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= 0001.3003.p (430 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312340|ref|YP_003776432.1| transporter transmembrane prote... 719 0.0 gi|300312509|ref|YP_003776601.1| arabinose efflux permease [Herb... 70 3e-13 gi|300313915|ref|YP_003778007.1| transmembrane arabinose efflux ... 67 2e-12 gi|300309575|ref|YP_003773667.1| proline/betaine transporter pro... 58 2e-09 gi|300312245|ref|YP_003776337.1| transmembrane efflux transmembr... 57 2e-09 >gi|300312340|ref|YP_003776432.1| transporter transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 421 Score = 719 bits (1856), Expect = 0.0, Method: Compositional matrix adjust. Identities = 363/416 (87%), Positives = 384/416 (92%), Gaps = 3/416 (0%) Query: 7 QHPVSP---PALAGFTRYQKTVGGLLAFLQFAVILDFMLMSPLGALIMPAMRITPQQFGL 63 HP +P P + GFT YQK V GLLAFLQFAVILDFMLMSPLGALIMP+M+ITPQQFGL Sbjct: 2 NHPATPSLSPPVQGFTPYQKIVTGLLAFLQFAVILDFMLMSPLGALIMPSMQITPQQFGL 61 Query: 64 VVSAYAFSAGASGLLTAGFADRFDRKRLLLFFYGGFVLGTVWCGLAQSFESLLLARIVTG 123 VVSAYAFSAGASGLLTAGFADRFDRKRLLLFFYGGFVLGTVWCGLAQSFESLLLARIVTG Sbjct: 62 VVSAYAFSAGASGLLTAGFADRFDRKRLLLFFYGGFVLGTVWCGLAQSFESLLLARIVTG 121 Query: 124 LFGGVIGSITLAIATDLFAPHLRGRVMGIIQTSFAASQVLGIPIGLYLSNTWNWHVPFLA 183 LFGGVIGSITLAIATDLFAPHLRGRVMG+IQTSFAASQVLGIPIGLYLSN WNWHVPFLA Sbjct: 122 LFGGVIGSITLAIATDLFAPHLRGRVMGVIQTSFAASQVLGIPIGLYLSNRWNWHVPFLA 181 Query: 184 MAGLGAVGGLVVSFKMQPVDAHLKLKQEHSAWMHLYHTIAEPRYLVAFATTALLMTGGFM 243 MA LG GGLVV +MQPVD HL LKQEHSAWMHLYHT+AEPRYL AFATTALLMTGGFM Sbjct: 182 MAALGLAGGLVVLVRMQPVDGHLTLKQEHSAWMHLYHTLAEPRYLTAFATTALLMTGGFM 241 Query: 244 LMPFSSAYLVGNLGIDLHHLPTVYLITGLCTITFGPLIGRAADKLGKLRVFFFGALLSII 303 LMPFSSAYLVGNLGID+ HLPT+YL+TGLCTI FGPLIGRAADKLGKLRVF FGA+LSII Sbjct: 242 LMPFSSAYLVGNLGIDMAHLPTIYLVTGLCTIAFGPLIGRAADKLGKLRVFLFGAVLSII 301 Query: 304 MVLIYTHLGPVTVPMIVLVNAVLFLGIFSRMIPFQALVSSVPAPTQRGSFNAVSASIQQL 363 MVLIYTHLG VTVPMIV VNAVLFLGIFSRMIPFQALVSSVPA TQRGSFNA+SASIQQL Sbjct: 302 MVLIYTHLGRVTVPMIVAVNAVLFLGIFSRMIPFQALVSSVPAATQRGSFNAISASIQQL 361 Query: 364 SGGVASVVAGQIVTLGADGQLLHFEVVGYVIVASTLLASVLVWRLNRDVQLRAAAA 419 SGGVASV+AG IVTL DG+L HF++VG+VIV +TLLASVLVWRL+RD+Q R +AA Sbjct: 362 SGGVASVIAGHIVTLAPDGRLGHFDIVGFVIVGTTLLASVLVWRLHRDLQARESAA 417 >gi|300312509|ref|YP_003776601.1| arabinose efflux permease [Herbaspirillum seropedicae SmR1] Length = 385 Score = 70.1 bits (170), Expect = 3e-13, Method: Compositional matrix adjust. Identities = 65/252 (25%), Positives = 114/252 (45%), Gaps = 9/252 (3%) Query: 56 ITPQQFGLVVSAYAFSAGASGLLTAGFADRFDRKRLLLFFYGGFVLGTVWCGLAQSFESL 115 +T G++VS YA A + A ++ RK+ L+ F+LG V C LA ++ L Sbjct: 35 VTAPAAGMLVSGYALGVAAGAPILAILTAKWPRKQALVGLMCLFILGNVLCALAPNYVFL 94 Query: 116 LLARIVTGLFGGVIGSITLAIATDLFAPHLRGRVMGIIQTSFAASQVLGIPIGLYLSNTW 175 ++AR+VT I +A +L AP R + + ++ T + +LG+P+G + Sbjct: 95 MVARVVTAFCHAAFFGIGSVVAAELVAPQKRAQAVALMFTGLTVANILGVPLGTAFGHAA 154 Query: 176 NWHVPFLAMAGLGAVGGLVVSFKMQPVDAHLKLKQEHSAWMHLYHTIAEPRYLVAFATTA 235 W F A+ +G + +++ + M P K+ + + +I + R ++ T+ Sbjct: 155 GWRSTFGAVTAIGVLAAIML-WTMLPK----KIPMQAGNIFQEFRSIIDTRVQLSLLTST 209 Query: 236 LLMTGGFMLMPFSSAYLVGNLGIDLHHLPTVYLITGLCTITFGPLI-GRAADKLGKLRVF 294 L F ++ + + L+ G V L+ G IT G L+ G+ AD KL Sbjct: 210 LASISMFSVITYIAYILLDVTGFTTQQESWVLLLFG-AGITVGGLVGGKLADW--KLMPV 266 Query: 295 FFGALLSIIMVL 306 G L I +VL Sbjct: 267 MCGVFLCIAVVL 278 >gi|300313915|ref|YP_003778007.1| transmembrane arabinose efflux transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 403 Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 70/266 (26%), Positives = 117/266 (43%), Gaps = 34/266 (12%) Query: 3 QPQPQHPVSPPALAGFTRYQKTV-GGLLAFLQFAVILDFMLMSPLGALIMPAMRITPQQF 61 P P P +P A A T+ + G LA FA+ + +++PL +P M F Sbjct: 2 NPPPLGPSAPSACASPTQAGSLLTAGFLALGTFAIGTEGFMIAPL----LPRMA---ADF 54 Query: 62 GLVVS-----------AYAFSAGASGLLTAGFADRFDRKRLLLFFYGGFVLGTVWCGLAQ 110 G+ V A S+ S +L+A +R+R+L+ F + + Sbjct: 55 GMSVPMVASLVVIFTLVLALSSPISTVLSAAM----NRRRVLIAAMTAFTAANLLAACSS 110 Query: 111 SFESLLLARIVTGLFGGVIGSITLAIATDLFAPHLRGRVMGIIQTSFAASQVLGIPIGLY 170 SF LL+AR++ + G+ A+A + AP RGR + I+ + LG+P+G Sbjct: 111 SFTGLLVARLLMAVAAGLYTPNASALAGAMVAPGQRGRALAIVSGGMTSPSALGLPLGAV 170 Query: 171 LSNTWNWHVPFLAMAGLGAV--GGLVVSFKMQPVDAHLKLK--QEHSAWMHLYHTIAEPR 226 + + + W FLA++ +GAV G+++ Q AHL + +E A I +P+ Sbjct: 171 VGHAFGWRATFLAVSAMGAVALAGILLGVPRQ-AGAHLHVAGLRERMA------VIGQPQ 223 Query: 227 YLVAFATTALLMTGGFMLMPFSSAYL 252 A T L G + P+ + YL Sbjct: 224 VQRLLAVTLLWSVGAYAAYPYIAPYL 249 >gi|300309575|ref|YP_003773667.1| proline/betaine transporter protein [Herbaspirillum seropedicae SmR1] Length = 433 Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 62/234 (26%), Positives = 103/234 (44%), Gaps = 23/234 (9%) Query: 76 GLLTAGFADRFDRKRLLLFFYGGFVLGTVWCGLAQSFESL--------LLARIVTGLF-G 126 G+L +ADR RK L +GT GLA ++ES+ ++AR++ G G Sbjct: 79 GILLGIYADRVGRKAALSVTILLMAVGTTMIGLAPTYESIGLFAPLIIVVARLLQGFSAG 138 Query: 127 GVIGSITLAIATDLFAPHLRGRVMGIIQTSFAASQVLGIPIGLYLSNT--------WNWH 178 G +GS T A T+ R IQ S + +LG +G +++ + W W Sbjct: 139 GEMGSAT-AFLTEYAPERERAYYSSWIQASIGVAVLLGAAVGTFVTASLDAAALASWGWR 197 Query: 179 VPFLAMAGLGAVGGLVVSFKMQPVDAHLKLKQEHSAWMHLYHTIAE-PRYLVA-FATTAL 236 +PFL +G VG + ++ L+ K + + L I PR A F+ L Sbjct: 198 LPFLLGIIIGPVG-YYIRHHLEETPTFLEEKDKTDS--PLKEVIRNFPRETSASFSMVIL 254 Query: 237 LMTGGFMLMPFSSAYLVGNLGIDLHHLPTVYLITGLCTITFGPLIGRAADKLGK 290 ++L+ + Y V L + ++ GLC + P++GR AD++G+ Sbjct: 255 WTVCTYVLLFYMPTYSVKVLKLPQTTGFIAGMVGGLCIMVLAPIVGRLADRIGR 308 >gi|300312245|ref|YP_003776337.1| transmembrane efflux transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 395 Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 51/226 (22%), Positives = 90/226 (39%), Gaps = 5/226 (2%) Query: 62 GLVVSAYAFSAGASGLLTAGFADRFDRKRLLLFFYGGFVLGTVWCGLAQSFESLLLARIV 121 GL+V+ YA L R RK LL+ FV+G + C +A + +L++ R+V Sbjct: 41 GLLVTGYALGVFVGAPLLTATTGRLPRKTLLVALMVVFVVGNLACAIAPDYTTLMIGRVV 100 Query: 122 TGLFGGVIGSITLAIATDLFAPHLRGRVMGIIQTSFAASQVLGIPIGLYLSNTWNWHVPF 181 G + +AT L + + ++ T + VLG+P G +L ++ W F Sbjct: 101 ASFAHGAFFGVGSVVATSLVPKEKQASAIALMFTGLTVANVLGVPFGTWLGQSYGWRATF 160 Query: 182 LAMAGLGAVGGLVVSFKMQPVDAHLKLKQEHSAWMHLYHTIAEPRYLVAFATTALLMTGG 241 A+ +G V++ V E + + + P+ ++ T L G Sbjct: 161 WAVTVIG-----VIALAATAVLVPRSQGGEETDFGKEVRVLMRPQVMLGLLMTVLGFGGV 215 Query: 242 FMLMPFSSAYLVGNLGIDLHHLPTVYLITGLCTITFGPLIGRAADK 287 F + + L G + + L+ GL + G+ ADK Sbjct: 216 FAAFTYIAPILTDLSGFPASAVSPILLLFGLGLVIGNLAGGKLADK 261 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 0.328 0.142 0.426 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: 1,178,849 Number of extensions: 48104 Number of successful extensions: 310 Number of sequences better than 1.0e-08: 13 Number of HSP's gapped: 312 Number of HSP's successfully gapped: 13 Length of query: 430 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 342 Effective length of database: 1,203,190 Effective search space: 411490980 Effective search space used: 411490980 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 132 (55.5 bits)