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= 0001.0067.p (323 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasm... 540 e-155 gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasm... 120 2e-28 gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasm... 74 1e-14 gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter peripl... 73 2e-14 gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasm... 64 2e-11 >gi|300310395|ref|YP_003774487.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 302 Score = 540 bits (1391), Expect = e-155, Method: Compositional matrix adjust. Identities = 277/283 (97%), Positives = 280/283 (98%) Query: 41 AQELSKLKIGMSFQEMNNPYFVSMKKALDDAAKSFGAKVIVTDAAHNVAKQIADIEDMLQ 100 AQE+SKLKIGMSFQEMNNPYFVSMKKALD+AAKS GAKVI TDAAHNVAKQIADIEDMLQ Sbjct: 20 AQEVSKLKIGMSFQEMNNPYFVSMKKALDEAAKSLGAKVIATDAAHNVAKQIADIEDMLQ 79 Query: 101 QNIDILLINPTDSAGVEAAVKAAKARNVIVVAVDANASGPVDMFVGSKNKDAGYQSCRAL 160 QNIDILLINPTDSAGVEAAVKAAKARNVIVVAVDANASGPVDMFVGSKNKDAGYQSCRAL Sbjct: 80 QNIDILLINPTDSAGVEAAVKAAKARNVIVVAVDANASGPVDMFVGSKNKDAGYQSCRAL 139 Query: 161 ADAIGGKGEVAILDGIPVVPILQRVEGCKQALGEYKDIKLVATQNGRQDRSVALGVVENM 220 ADAIGGKGEVAILDGIPVVPILQRVEGCKQAL EYKDIKLVATQNGRQDRSVALGVVENM Sbjct: 140 ADAIGGKGEVAILDGIPVVPILQRVEGCKQALAEYKDIKLVATQNGRQDRSVALGVVENM 199 Query: 221 IQSRPNLKGIFSVNDGGAMGALAAIQGSGKDIKLTSVDGAPEAVKAIADGGPFIETTAQF 280 IQSRPNLKGIFSVNDGGAMGALAAIQGSGKDIKLTSVDGAPEAVKAIADGGPF+ETTAQF Sbjct: 200 IQSRPNLKGIFSVNDGGAMGALAAIQGSGKDIKLTSVDGAPEAVKAIADGGPFVETTAQF 259 Query: 281 PRDQVRVGLAMALAKKWGARVVPKEVPIDVMPVTKKNAAGFSW 323 PRDQVRVGLAMALAKKWGARVVPKEVPIDVMPVTKKNAAGFSW Sbjct: 260 PRDQVRVGLAMALAKKWGARVVPKEVPIDVMPVTKKNAAGFSW 302 >gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 316 Score = 120 bits (300), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 103/317 (32%), Positives = 170/317 (53%), Gaps = 16/317 (5%) Query: 18 MKKALTALALSTATLVAFTAPASAQELSKLKIGMSFQEMNNPYFVSMKKALDDAAKSFG- 76 M K A+A ST L A PA A + +G++ ++ NP+FV++ K + A Sbjct: 1 MIKNTIAIACSTLLLAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINP 60 Query: 77 -AKVIVTDAAHNVAKQIADIEDMLQQNIDILLINPTDSAGVEAAVKAAKARNVIVVAVDA 135 AKV V + +++ Q+ IE+ + +D++++N DS GV AVK A+ + IVV Sbjct: 61 DAKVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQ-KAGIVVVAVD 119 Query: 136 NASGPVDMFVGSKNKDAGYQSCRALADAIGGKGEVAILDGIPVVPILQRVEGCKQALGEY 195 A+ D+ V S N AG +SC+ LA+ + GKG V I++G PV ++ RV GCK + Sbjct: 120 VAAAGADVTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKS 179 Query: 196 KDIKLVA-TQNGRQDRSVALGVVENMIQSRPNLKGIFSVNDGGAMGA-LAAIQGSGKDIK 253 IK+++ QN R + + N++ ++P + +F++ND A+GA LA Q DIK Sbjct: 180 PGIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIK 239 Query: 254 -LTSVDGAPEAVKAIADGGP-FIETTAQFPR----DQVRVGLAMALAKKWGARVVPKEVP 307 ++ VDGAP+A +A+ D F + AQ P + V +G A+ + +V K +P Sbjct: 240 WISGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKV--KLLP 297 Query: 308 IDVMPVTKKNAAGFS-W 323 + + +T+ N A + W Sbjct: 298 VKL--ITRDNVADYQGW 312 >gi|300311608|ref|YP_003775700.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 314 Score = 74.3 bits (181), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 77/296 (26%), Positives = 136/296 (45%), Gaps = 23/296 (7%) Query: 14 METAMKKALTALALSTATLVAFTAPASAQELSKLKIGMSFQEMNNPYFVSMKKALDDAAK 73 M ++ AL+ A L A AQ +K K+ + + + N +F++M+ + K Sbjct: 1 MNKFTRRHFAIAALACAVL---PGAAMAQTPAKPKVALVMKSLANEFFLNMENGAREYQK 57 Query: 74 SFGAKV-IVTDA---AHNVAKQIADIEDMLQQNIDILLINPTDSAGVEAAVKAAKARNVI 129 + +K ++ + + A QI +E M+ ++ L+I P DS + VK A +I Sbjct: 58 ANASKFDLIANGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGII 117 Query: 130 VVAVD-------ANASGPVDMFVGSKNKDAGYQSCRALADAIGGKGEVAILDGIPVV-PI 181 VV +D G FVG N+ + L + +VAI++G+ Sbjct: 118 VVNIDNKLDDAALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNA 177 Query: 182 LQRVEGCKQALGEYKDI--KLVATQNGRQDRSVALGVVENMIQSRPNLKGIFSVNDGGAM 239 QR G + A+ KD+ +V Q+G+ + V +++ + P++K I + ND A+ Sbjct: 178 QQRTLGFQDAM---KDVGANVVTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMAL 234 Query: 240 GALAAIQGSGK--DIKLTSVDGAPEAVKAIADGGPFIETTAQFPRDQVRVGLAMAL 293 GA+AAI+ +GK ++L D A+K + G + T QF + Q G+ AL Sbjct: 235 GAVAAIRAAGKTGKVQLVGYDNI-NAIKPMLKDGRVLATVDQFAQQQAVFGIETAL 289 >gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 338 Score = 73.2 bits (178), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 78/269 (28%), Positives = 133/269 (49%), Gaps = 18/269 (6%) Query: 14 METAMKKALTALALSTATLVAFTAPASAQELSKLKIGMSFQEMNNPYFVSMKKALDDAAK 73 M+ +KK T LAL T T ++ A ++ + KIG S ++ + + AA+ Sbjct: 1 MKAMLKK--TVLALMTVTTLSMVAGSAMADAKNPKIGFSIDDLRVERWARDRDFFTAAAE 58 Query: 74 SFGAKVIVTDAAHNVAKQIADIEDMLQQNIDILLINPTDSAGVEAAVKAAKARNVIVVAV 133 GAKV V A + +QI+ IE+++ + +D+++I P ++ + +K AK + V++ Sbjct: 59 KLGAKVYVQSADASEQRQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSY 118 Query: 134 DA---NASGPVDMFVGSKNKDAGYQSCRALADAIGGKGEVAILDGIPVVPILQRV-EGCK 189 D NA VD ++ N+ G + + KG +L G P + EG Sbjct: 119 DRLILNAD--VDAYISFDNEKVGEMQAEGIL-KVKNKGNFFLLGGSPTDNNAKMFREGQM 175 Query: 190 QALGEY---KDIKLVATQNGRQ-DRSVALGVVENMIQSRPN-LKGIFSVND---GGAMGA 241 +AL Y DIK+V Q ++ + + AL +VEN + + N + I + ND GGA+ A Sbjct: 176 KALKPYIDKGDIKIVGQQWVKEWNPTEALSIVENALTANNNKIDAIVASNDGTAGGAIQA 235 Query: 242 LAAIQGSGKDIKLTSVDGAPEAVKAIADG 270 LAA + +GK + ++ D AVK + G Sbjct: 236 LAAQKLAGK-VPVSGQDADLAAVKRVVAG 263 >gi|300310366|ref|YP_003774458.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 63.5 bits (153), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 64/261 (24%), Positives = 123/261 (47%), Gaps = 16/261 (6%) Query: 24 ALALSTATLVAFTAPASAQELSKLKIGMSFQEMNNPYFVSMKKALDDAAKSFGAKVIVTD 83 A+ LS + A + PA A + L +G S + + + ++ DAAK G + D Sbjct: 12 AICLSLGS-SAMSLPAFAAD-KPLTMGFSQVGAESEWRTANTVSIKDAAKQAGVNLKFAD 69 Query: 84 AAHNVAKQIADIEDMLQQNIDILLINPTDSAGVEAAVKAAKARNVIVV----AVDANASG 139 A Q+ I + Q +D++ +P +G E ++ AKA + V+ AV+ + Sbjct: 70 AQQKQENQVKAIRSFIAQKVDVIAFSPVVESGWETVLREAKAAKIPVILTDRAVNVSDKS 129 Query: 140 PVDMFVGSKNKDAGYQSCRALADAIGG--KGEVAILD---GIPVVPILQRVEGCKQALGE 194 F+GS + G ++ R L + G++ I++ + P + R G ++ + Sbjct: 130 LYVTFIGSDFVEEGRRAGRWLLEKAKSMPAGDINIVELQGTVGSAPAIDRKAGFEEVIKG 189 Query: 195 YKDIKLVATQNGRQDRSVALGVVENMIQSR-PNLKGIFSVNDGGAMGALAAIQGS----G 249 +K++ +Q G R+ V+E +++ + +++ ND A+GA+ AI+ + G Sbjct: 190 EPRLKIIRSQTGDFTRAKGKEVMEAFLKAEGKKINVLYAHNDDMAIGAIQAIEEAGMKPG 249 Query: 250 KDIKLTSVDGAPEAVKAIADG 270 KDI + S+DG A +A+ G Sbjct: 250 KDIIIISIDGVKGAFEAMMAG 270 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 0.315 0.131 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: 880,290 Number of extensions: 34137 Number of successful extensions: 158 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 150 Number of HSP's successfully gapped: 7 Length of query: 323 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 238 Effective length of database: 1,217,395 Effective search space: 289740010 Effective search space used: 289740010 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: 131 (55.1 bits)