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= 0011.0248.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... 629 0.0 gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasm... 129 3e-31 gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasm... 75 5e-15 gi|300310384|ref|YP_003774476.1| sugar ABC transporter periplasm... 70 3e-13 gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasm... 68 9e-13 >gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 316 Score = 629 bits (1621), Expect = 0.0, Method: Compositional matrix adjust. Identities = 316/316 (100%), Positives = 316/316 (100%) Query: 1 MIKNTIAIACSTLLLAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINP 60 MIKNTIAIACSTLLLAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINP Sbjct: 1 MIKNTIAIACSTLLLAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINP 60 Query: 61 DAKVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDV 120 DAKVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDV Sbjct: 61 DAKVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDV 120 Query: 121 AAAGADVTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKSP 180 AAAGADVTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKSP Sbjct: 121 AAAGADVTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKSP 180 Query: 181 GIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIKW 240 GIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIKW Sbjct: 181 GIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIKW 240 Query: 241 ISGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLPVKL 300 ISGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLPVKL Sbjct: 241 ISGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLPVKL 300 Query: 301 ITRDNVADYQGWVPAK 316 ITRDNVADYQGWVPAK Sbjct: 301 ITRDNVADYQGWVPAK 316 >gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 302 Score = 129 bits (324), Expect = 3e-31, Method: Compositional matrix adjust. Identities = 96/295 (32%), Positives = 164/295 (55%), Gaps = 16/295 (5%) Query: 23 MAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPDAKVTVVSSKYDLNTQVGQIEN 82 MA + +G++ ++ NP+FV++ K + A + AKV + +++ Q+ IE+ Sbjct: 19 MAQEVSKLKIGMSFQEMNNPYFVSMKKALDEAAKSLG--AKVIATDAAHNVAKQIADIED 76 Query: 83 FIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDVAAAG-ADVTVMSDNTMAGAESC 141 + +D++++N DS GV AVK A+ ++VVAVD A+G D+ V S N AG +SC Sbjct: 77 MLQQNIDILLINPTDSAGVEAAVKAAKARNVIVVAVDANASGPVDMFVGSKNKDAGYQSC 136 Query: 142 KFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKSPGIKILSDNQNAGGSRDGGMTT 201 + LA+ + GKG V I++G PV ++ RV GCK + IK+++ QN R + Sbjct: 137 RALADAIGGKGEVAILDGIPVVPILQRVEGCKQALAEYKDIKLVA-TQNGRQDRSVALGV 195 Query: 202 MSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIKWISGVDGAPDAERALKDSKSLF 261 + N++ ++P + +F++ND A+GA AI Q DIK ++ VDGAP+A +A+ D F Sbjct: 196 VENMIQSRPNLKGIFSVNDGGAMGALAAI-QGSGKDIK-LTSVDGAPEAVKAIADGGP-F 252 Query: 262 AASPAQDPYGMAAESVAIGYAVMNGRAPQQKV--KLLPVKL--ITRDNVADYQGW 312 + AQ P + V +G A+ + +V K +P+ + +T+ N A + W Sbjct: 253 VETTAQFPR----DQVRVGLAMALAKKWGARVVPKEVPIDVMPVTKKNAAGFS-W 302 >gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 75.5 bits (184), Expect = 5e-15, Method: Compositional matrix adjust. Identities = 81/265 (30%), Positives = 125/265 (47%), Gaps = 18/265 (6%) Query: 7 AIACSTLLLAAAAQ-PAMAADKPLKSVGVTVGDLANPFFVAIAKGAES--GAHKINPDAK 63 A+AC+ L AA AQ PA KP V + + LAN FF+ + GA A+ D Sbjct: 13 ALACAVLPGAAMAQTPA----KP--KVALVMKSLANEFFLNMENGAREYQKANASKFDLI 66 Query: 64 VTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVD---- 119 + + D Q+ +E I +KV+ +V+ ADSK + P VKKA AGI+VV +D Sbjct: 67 ANGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVNIDNKLD 126 Query: 120 ---VAAAGADVTVMSDNTMAGAE-SCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAE 175 + G V + + GA+ + +L ++LQ V I+ G + + T + Sbjct: 127 DAALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQRTLGFQD 186 Query: 176 FKKSPGIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKR 235 K G +++ Q+ D G +++L A P I A+ A ND A+GA AIR A + Sbjct: 187 AMKDVGANVVT-VQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAAIRAAGK 245 Query: 236 SDIKWISGVDGAPDAERALKDSKSL 260 + + G D + LKD + L Sbjct: 246 TGKVQLVGYDNINAIKPMLKDGRVL 270 >gi|300310384|ref|YP_003774476.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 312 Score = 69.7 bits (169), Expect = 3e-13, Method: Compositional matrix adjust. Identities = 87/290 (30%), Positives = 131/290 (45%), Gaps = 30/290 (10%) Query: 1 MIKNTIAIACSTLLLAAAAQPAMAADK--PLKSVGVTVGDLANPFFVAIAKGAESGAHKI 58 M KN + A L A A A A + PL S G + F+ A+ ++GA + Sbjct: 1 MFKNKLLGAALGLAFAMGASAAQAQEAYIPLISKG-----FQHQFWQAV----KAGADQA 51 Query: 59 NPDAKVTVV----SSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIV 114 D KV V ++ ++ Q+ + +A K I A DSK P +KKAQ A I Sbjct: 52 GKDYKVKVTFEGPETEAMVDKQIDMLSAALAKKPQAIGFAALDSKAAIPLLKKAQAAKIP 111 Query: 115 VVAVDVAAAGAD-----VTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAV-MDR 168 VVA D +G D T +DN A A + +AE + +G V +V S +DR Sbjct: 112 VVAFD---SGVDSDIPVTTATTDNRAAAALAADKMAELVGKEGEVAVVAHDQTSRTGVDR 168 Query: 169 VTGCKAEFKKS-PGIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAE 227 G K + P IK++S AG T S +L A PKI +F N+ +AIG Sbjct: 169 RDGFLERIKSAYPKIKVVSVQYGAGDQLKSTEVTKS-ILQAYPKIKGIFGTNEGSAIGVV 227 Query: 228 LAIRQAKRSDIKWISGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESV 277 +++ KR I I G D + A+++ + A + Q+P G+ ++V Sbjct: 228 NGVKEMKRKII--IIGYDSGKQQKDAIRE--GIMAGAITQNPVGIGYKTV 273 >gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 68.2 bits (165), Expect = 9e-13, Method: Compositional matrix adjust. Identities = 79/257 (30%), Positives = 120/257 (46%), Gaps = 20/257 (7%) Query: 10 CSTLLLAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPDAKVTVVSS 69 C +L +A + PA AADKPL ++G + + + A + A + + K Sbjct: 14 CLSLGSSAMSLPAFAADKPL-TMGFSQVGAESEWRTANTVSIKDAAKQAGVNLKFADAQQ 72 Query: 70 KYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDVAAAGADVTV 129 K + QV I +FIA KVD+I + G +++A+ A I V+ D A +D ++ Sbjct: 73 KQE--NQVKAIRSFIAQKVDVIAFSPVVESGWETVLREAKAAKIPVILTDRAVNVSDKSL 130 Query: 130 M-----SDNTMAGAESCKFLAEKLQ----GKGNVVIVNGPPVSA-VMDRVTGCKAEFKKS 179 SD G + ++L EK + G N+V + G SA +DR G + K Sbjct: 131 YVTFIGSDFVEEGRRAGRWLLEKAKSMPAGDINIVELQGTVGSAPAIDRKAGFEEVIKGE 190 Query: 180 PGIKILSDNQNAGGSRDGGMTTMSNLLAAQ-PKIDAVFAINDPTAIGAELAIRQA----- 233 P +KI+ +Q +R G M L A+ KI+ ++A ND AIGA AI +A Sbjct: 191 PRLKIIR-SQTGDFTRAKGKEVMEAFLKAEGKKINVLYAHNDDMAIGAIQAIEEAGMKPG 249 Query: 234 KRSDIKWISGVDGAPDA 250 K I I GV GA +A Sbjct: 250 KDIIIISIDGVKGAFEA 266 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 0.129 0.360 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: 875,675 Number of extensions: 33014 Number of successful extensions: 129 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 122 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 (22.0 bits) S2: 130 (54.7 bits)