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= 0002.0143.p (371 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... 172 3e-44 gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotrans... 170 1e-43 gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent a... 166 3e-42 gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent a... 100 3e-22 gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-... 84 2e-17 >gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 366 Score = 172 bits (437), Expect = 3e-44, Method: Compositional matrix adjust. Identities = 130/346 (37%), Positives = 175/346 (50%), Gaps = 20/346 (5%) Query: 22 GPYTAKCHAWLQERTASHKVLLTHSCTAALEMAALLLDIQPGDEIIMPSYTFVSTANAFV 81 GP + A L+ T + + S T AL ++ + LDI+PGDEII +TFV+TA V Sbjct: 37 GPEVRELEAALEAYTGAKHCITVASGTEALLISLMALDIKPGDEIITTPFTFVATAEVMV 96 Query: 82 LRGGIPVFVDIREDTLNLDERLIEQAITSRTRAIVPVHYAGVACEMDAILAIARQHG-LH 140 L G PVFVD+ DT N+D RLIE ITS+T+AI+PV G A +MD I AIA +HG L Sbjct: 97 LLGAKPVFVDVEPDTGNIDVRLIEARITSKTKAIMPVSLYGQAADMDEINAIAARHGNLP 156 Query: 141 VVEDAAQGVMSTYKGRALGAIGDLGAYSFHETKNV-ISGEGGALLVNQPALAQRAEIIRE 199 V+EDAAQ +TYKGR G + +G SF +K + G+GGA+ N A+A IR Sbjct: 157 VIEDAAQSFGATYKGRKSGNLSSIGCTSFFPSKPLGCYGDGGAIFTNDDAIALACRQIR- 215 Query: 200 KGTDRSRFFRGEVDKYTWQEVGSSFLPGELIAAFLWAQLEGADAITDARLAAWHRYDEQL 259 G+ +Y VG L A + A+LE D + RLA RY+ L Sbjct: 216 --------VHGQSQRYVHTRVGVGGRMDTLQCAIVLAKLERFDWEIEQRLALGSRYNSLL 267 Query: 260 AQAEQDGLLRRPVVPDGCVHNAHMYYVIVPQAGQRQQVLDALKQEGIGAVFHY-VPLHSS 318 A G+ R PD A Y V++ R+ V AL+ GI HY VPL+ Sbjct: 268 DAA---GIARIQQRPDRDSVFAQ-YTVLL---DNREAVQAALQNAGIPTAVHYPVPLNRQ 320 Query: 319 PAGLRYGRVSGAMDITDLQSERLIRLPLWAGLTVQQQDKVIDILTS 364 PA G + D + R++ LP+ L QD ++ L S Sbjct: 321 PAYRHLGD-PDQTPVADQLAARVMSLPMSPDLEHTAQDSIVAALRS 365 >gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotransferase family protein [Herbaspirillum seropedicae SmR1] Length = 388 Score = 170 bits (431), Expect = 1e-43, Method: Compositional matrix adjust. Identities = 124/353 (35%), Positives = 170/353 (48%), Gaps = 34/353 (9%) Query: 31 WLQERTASHKVLLTHSCTAALEMAALLLDIQPGDEIIMPSYTFVSTANAFVLRGGIPVFV 90 W A H + +T SCT AL ++ L PGDE I+P++T+++TAN GG VF Sbjct: 40 WSAFTGARHSIAVT-SCTTALHLSLAALGFGPGDEAIVPAFTWIATANVIEHLGGKVVFC 98 Query: 91 DIREDTLNLDERLIEQAITSRTRAIVPVHYAGVACEMDAILAIARQHGLHVVEDAAQGVM 150 DI +T NLD + ITSRT+AI+PVH G+A EMD I +A+QHGL VVEDAA G Sbjct: 99 DIDLNTFNLDVAALRSKITSRTKAILPVHLFGLAAEMDQINDVAKQHGLWVVEDAACGFG 158 Query: 151 STYKGRALGAIGDLGAYSFHETKNVISGEGGALLVNQPALAQRAEIIREKG---TDRSRF 207 S Y G+ +G +GD G +SFH K + +GEGG + + ALA++ +R+ G TD R Sbjct: 159 SRYHGKHVGVLGDTGCFSFHPRKAITTGEGGMITTDNDALAEKLRRLRDHGAAMTDLQRH 218 Query: 208 FRGE----VDKYTWQEVGSSFLPGELIAAFLWAQLEGADAITDARLAAWHRYDEQLAQAE 263 D + G + ++ AA AQ+E AD I R RYD A Sbjct: 219 LGARPYLLADH---PDAGYNQRMTDIQAALGAAQMERADDIIAERRRLAERYDAAFADLS 275 Query: 264 QDGLLRRPVVPDGCVHNAHMYYVIV-PQA----------GQRQQVLDALKQEGIGA---- 308 LR P DG H Y + P+ R +D+L+Q GI Sbjct: 276 ---WLRTPAHVDGLEHGYQSYPCLFQPEPVNTDSIERINAARNAWMDSLQQAGISTRPAT 332 Query: 309 -VFHYVPLHSSPAGLRYGRVSGAMDITDLQSERLIRLPLWAGLTVQQQDKVID 360 H + + L+ A D I LPL+ G+T +QD VI+ Sbjct: 333 HAVHMLTFYREKYALKPADFPNAWAANDCS----ISLPLFHGMTQAEQDFVIE 381 >gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 373 Score = 166 bits (420), Expect = 3e-42, Method: Compositional matrix adjust. Identities = 107/345 (31%), Positives = 170/345 (49%), Gaps = 5/345 (1%) Query: 22 GPYTAKCHAWLQERTASHKVLLTHSCTAALEMAALLLDIQPGDEIIMPSYTFVSTANAFV 81 GP L + V +S T +E+A + + PGDE+I ++V+TAN + Sbjct: 33 GPKVQAFEKALSDYLGGRIVRTFNSGTCTMEIALRIAGVGPGDEVITTPISWVATANVIL 92 Query: 82 LRGGIPVFVDIREDTLNLDERLIEQAITSRTRAIVPVHYAGVACEMDAILAIARQHGLHV 141 G PVF DI T N+D +E AIT RT+A++PV+ +G+ +MD + AIA +H L V Sbjct: 93 ETGATPVFADIDPITRNIDLDKLEAAITPRTKAVIPVYLSGLPVDMDRLYAIAAKHKLRV 152 Query: 142 VEDAAQGVMSTYKGRALGAIGDLGAYSFHETKNVISGEGGALLVNQPALAQRAEIIREKG 201 VEDAAQ + ST+ G+ +GA GD ++S KN+ S EGG L++N A+ AE R +G Sbjct: 153 VEDAAQALGSTWNGKRIGAFGDFVSFSLQANKNITSSEGGFLVLNNAEEARLAEKYRLQG 212 Query: 202 TDRSRFFRGEVDKYTWQEVGSSFLPGELIAAFLWAQLEGADAITDARLAAWHRYDEQLAQ 261 RS F EVD +G F ++ AA Q DAIT R Y Sbjct: 213 VTRSGFDGLEVDV-----LGGKFNMTDVAAAIGLGQFAHIDAITAHRKELARHYFACFGS 267 Query: 262 AEQDGLLRRPVVPDGCVHNAHMYYVIVPQAGQRQQVLDALKQEGIGAVFHYVPLHSSPAG 321 + + V D N HM+ +++P+ R ++ + ++ IG +HY +H Sbjct: 268 DFESRYGAQLPVADFENSNWHMFQLVLPERITRAAFMEKMMEKQIGIGYHYPAIHLLKLY 327 Query: 322 LRYGRVSGAMDITDLQSERLIRLPLWAGLTVQQQDKVIDILTSTL 366 G G + + +R++ LP++ ++ + ++ + S L Sbjct: 328 RERGFGEGMFPVAERVGQRIVSLPMFNTMSKDDVVRSVETVKSVL 372 >gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 382 Score = 99.8 bits (247), Expect = 3e-22, Method: Compositional matrix adjust. Identities = 90/315 (28%), Positives = 141/315 (44%), Gaps = 17/315 (5%) Query: 46 SCTAALEMAALLLDIQPGDEIIMPSYTFVSTANAFVLRGGIPVFVDIREDTLNLDERLIE 105 S T AL +A + I+ GDE+I +Y++ +A L G PVF DI + NL + Sbjct: 57 SGTVALMLALRAMGIRAGDEVIASAYSWHQIVHAITLVGATPVFADIDYWSGNLAPHKVA 116 Query: 106 QAITSRTRAIVPVHYAGVACEMDAILAIARQHGLHVVEDAAQGVMSTYKGRALGAIGDLG 165 I+ RTRAIV + G +A+ HGL ++ED+++ + S Y+GR +G GD+ Sbjct: 117 DKISQRTRAIVVGNCNGHPAAWTEFRQLAQAHGLRLIEDSSEAIGSRYQGRVVGNFGDIA 176 Query: 166 AYSFHETKNVISGEGGALLVNQPALAQRAEIIREKG-TDRSRFFRGEVDKYTWQEVGSSF 224 + F + + GEG L+ + P LA +R + +DR + Q GS Sbjct: 177 IFDFSQPSALCCGEGAMLVTDDPELASELHYMRNRNLSDRQSI--AVASRVPMQ--GSM- 231 Query: 225 LPGELIAAFLWAQLEGADAITDARLAAWHRYDEQLAQAEQDGLLRRPVVPDGCVHNAHMY 284 +L AA AQLE D I R Y E + E G+ + PD V + Sbjct: 232 --SDLSAAIGIAQLERLDEILMRRKQVEAYYLEHVQFFE--GIKPPYIGPD--VEEVYWM 285 Query: 285 YVIVPQAGQ-----RQQVLDALKQEGIGAVFHYVPLHSSPAGLRYGRVSGAMDITDLQSE 339 +V + R Q+++ L + + A PLH R+ G + +T+ ++ Sbjct: 286 LYLVHLGTRFTRTMRNQIIEDLASQEVEAAAWCQPLHQQFYYSRFDCKRGDLLLTEKIAD 345 Query: 340 RLIRLPLWAGLTVQQ 354 R I LPL L + Sbjct: 346 RCIALPLHGHLNTDE 360 >gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-dehydrase [Herbaspirillum seropedicae SmR1] Length = 390 Score = 84.0 bits (206), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 51/175 (29%), Positives = 84/175 (48%), Gaps = 1/175 (0%) Query: 31 WLQERTASHKVLLTHSCTAAL-EMAALLLDIQPGDEIIMPSYTFVSTANAFVLRGGIPVF 89 W + + V + +A L MA L L G E+I+P T++S + G PVF Sbjct: 43 WSEWLGVKYSVFVNSGASANLLSMAVLKLRHPEGGEVIVPPLTWISDVATVIQNGFTPVF 102 Query: 90 VDIREDTLNLDERLIEQAITSRTRAIVPVHYAGVACEMDAILAIARQHGLHVVEDAAQGV 149 DI +L + I IT RTRA+ H G D +LA + + ++ED + Sbjct: 103 ADIDPRSLAMAPEQILAKITERTRAVFLTHVQGFDGLTDELLAELERRNIPLIEDVCESH 162 Query: 150 MSTYKGRALGAIGDLGAYSFHETKNVISGEGGALLVNQPALAQRAEIIREKGTDR 204 +T+ G+ LG+ G + +SF+ ++ + EGG + N P + Q+ ++R G R Sbjct: 163 GATHNGQRLGSFGWMSNFSFYYAHHMSTIEGGMVCTNDPEVYQQVRMLRSHGMVR 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 0.136 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: 1,226,922 Number of extensions: 55463 Number of successful extensions: 175 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 168 Number of HSP's successfully gapped: 5 Length of query: 371 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 284 Effective length of database: 1,207,925 Effective search space: 343050700 Effective search space used: 343050700 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)