159 Query: 130 YSAPT-VYYSWGMFYRKDLFKKVGIASEPKTWDEFLEACKKLKAAGIAPVAVGGRDAWTL 188 +AP ++ ++Y +FK+ + S PKTWDEF + KKL+ +G+ P+A +AW L Sbjct: 160 VAAPLGIHRINSLYYNVAVFKRYNL-SPPKTWDEFDQIVKKLQGSGVVPLAQSA-EAWQL 217 Query: 189 AGWFDYLDLRINGNAFHQQLMA--GDIAYTDPRVKKVYTTWKSL-------IDNKIFIDN 239 A F+ L L +G A++++L AY D R+ + ++L + + + + Sbjct: 218 ATLFENLALAESGPAYYRKLFVEMSPAAYLDARMLHILKRLRALAGAMAQPVRERPWTEV 277 Query: 240 ALSYDLDGAQPFLFQGKAAMMLMGTFIAKG 269 A S + G+AAM++MG + AKG Sbjct: 278 ARS---------MVSGEAAMLIMGDW-AKG 297 >gi|300313992|ref|YP_003778084.1| extracellular solute-binding, family 1 protein [Herbaspirillum seropedicae SmR1] Length = 473 Score = 63.5 bits (153), Expect = 3e-11, Method: Compositional matrix adjust. Identities = 69/287 (24%), Positives = 127/287 (44%), Gaps = 10/287 (3%) Query: 42 QSTVDEFKKANPDVDVKVSFMEEEAYKVQL-PGWLSTQAPDIINWHNGERMAFYASRGLL 100 Q D F +P V + + FM + + L P + PDI++ + A A +GLL Sbjct: 92 QRVCDGFMHEHPGVRINLQFMIGNSVEENLKPRATTDSLPDIVSVNASPYTASLADQGLL 151 Query: 101 EDLSEDWKKNGWDSTYASTKEASSWQGKQYSAPTVYYSWGMFYRKDLFKKVGIASEPKTW 160 DL + +G +E ++ G ++ P+ + ++Y DLF++ GI + P + Sbjct: 152 ADLGQTRSWHGLLDIL--QREWTAPGGCRFGLPSGVATTLIYYHPDLFERAGIQALPGDF 209 Query: 161 DEFLEACKKLKAAGIAPVAVGGRDAWTLA-GWFDYLDLRINGNA---FHQQLMAGDIAYT 216 ++FL A L+ AGI P+A+ G L G F Y + ++ + Q + G +A Sbjct: 210 EQFLAAGAALRRAGITPLALSGGFPNMLGNGPFSYGFANLVASSTPDWRQHIANGTLALD 269 Query: 217 DPRVKKVYTTWKSLIDNKIFIDNALSYDLDGAQPFLFQGKAAMMLMGTFIAKGFPAKLAP 276 + + V++ ++L+ + + L D +G+AAM G++ A Sbjct: 270 NAQGWAVFSRLRTLMTRHLVQADCLRAGYDATLRQFAEGRAAMTFQGSWAAGVLMQGRGQ 329 Query: 277 EMGYFQFPIIDANVPTAEEGPTES---IHIPAKARNKADAHRFIAFV 320 +G F P D + P +E+ I AR++ A RF+ ++ Sbjct: 330 PVGVFVPPWNDKDQPRQAVIGSETGFAIAQRISARHRQAAARFLDYL 376 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 0.317 0.132 0.403 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: 1,276,289 Number of extensions: 55403 Number of successful extensions: 177 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 175 Number of HSP's successfully gapped: 4 Length of query: 412 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 324 Effective length of database: 1,203,190 Effective search space: 389833560 Effective search space used: 389833560 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 (21.7 bits) S2: 132 (55.5 bits)