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= 0002.0158.p (376 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent a... 182 5e-47 gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis... 179 4e-46 gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotrans... 174 1e-44 gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent a... 106 4e-24 gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-... 88 9e-19 >gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 373 Score = 182 bits (461), Expect = 5e-47, Method: Compositional matrix adjust. Identities = 118/319 (36%), Positives = 169/319 (52%), Gaps = 11/319 (3%) Query: 54 HSCTAALEMAALLLDIKPGDEIIMPSFTFVSTANAFVLRGGVPVFVDIREDTLNLDERLI 113 +S T +E+A + + PGDE+I ++V+TAN + G PVF DI T N+D + Sbjct: 56 NSGTCTMEIALRIAGVGPGDEVITTPISWVATANVILETGATPVFADIDPITRNIDLDKL 115 Query: 114 EAAITTRTKAIVPVHYAGVACEMDTIMDIAVRHGLRVVEDAAQGVMSKYKGKALGSIGDF 173 EAAIT RTKA++PV+ +G+ +MD + IA +H LRVVEDAAQ + S + GK +G+ GDF Sbjct: 116 EAAITPRTKAVIPVYLSGLPVDMDRLYAIAAKHKLRVVEDAAQALGSTWNGKRIGAFGDF 175 Query: 174 GAFSFHETKNVISGEGGALLVNDKSAALRAEIIREKGTDRSRFFRGEVDKYTWQEVGSSF 233 +FS KN+ S EGG L++N+ A AE R +G RS F EVD +G F Sbjct: 176 VSFSLQANKNITSSEGGFLVLNNAEEARLAEKYRLQGVTRSGFDGLEVDV-----LGGKF 230 Query: 234 LPGELIAAFLWAQLEESETITARRLHSWEHYHAALAS-LESKGVLRRPVVPDACQHNAHM 292 ++ AA Q + ITA R HY A S ES+ + PV D N HM Sbjct: 231 NMTDVAAAIGLGQFAHIDAITAHRKELARHYFACFGSDFESRYGAQLPVA-DFENSNWHM 289 Query: 293 YYVLLAPGINRQQVLAELKRNQINSVFHYVPLHSSPAGLRYGRAHGELNWTVTQ--SERL 350 + ++L I R + ++ QI +HY +H L R GE + V + +R+ Sbjct: 290 FQLVLPERITRAAFMEKMMEKQIGIGYHYPAIHL--LKLYRERGFGEGMFPVAERVGQRI 347 Query: 351 VRLPMFVGLEESQQDRVVD 369 V LPMF + + R V+ Sbjct: 348 VSLPMFNTMSKDDVVRSVE 366 >gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 366 Score = 179 bits (453), Expect = 4e-46, Method: Compositional matrix adjust. Identities = 131/344 (38%), Positives = 176/344 (51%), Gaps = 26/344 (7%) Query: 31 GPFTKRCHQWIETNTSCAKALLTHSCTAALEMAALLLDIKPGDEIIMPSFTFVSTANAFV 90 GP + +E T + S T AL ++ + LDIKPGDEII FTFV+TA V Sbjct: 37 GPEVRELEAALEAYTGAKHCITVASGTEALLISLMALDIKPGDEIITTPFTFVATAEVMV 96 Query: 91 LRGGVPVFVDIREDTLNLDERLIEAAITTRTKAIVPVHYAGVACEMDTIMDIAVRHG-LR 149 L G PVFVD+ DT N+D RLIEA IT++TKAI+PV G A +MD I IA RHG L Sbjct: 97 LLGAKPVFVDVEPDTGNIDVRLIEARITSKTKAIMPVSLYGQAADMDEINAIAARHGNLP 156 Query: 150 VVEDAAQGVMSKYKGKALGSIGDFGAFSFHETKNV-ISGEGGALLVNDKSAALRAEIIRE 208 V+EDAAQ + YKG+ G++ G SF +K + G+GGA+ ND + AL IR Sbjct: 157 VIEDAAQSFGATYKGRKSGNLSSIGCTSFFPSKPLGCYGDGGAIFTNDDAIALACRQIR- 215 Query: 209 KGTDRSRFFRGEVDKYTWQEVGSSFLPGELIAAFLWAQLEESETITARRLHSWEHYHAAL 268 G+ +Y VG L A + A+LE + +RL Y++ Sbjct: 216 --------VHGQSQRYVHTRVGVGGRMDTLQCAIVLAKLERFDWEIEQRLALGSRYNSL- 266 Query: 269 ASLESKGVLRRPVVPDACQHNAHMYYVLLAPGINRQQVLAELKRNQINSVFHY-VPLHSS 327 L++ G+ R PD A Y VLL NR+ V A L+ I + HY VPL+ Sbjct: 267 --LDAAGIARIQQRPDRDSVFAQ-YTVLLD---NREAVQAALQNAGIPTAVHYPVPLNRQ 320 Query: 328 PAGLRYGRAHGELNWTVTQSE---RLVRLPMFVGLEESQQDRVV 368 PA R G+ + T + R++ LPM LE + QD +V Sbjct: 321 PA----YRHLGDPDQTPVADQLAARVMSLPMSPDLEHTAQDSIV 360 >gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotransferase family protein [Herbaspirillum seropedicae SmR1] Length = 388 Score = 174 bits (440), Expect = 1e-44, Method: Compositional matrix adjust. Identities = 123/388 (31%), Positives = 183/388 (47%), Gaps = 26/388 (6%) Query: 1 MTIPFNRPYMVGKELDYIIQAKQGNMLAGDGPFTKRCHQWIETNTSCAKALLTHSCTAAL 60 M +P R + E+ ++ A N GP + + T ++ SCT AL Sbjct: 1 MNVPIARTSLTEAEIQSVL-APLSNGWLVQGPKVREFEEKWSAFTGARHSIAVTSCTTAL 59 Query: 61 EMAALLLDIKPGDEIIMPSFTFVSTANAFVLRGGVPVFVDIREDTLNLDERLIEAAITTR 120 ++ L PGDE I+P+FT+++TAN GG VF DI +T NLD + + IT+R Sbjct: 60 HLSLAALGFGPGDEAIVPAFTWIATANVIEHLGGKVVFCDIDLNTFNLDVAALRSKITSR 119 Query: 121 TKAIVPVHYAGVACEMDTIMDIAVRHGLRVVEDAAQGVMSKYKGKALGSIGDFGAFSFHE 180 TKAI+PVH G+A EMD I D+A +HGL VVEDAA G S+Y GK +G +GD G FSFH Sbjct: 120 TKAILPVHLFGLAAEMDQINDVAKQHGLWVVEDAACGFGSRYHGKHVGVLGDTGCFSFHP 179 Query: 181 TKNVISGEGGALLVNDKSAALRAEIIREKG---TDRSRFFRGE----VDKYTWQEVGSSF 233 K + +GEGG + ++ + A + +R+ G TD R D + G + Sbjct: 180 RKAITTGEGGMITTDNDALAEKLRRLRDHGAAMTDLQRHLGARPYLLADH---PDAGYNQ 236 Query: 234 LPGELIAAFLWAQLEESETITARRLHSWEHYHAALASLESKGVLRRPVVPDACQHNAHMY 293 ++ AA AQ+E ++ I A R E Y AA A L LR P D +H Y Sbjct: 237 RMTDIQAALGAAQMERADDIIAERRRLAERYDAAFADLS---WLRTPAHVDGLEHGYQSY 293 Query: 294 YVLLAPGINRQQVLAELK--RNQINSVFHYVPLHSSPAGL----------RYGRAHGELN 341 L P + + RN + + PA +Y + Sbjct: 294 PCLFQPEPVNTDSIERINAARNAWMDSLQQAGISTRPATHAVHMLTFYREKYALKPADFP 353 Query: 342 WTVTQSERLVRLPMFVGLEESQQDRVVD 369 ++ + LP+F G+ +++QD V++ Sbjct: 354 NAWAANDCSISLPLFHGMTQAEQDFVIE 381 >gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 382 Score = 106 bits (264), Expect = 4e-24, Method: Compositional matrix adjust. Identities = 91/357 (25%), Positives = 156/357 (43%), Gaps = 14/357 (3%) Query: 3 IPFNRPYMVGKELDYIIQAKQGNMLAGDGPFTKRCHQWIETNTSCAKALLTHSCTAALEM 62 I + P + +EL+ + + + L+ GP + + + S T AL + Sbjct: 6 IKLSDPDVSTRELEAVTRVLVSSGLSA-GPVVESFENEFASYLGRTYGVAAASGTVALML 64 Query: 63 AALLLDIKPGDEIIMPSFTFVSTANAFVLRGGVPVFVDIREDTLNLDERLIEAAITTRTK 122 A + I+ GDE+I ++++ +A L G PVF DI + NL + I+ RT+ Sbjct: 65 ALRAMGIRAGDEVIASAYSWHQIVHAITLVGATPVFADIDYWSGNLAPHKVADKISQRTR 124 Query: 123 AIVPVHYAGVACEMDTIMDIAVRHGLRVVEDAAQGVMSKYKGKALGSIGDFGAFSFHETK 182 AIV + G +A HGLR++ED+++ + S+Y+G+ +G+ GD F F + Sbjct: 125 AIVVGNCNGHPAAWTEFRQLAQAHGLRLIEDSSEAIGSRYQGRVVGNFGDIAIFDFSQPS 184 Query: 183 NVISGEGGALLVNDKSAALRAEIIREKG-TDRSRFFRGEVDKYTWQEVGSSFLPGELIAA 241 + GEG L+ +D A +R + +DR + Q S +L AA Sbjct: 185 ALCCGEGAMLVTDDPELASELHYMRNRNLSDRQSI--AVASRVPMQGSMS-----DLSAA 237 Query: 242 FLWAQLEESETITARRLHSWEHYHAALASLESKGVLRRPVVPDACQHNAHMYYVLLAPGI 301 AQLE + I RR +Y + E G+ + PD + +Y V L Sbjct: 238 IGIAQLERLDEILMRRKQVEAYYLEHVQFFE--GIKPPYIGPDVEEVYWMLYLVHLGTRF 295 Query: 302 N---RQQVLAELKRNQINSVFHYVPLHSSPAGLRYGRAHGELNWTVTQSERLVRLPM 355 R Q++ +L ++ + PLH R+ G+L T ++R + LP+ Sbjct: 296 TRTMRNQIIEDLASQEVEAAAWCQPLHQQFYYSRFDCKRGDLLLTEKIADRCIALPL 352 >gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-dehydrase [Herbaspirillum seropedicae SmR1] Length = 390 Score = 88.2 bits (217), Expect = 9e-19, Method: Compositional matrix adjust. Identities = 62/220 (28%), Positives = 103/220 (46%), Gaps = 11/220 (5%) Query: 1 MTIPFNRPYMVGKELDYIIQ-AKQGNMLAGDGP----FTKRCHQWIETNTSCAKALLTHS 55 M P R ++ ++LD +I+ +Q + + +GP F K +W+ S + +S Sbjct: 2 MKYPLMRNNILREDLDAVIEHLRQDDPILTNGPNVRAFEKEWSEWLGVKYS----VFVNS 57 Query: 56 CTAA--LEMAALLLDIKPGDEIIMPSFTFVSTANAFVLRGGVPVFVDIREDTLNLDERLI 113 +A L MA L L G E+I+P T++S + G PVF DI +L + I Sbjct: 58 GASANLLSMAVLKLRHPEGGEVIVPPLTWISDVATVIQNGFTPVFADIDPRSLAMAPEQI 117 Query: 114 EAAITTRTKAIVPVHYAGVACEMDTIMDIAVRHGLRVVEDAAQGVMSKYKGKALGSIGDF 173 A IT RT+A+ H G D ++ R + ++ED + + + G+ LGS G Sbjct: 118 LAKITERTRAVFLTHVQGFDGLTDELLAELERRNIPLIEDVCESHGATHNGQRLGSFGWM 177 Query: 174 GAFSFHETKNVISGEGGALLVNDKSAALRAEIIREKGTDR 213 FSF+ ++ + EGG + ND + ++R G R Sbjct: 178 SNFSFYYAHHMSTIEGGMVCTNDPEVYQQVRMLRSHGMVR 217 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 0.321 0.135 0.402 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: 1,181,747 Number of extensions: 48961 Number of successful extensions: 150 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 144 Number of HSP's successfully gapped: 5 Length of query: 376 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 289 Effective length of database: 1,207,925 Effective search space: 349090325 Effective search space used: 349090325 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)