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= 0003.0001.p (435 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313089|ref|YP_003777181.1| glycerol-3-phosphate ABC transp... 794 0.0 gi|300311925|ref|YP_003776017.1| glycerol-3-phosphate ABC transp... 253 2e-68 gi|300312387|ref|YP_003776479.1| sugar ABC transporter periplasm... 128 8e-31 >gi|300313089|ref|YP_003777181.1| glycerol-3-phosphate ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 437 Score = 794 bits (2050), Expect = 0.0, Method: Compositional matrix adjust. Identities = 372/431 (86%), Positives = 402/431 (93%) Query: 5 VKTFAAAALLATMTTSAFAVTDIAWWHSMTGALGERVNAMADEFNKSQSDYKVTPVYKGT 64 +KT A +LAT+T+SAFA T I WWHSMTGALGERVNA+AD+FNK+Q DYK+ PVYKGT Sbjct: 4 MKTLIATGVLATITSSAFAATAITWWHSMTGALGERVNALADDFNKTQGDYKIVPVYKGT 63 Query: 65 YDESMAAAIAAYRAGNAPNILQIFEVGTATMVYSKGAIKPVYEVMQQAGEKFDQNAYVPA 124 YDESM+AAIAAYRAGNAP ILQ+FEVGTATM+Y+KGA+KPVYEVM QAGEKFDQNAYVPA Sbjct: 64 YDESMSAAIAAYRAGNAPAILQVFEVGTATMIYAKGAVKPVYEVMHQAGEKFDQNAYVPA 123 Query: 125 VSGYYSTAKGMMSFPFNSSTTIMFYNKDLFAKAGLDPNKPPATWQDFVGMAAKMKASGIT 184 V+GYYST KGMMSFPFNSSTTIMFYNKD+FAKAGLDP KPP TWQ+FVGMAAK+KASG Sbjct: 124 VAGYYSTPKGMMSFPFNSSTTIMFYNKDMFAKAGLDPEKPPVTWQEFVGMAAKIKASGAA 183 Query: 185 CPYTTTWQSWVHLESFSAWHNTETATKSNGFGGLDARLKINGPLQVRHIENMSNWAKQGY 244 C YTTTWQSWVHLESFS WHN E ATK+NGFGGLDARLK+N PL VRHIEN+SNWAKQGY Sbjct: 184 CAYTTTWQSWVHLESFSTWHNVELATKNNGFGGLDARLKMNSPLHVRHIENLSNWAKQGY 243 Query: 245 FIYAGRKDEANAKFNAGECAIITGSSSAYADIRKNAKFKFGVAPLPYYSDVQGAPQNTVI 304 F YAGRKDEANAKFNAGECAIITGSSSAYADIRKNAKFKFGVA LPYY+DVQGAPQNTVI Sbjct: 244 FTYAGRKDEANAKFNAGECAIITGSSSAYADIRKNAKFKFGVATLPYYNDVQGAPQNTVI 303 Query: 305 GGASLWVMGGKKADEYKGVAKFFTYLSKPEVQAKWHQETGYLPVTKAAYEITQKSGFYER 364 GGASLWVM GKKADEYKGVAKFF+YLSKPEV AKWHQ+TGYLPVTKAAYE+T+ SGFYER Sbjct: 304 GGASLWVMNGKKADEYKGVAKFFSYLSKPEVAAKWHQDTGYLPVTKAAYELTKSSGFYER 363 Query: 365 NPGTDVAVKQMIVKTTDKSRGIRLGNYAQIRTVIDEELENVWTGKKAPKEALDSAVKRGD 424 NPGTDVAVKQMIVKTT+KSRG+RLGNYAQ+RTV DEELENVWTGKK+ K+ALDSAVKRGD Sbjct: 364 NPGTDVAVKQMIVKTTEKSRGLRLGNYAQVRTVFDEELENVWTGKKSAKDALDSAVKRGD 423 Query: 425 ELLARFEKANK 435 ELLARFEKANK Sbjct: 424 ELLARFEKANK 434 >gi|300311925|ref|YP_003776017.1| glycerol-3-phosphate ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 452 Score = 253 bits (647), Expect = 2e-68, Method: Compositional matrix adjust. Identities = 142/407 (34%), Positives = 216/407 (53%), Gaps = 12/407 (2%) Query: 29 WWHSMTGALGERVNAMADEFNKSQSDYKVTPVYKGTYDESMAAAIAAYRAGNAPNILQIF 88 +W S GA+ + V + FN +Q ++V V GTY+++M IA YRA P +++I+ Sbjct: 42 FWSSHAGAMAQAVRQLCAGFNAAQQQHQVRCVVPGTYEQTMQKTIATYRAAQQPALVEIY 101 Query: 89 EVGTATMVYSKGAIKPVYEVMQQAGEKFDQNAYVPAVSGYYSTAKGMM-SFPFNSSTTIM 147 +VGT M+ S GAI PV+++M G + D Y+PA+ GYY+ A+G S PFN ST ++ Sbjct: 102 DVGTLDMMLS-GAIVPVHQLMADHGYRVDWQDYLPAIRGYYTDAQGQFDSLPFNVSTAVL 160 Query: 148 FYNKDLFAKAGLDPNKPPATWQDFVGMAAKMKASGITCPYTTTWQSWVHLESFSAWHNTE 207 + N D +AG+ + P+TW++ A +++A+G TCP + + W+ LE S Sbjct: 161 YLNTDQLRQAGI--STLPSTWRELEQTARQLRAAGQTCPLVSDFNPWILLEQVSTIEGAP 218 Query: 208 TATKSNGFGGLDARLKINGPLQVRHIENMSNWAKQGYFIYAG--RKDEANAKFNAGECAI 265 A NG GL A + L +R ++ + W +Q + A R F GECA+ Sbjct: 219 IADHDNGHQGLAAHYLFDQGLHLRFMQQLQRWHQQHLLVEAAATRTGRHTLAFTTGECAM 278 Query: 266 ITGSSSAYADIRKNAKFKFGVAPLPYYSDVQGAPQNTVIGGASLWVMGGKKADEYKGVAK 325 + S+SA+ I ++ V PLP ++D G N+V GGASLWVM G Y VA Sbjct: 279 LFDSTSAWHAIARSGLPHVAVRPLPIHAD--GQRHNSVPGGASLWVMKGFDRQVYAAVAA 336 Query: 326 FFTYLSKPEVQAKWHQETGYLPVTK-AAYEITQKSGFYERNPGTDVAVKQMIVKTTDKSR 384 F YL +P+ Q ++TGYLPVT+ A +I Y P VA + + Sbjct: 337 FIAYLQQPQNQRLLARQTGYLPVTRQVAAQIMDDPDHY---PAAVVAGIHSLDAASQPGV 393 Query: 385 GIRLGNYAQIRTVIDEELENVWTGKKAPKEALDSAVKRGDELLARFE 431 G RLG + Q+R E+++ +G++ +AL A +RGD LL RF Sbjct: 394 GPRLGFFPQLRLAWTEQVQMALSGQQDMAQALSKARQRGDALLQRFR 440 >gi|300312387|ref|YP_003776479.1| sugar ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 430 Score = 128 bits (322), Expect = 8e-31, Method: Compositional matrix adjust. Identities = 103/411 (25%), Positives = 184/411 (44%), Gaps = 37/411 (9%) Query: 35 GALGERVNAMADEFNKSQSDYKVTPVYKGTYDESMAAAIAAYRAGNAPNILQIFEVGTAT 94 GA+ + +++M +F K+ D KV +Y GTY ES+ A+ A++ G P + + T Sbjct: 40 GAVTKTIDSMVADFEKAHPDIKVKAIYAGTYQESIVKALTAFKGGTPPTLAVLLSTDLFT 99 Query: 95 MVYSKGAIKPVYEVMQQAGEKFDQNAYVPAVSGYYSTAKGMMS----------FPFNSST 144 ++ + AI P+ + A +K ++G+Y KG M PF ST Sbjct: 100 LI-DENAILPIDSLASSAEDK-------KWIAGFY---KGFMENSQTEGKTWGIPFQRST 148 Query: 145 TIMFYNKDLFAKAGLDPNKPPATWQDFVGMAAKMKASGITCPYTTTWQSWVHLESFSAWH 204 +M+YNK LF +AGL+P+K PA W + V A K+ T W + F W Sbjct: 149 IVMYYNKALFKEAGLNPDKAPANWNEMVEAAKKLTKRD-AAGNVTQWGVKIPSTGFGYWM 207 Query: 205 NTETATKSNGFGGLDA---RLKINGPLQVRHIENMSNWAKQGYFIYAGRKDEANA--KFN 259 + T SN +++ + + P V+ +++ + + + AG + F Sbjct: 208 -FQAMTASNDTLLMNSAGTKTYFDKPGAVQALQHWVDLTTKEKVMPAGSIEWGTTPKDFL 266 Query: 260 AGECAIITGSSSAYADIRKNAKFKFGVAPLPYYSDVQGAPQNTVIGGASLWVMGGKKADE 319 + A++ ++ +IR NA F FGVA LP G+P GG + +V E Sbjct: 267 EQKAAMVWTTTGNLTNIRTNASFPFGVAMLPGIKH-PGSP----TGGGNFYVFNKTSPAE 321 Query: 320 YKGVAKFFTYLSKPEVQAKWHQETGYLPVTKAAYEITQKSGFYERNPGTDVAVKQMIVKT 379 + KF + ++P A+W TGY+ + A++ + + + P DVA +QM Sbjct: 322 QQAAMKFIRFATEPARAAQWSIATGYVAPRQDAWDTPEMKKYLQDVPAADVAREQMKYGV 381 Query: 380 TDKSRGIRLGNYAQIRTVIDEELENVWTGKKAPKEALDSAVKRGDELLARF 430 + S + ++ +++ L+ + K P+ AL A + + +L + Sbjct: 382 AELST----HDNQRVTKALNDNLQAALSDTKTPEAALKDAQREAERILRSY 428 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 0.129 0.386 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: 1,262,087 Number of extensions: 50943 Number of successful extensions: 142 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 134 Number of HSP's successfully gapped: 3 Length of query: 435 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 347 Effective length of database: 1,203,190 Effective search space: 417506930 Effective search space used: 417506930 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: 132 (55.5 bits)