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= 0028.0243.p (388 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis... 169 3e-43 gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent a... 127 2e-30 gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotrans... 124 1e-29 gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent a... 115 7e-27 gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-... 82 1e-16 >gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 366 Score = 169 bits (429), Expect = 3e-43, Method: Compositional matrix adjust. Identities = 114/350 (32%), Positives = 179/350 (51%), Gaps = 14/350 (4%) Query: 29 DLYRHNEPLEPEISKVFQNFLARGWYVLGAEVTAFEREFAAYCGTEYALGVANGTDALEL 88 DL L+ I+ Q L G Y++G EV E AY G ++ + VA+GT+AL + Sbjct: 9 DLKSQYRALKDAINSRIQKVLDHGQYIMGPEVRELEAALEAYTGAKHCITVASGTEALLI 68 Query: 89 ALRTAGVEAGDRVALVANAGGYGTFAVNA-----IGAVPVYVDVDAFSLNMDVLALERAL 143 +L ++ GD + TF A +GA PV+VDV+ + N+DV +E A Sbjct: 69 SLMALDIKPGDEIITTPF-----TFVATAEVMVLLGAKPVFVDVEPDTGNIDVRLIE-AR 122 Query: 144 QASSISAIIVTHLYGRLANIEEISRLARDQG-VKLIEDCAQAHGAVRDGKKAGSWGDLAT 202 S AI+ LYG+ A+++EI+ +A G + +IED AQ+ GA G+K+G+ + Sbjct: 123 ITSKTKAIMPVSLYGQAADMDEINAIAARHGNLPVIEDAAQSFGATYKGRKSGNLSSIGC 182 Query: 203 FSFYPTKNLGALGDGGALTMNAPDVAERAKQLRQYGWTQKYRSTVIGGRNSRLDEVQAAI 262 SF+P+K LG GDGGA+ N +A +Q+R +G +Q+Y T + G R+D +Q AI Sbjct: 183 TSFFPSKPLGCYGDGGAIFTNDDAIALACRQIRVHGQSQRYVHTRV-GVGGRMDTLQCAI 241 Query: 263 LRIKLPYLDRWNARRRAIFDLYGKLLRHPQIT-LPAPSGPDHVGHLYVIRCGQRDSLSAH 321 + KL D +R A+ Y LL I + D V Y + R+++ A Sbjct: 242 VLAKLERFDWEIEQRLALGSRYNSLLDAAGIARIQQRPDRDSVFAQYTVLLDNREAVQAA 301 Query: 322 LRTMQVPHDIHFPVPDHRQEMFNGRFAADILPVTECACNEVLTLPCFPEM 371 L+ +P +H+PVP +RQ + D PV + V++LP P++ Sbjct: 302 LQNAGIPTAVHYPVPLNRQPAYRHLGDPDQTPVADQLAARVMSLPMSPDL 351 >gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 373 Score = 127 bits (318), Expect = 2e-30, Method: Compositional matrix adjust. Identities = 99/352 (28%), Positives = 170/352 (48%), Gaps = 18/352 (5%) Query: 38 EPEISKVFQNFLARGWYVLGAEVTAFEREFAAYCGTEYALGVANGTDALELALRTAGVEA 97 EP I+ V + L GW G +V AFE+ + Y G +GT +E+ALR AGV Sbjct: 15 EPTIAAVGE-VLRSGWITSGPKVQAFEKALSDYLGGRIVRTFNSGTCTMEIALRIAGVGP 73 Query: 98 GDRVALVANAGGYGTFAVNAIGAVPVYVDVDAFSLNMDVLALERALQASSISAIIVTHLY 157 GD V + + GA PV+ D+D + N+D+ LE A+ + A+I +L Sbjct: 74 GDEVITTPISWVATANVILETGATPVFADIDPITRNIDLDKLEAAITPRT-KAVIPVYLS 132 Query: 158 GRLANIEEISRLARDQGVKLIEDCAQAHGAVRDGKKAGSWGDLATFSFYPTKNLGALGDG 217 G +++ + +A ++++ED AQA G+ +GK+ G++GD +FS KN+ + +G Sbjct: 133 GLPVDMDRLYAIAAKHKLRVVEDAAQALGSTWNGKRIGAFGDFVSFSLQANKNITS-SEG 191 Query: 218 GALTMNAPDVAERAKQLRQYGWTQK----YRSTVIGGRNSRLDEVQAAILRIKLPYLDRW 273 G L +N + A A++ R G T+ V+GG+ + D V AAI + ++D Sbjct: 192 GFLVLNNAEEARLAEKYRLQGVTRSGFDGLEVDVLGGKFNMTD-VAAAIGLGQFAHIDAI 250 Query: 274 NARRRAI----FDLYGKLLRHPQ-ITLPAPSGPDHVGHLYVIRCGQRDSLSAHLRTM--- 325 A R+ + F +G LP + H++ + +R + +A + M Sbjct: 251 TAHRKELARHYFACFGSDFESRYGAQLPVADFENSNWHMFQLVLPERITRAAFMEKMMEK 310 Query: 326 QVPHDIHFPVPDHRQEMFNGR-FAADILPVTECACNEVLTLPCFPEMTDEEV 376 Q+ H+P H +++ R F + PV E +++LP F M+ ++V Sbjct: 311 QIGIGYHYPAI-HLLKLYRERGFGEGMFPVAERVGQRIVSLPMFNTMSKDDV 361 >gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotransferase family protein [Herbaspirillum seropedicae SmR1] Length = 388 Score = 124 bits (312), Expect = 1e-29, Method: Compositional matrix adjust. Identities = 104/382 (27%), Positives = 169/382 (44%), Gaps = 46/382 (12%) Query: 38 EPEISKVFQNFLARGWYVLGAEVTAFEREFAAYCGTEYALGVANGTDALELALRTAGVEA 97 E EI V L+ GW V G +V FE +++A+ G +++ V + T AL L+L G Sbjct: 12 EAEIQSVLAP-LSNGWLVQGPKVREFEEKWSAFTGARHSIAVTSCTTALHLSLAALGFGP 70 Query: 98 GDRVALVANAGGYGTFAVNAIGAVPVYVDVDAFSLNMDVLALERALQASSISAIIVTHLY 157 GD + A + +G V+ D+D + N+DV AL R+ S AI+ HL+ Sbjct: 71 GDEAIVPAFTWIATANVIEHLGGKVVFCDIDLNTFNLDVAAL-RSKITSRTKAILPVHLF 129 Query: 158 GRLANIEEISRLARDQGVKLIEDCAQAHGAVRDGKKAGSWGDLATFSFYPTKNLGALGDG 217 G A +++I+ +A+ G+ ++ED A G+ GK G GD FSF+P K + G+G Sbjct: 130 GLAAEMDQINDVAKQHGLWVVEDAACGFGSRYHGKHVGVLGDTGCFSFHPRKAI-TTGEG 188 Query: 218 GALTMNAPDVAERAKQLRQYGWTQKYRSTVIGGR------------NSRLDEVQAAILRI 265 G +T + +AE+ ++LR +G +G R N R+ ++QAA+ Sbjct: 189 GMITTDNDALAEKLRRLRDHGAAMTDLQRHLGARPYLLADHPDAGYNQRMTDIQAALGAA 248 Query: 266 KLPYLDRWNARRRAIFDLYGKLL--------------------RHPQITLPAPSGPDHVG 305 ++ D A RR + + Y +P + P P D + Sbjct: 249 QMERADDIIAERRRLAERYDAAFADLSWLRTPAHVDGLEHGYQSYPCLFQPEPVNTDSIE 308 Query: 306 HLYVIRCGQRDSL-SAHLRTMQVPHDIHFPVPDHRQEMFNGRFA---ADILPVTECACNE 361 + R DSL A + T H +H + ++A AD P A + Sbjct: 309 RINAARNAWMDSLQQAGISTRPATHAVHMLT------FYREKYALKPAD-FPNAWAANDC 361 Query: 362 VLTLPCFPEMTDEEVEWVSKHV 383 ++LP F MT E ++V + V Sbjct: 362 SISLPLFHGMTQAEQDFVIEQV 383 >gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 382 Score = 115 bits (288), Expect = 7e-27, Method: Compositional matrix adjust. Identities = 100/342 (29%), Positives = 163/342 (47%), Gaps = 29/342 (8%) Query: 57 GAEVTAFEREFAAYCGTEYALGVANGTDALELALRTAGVEAGDRVALVANAGGYGTFAVN 116 G V +FE EFA+Y G Y + A+GT AL LALR G+ AGD V A + A+ Sbjct: 33 GPVVESFENEFASYLGRTYGVAAASGTVALMLALRAMGIRAGDEVIASAYSWHQIVHAIT 92 Query: 117 AIGAVPVYVDVDAFSLNMDVLALERALQASSISAIIVTHLYGRLANIEEISRLARDQGVK 176 +GA PV+ D+D +S N+ + + + AI+V + G A E +LA+ G++ Sbjct: 93 LVGATPVFADIDYWSGNLAPHKVADKI-SQRTRAIVVGNCNGHPAAWTEFRQLAQAHGLR 151 Query: 177 LIEDCAQAHGAVRDGKKAGSWGDLATFSFYPTKNLGALGDGGALTMNAPDVAERAKQLRQ 236 LIED ++A G+ G+ G++GD+A F F L G+G L + P++A +R Sbjct: 152 LIEDSSEAIGSRYQGRVVGNFGDIAIFDFSQPSAL-CCGEGAMLVTDDPELASELHYMRN 210 Query: 237 YGWTQKYRSTVIGGR---NSRLDEVQAAILRIKLPYLDRWNARRRAIFDLYGKLLRHPQI 293 + + +S + R + ++ AAI +L LD RR+ + Y + ++ + Sbjct: 211 RNLSDR-QSIAVASRVPMQGSMSDLSAAIGIAQLERLDEILMRRKQVEAYYLEHVQFFEG 269 Query: 294 TLPAPSGPD---HVGHLYVIRCGQRDSLSAHLRTM--QVPHDI--------HFPVPDHRQ 340 P GPD LY++ G R + RTM Q+ D+ + P H Q Sbjct: 270 IKPPYIGPDVEEVYWMLYLVHLGTRFT-----RTMRNQIIEDLASQEVEAAAWCQPLH-Q 323 Query: 341 EMFNGRF---AADILPVTECACNEVLTLPCFPEMTDEEVEWV 379 + + RF D+L +TE + + LP + +EV ++ Sbjct: 324 QFYYSRFDCKRGDLL-LTEKIADRCIALPLHGHLNTDEVHFI 364 >gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-dehydrase [Herbaspirillum seropedicae SmR1] Length = 390 Score = 81.6 bits (200), Expect = 1e-16, Method: Compositional matrix adjust. Identities = 69/246 (28%), Positives = 113/246 (45%), Gaps = 27/246 (10%) Query: 57 GAEVTAFEREFAAYCGTEYALGVANGTDA--LELALRTAGVEAGDRVALVANAGGYGTFA 114 G V AFE+E++ + G +Y++ V +G A L +A+ G V + Sbjct: 33 GPNVRAFEKEWSEWLGVKYSVFVNSGASANLLSMAVLKLRHPEGGEVIVPPLTWISDVAT 92 Query: 115 VNAIGAVPVYVDVDAFSLNMDVLALERALQ--ASSISAIIVTHLYGRLANIEEISRLARD 172 V G PV+ D+D SL M A E+ L A+ +TH+ G +E+ Sbjct: 93 VIQNGFTPVFADIDPRSLAM---APEQILAKITERTRAVFLTHVQGFDGLTDELLAELER 149 Query: 173 QGVKLIEDCAQAHGAVRDGKKAGSWGDLATFSFYPTKNLGALGDGGALTMNAPDVAERAK 232 + + LIED ++HGA +G++ GS+G ++ FSFY ++ + +GG + N P+V ++ + Sbjct: 150 RNIPLIEDVCESHGATHNGQRLGSFGWMSNFSFYYAHHMSTI-EGGMVCTNDPEVYQQVR 208 Query: 233 QLRQYGWTQK---------YRST----------VIGGRNSRLDEVQAAILRIKLPYLDRW 273 LR +G ++ YR N R E+ A + R +L LD Sbjct: 209 MLRSHGMVREATDDDLKLGYRQDNPQLNPDFIFAFPAYNVRNTEIGAIMGRSQLKRLDAN 268 Query: 274 NARRRA 279 ARR A Sbjct: 269 CARRTA 274 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 0.322 0.137 0.419 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: 1,270,153 Number of extensions: 55594 Number of successful extensions: 214 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 201 Number of HSP's successfully gapped: 5 Length of query: 388 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 301 Effective length of database: 1,207,925 Effective search space: 363585425 Effective search space used: 363585425 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 131 (55.1 bits)